From tsyu80 at gmail.com  Wed Aug  1 00:38:04 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Wed, 1 Aug 2012 00:38:04 -0400
Subject: Qt-MPL image viewer
In-Reply-To: <CAEym_HrvrzWgSeYroP9MU3S9xj-io257=jCOsuRs58y64-Jc3g@mail.gmail.com>
References: <CAEym_HrvrzWgSeYroP9MU3S9xj-io257=jCOsuRs58y64-Jc3g@mail.gmail.com>
Message-ID: <CAEym_Hps2g9xL3MEj3ox1=ioFejUSdicNA8T5idgEwwcZFTWNA@mail.gmail.com>

On Sat, Jul 28, 2012 at 10:08 AM, Tony Yu <tsyu80 at gmail.com> wrote:

> So I've been hacking on a new implementation of an
> image-viewer/interactive-image-processor. See PR 229:
>
>     https://github.com/scikits-image/scikits-image/pull/229
>
> The previous implementation was written purely in Matplotlib, partly for
> portability. Unfortunately, I found this implementation a bit limiting
> because Matplotlib doesn't provide quite-enough widget support. In
> addition, there was no way to add custom toolbars or menus without getting
> toolkit-specific.
>
> So, I've added a new implementation that requires PyQt but also uses
> Matplotlib because of the wealth of plotting functionality that it provides.
>
> There's a lot that I added in my original implementation that needs to be
> updated for this implementation (an image collection viewer, and Guillaume
> Gay's contrast setter and line-profile plugins). I'm of the opinion,
> however, that these should be implemented later in order to reduce the work
> to review this PR (that's actually why I moved the line profile plugin<https://github.com/tonysyu/scikits-image/blob/qtmpl-lineprofile/skimage/viewer/plugins/lineprofile.py>to a separate branch).
>
> Overall, I'm pretty happy with the current implementation. The basic idea
> is that there's a viewer class (to view images, of course). You can then
> connect plugins to the viewer, which typically calls some sort of filter
> function, but that's in no way a requirement (for example, the line-profile
> plugin measures values in the image). Also, there are widgets that get
> attached to these plugins (currently, just a slider and a combo box) to
> adjust filtering or plugin parameters.
>
> There are two ways to implement a plugin: The first is by subclassing the
> base `Plugin` class<https://github.com/tonysyu/scikits-image/blob/qtmpl-viewer/skimage/viewer/plugins/canny.py>.
> The second (which I shamelessly stole from Bokeh) instantiates a plugin
> and just adds widgets<https://github.com/tonysyu/scikits-image/blob/qtmpl-viewer/viewer_examples/plugins/canny_simple.py>(using the addition operator) to control filter parameters. The first is
> probably more flexible, while the second is convenient for people who may
> not be as comfortable with object-oriented programming (plus I think it
> reads really well).
>
> It's a big PR, but I'd really appreciate comments and suggestions.
>
> Cheers,
> -Tony
>
> P.S. Stefan: In a separate branch, I've added the Hough Transform plugin
> you so desired. Right now it's a little hacky, partly because I haven't yet
> built the infrastructure to support this type of plot (not only does it
> plot an overlay but also Matplotlib lines; in addition, parameters have to
> be delegated to two different functions). Nevertheless, the implementation
> is surprisingly short<https://github.com/tonysyu/scikits-image/blob/qtmpl-houghplugin/viewer_examples/plugins/hough_transform_simple.py>,
> despite not adding anything else to support this use case.
>


Update: I just added a CollectionViewer class (to view image collections)
to a separate branch that reimplements the CollectionViewer from the
original (pure-MPL) PR:

https://github.com/tonysyu/scikits-image/commit/c942db45ee0c663a5a70f8346a84d40795261af3

Cheers,
-Tony
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From tsyu80 at gmail.com  Thu Aug  2 21:28:54 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Thu, 2 Aug 2012 21:28:54 -0400
Subject: Bug in regionprops
In-Reply-To: <CABDkGQnROFkrtByJ5Bp-sOtBvPji-Rh8uHmQdcgscZS78zKy1w@mail.gmail.com>
References: <8484359e-e413-47cd-a3ba-90a02e19a75e@googlegroups.com> <CABDkGQnROFkrtByJ5Bp-sOtBvPji-Rh8uHmQdcgscZS78zKy1w@mail.gmail.com>
Message-ID: <CAEym_Hp2yYspV=bjA0FgCZNgn1cO9QVnzWNHdWh6RX21z204Qw@mail.gmail.com>

On Tue, Jul 31, 2012 at 4:42 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> Hi Jeff
>
> On Jul 31, 2012 9:07 AM, "jeff witz" <witzjean at gmail.com> wrote:
> >
> > I must use regionprops in order to identify a lot of el
>
>> Hello,
>>
>> I must use regionprops in order to identify a lot of ellipse in a
>> picture. I have constated a mistake in the implementation of the
>> 'Orientation' identification.
>> in skimage/measure/_regionprops.py at line 298 the function atan is used
>> to recover the angle. In my case I constate that a lot of the ellipse are
>> correctly identified using atan, but in some cases the 'MinorAxisLength'
>> and the 'MajorAxisLength' are swapped. You can solve this issue using the
>> atan2 function that take into account the trigonometric quadrant.
>>
>> Best Regards,
>>
>>
>>
>> Hi Jeff,

Thanks for the bug report. Johannes just added a PR to fix this issue:

https://github.com/scikits-image/scikits-image/pull/238

Do you have a short, self-contained example that you could submit as a
test. If you're comfortable with git, you can submit a PR to his branch
with the test. If not, maybe you could just post the example to this list,
and one of us can add it to the PR?

Thanks,
-Tony
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From tsyu80 at gmail.com  Sat Aug  4 10:42:15 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Sat, 4 Aug 2012 10:42:15 -0400
Subject: Bug in regionprops
In-Reply-To: <CAEym_Hp2yYspV=bjA0FgCZNgn1cO9QVnzWNHdWh6RX21z204Qw@mail.gmail.com>
References: <8484359e-e413-47cd-a3ba-90a02e19a75e@googlegroups.com>
 <CABDkGQnROFkrtByJ5Bp-sOtBvPji-Rh8uHmQdcgscZS78zKy1w@mail.gmail.com> <CAEym_Hp2yYspV=bjA0FgCZNgn1cO9QVnzWNHdWh6RX21z204Qw@mail.gmail.com>
Message-ID: <CAEym_Hr_Vie320kv+5gk8yfHoE29Tj3ehAmq+GLgYPG2_=D4fg@mail.gmail.com>

On Thu, Aug 2, 2012 at 9:28 PM, Tony Yu <tsyu80 at gmail.com> wrote:

>
>
> On Tue, Jul 31, 2012 at 4:42 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:
>
>> Hi Jeff
>>
>> On Jul 31, 2012 9:07 AM, "jeff witz" <witzjean at gmail.com> wrote:
>> >
>> > I must use regionprops in order to identify a lot of el
>>
>>> Hello,
>>>
>>> I must use regionprops in order to identify a lot of ellipse in a
>>> picture. I have constated a mistake in the implementation of the
>>> 'Orientation' identification.
>>> in skimage/measure/_regionprops.py at line 298 the function atan is used
>>> to recover the angle. In my case I constate that a lot of the ellipse are
>>> correctly identified using atan, but in some cases the 'MinorAxisLength'
>>> and the 'MajorAxisLength' are swapped. You can solve this issue using the
>>> atan2 function that take into account the trigonometric quadrant.
>>>
>>> Best Regards,
>>>
>>>
>>>
>>> Hi Jeff,
>
> Thanks for the bug report. Johannes just added a PR to fix this issue:
>
> https://github.com/scikits-image/scikits-image/pull/238
>
> Do you have a short, self-contained example that you could submit as a
> test. If you're comfortable with git, you can submit a PR to his branch
> with the test. If not, maybe you could just post the example to this list,
> and one of us can add it to the PR?
>
> Thanks,
> -Tony
>

For some reason, Johannes's emails aren't showing up on the list, so I'll
follow up to prevent duplicate work: Johannes added a test, and PR 238 has
been merged.

Cheers,
-Tony
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From stefan at sun.ac.za  Thu Aug  9 01:31:58 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 8 Aug 2012 22:31:58 -0700
Subject: EuroSciPy sprint
Message-ID: <CABDkGQk5s+SGHcE9QYDbeXLff4-O=A6hoQx6gHRwDXqZEExipw@mail.gmail.com>

Hi, everyone

We'll be sprinting at EuroSciPy, and would like to solicit ideas.
Currently, the sprint description reads as follows.  I'd love to hear
other suggestions!

"""

scikits-image is a collection of algorithms for image processing. See
http://skimage.org for more detail.

Ideas for the sprint:

- Add text, anti-aliasing to the draw module
- Integrate Tony's visualization tools
- Add binary features (BRIEF, BRISK, FREAK)
- Update the user guide
- Better video loading
- Hough transform parameter space explorer

Outstanding challenges:

- Blurring kernel estimation: http://bit.ly/Nril3u
- http://stackoverflow.com/questions/10196198/how-to-remove-convexity-defects-in-sudoku-square/11366549#11366549

And write up this one as an example:

- http://stackoverflow.com/questions/8686926/python-image-processing-help-needed-for-corner-detection-in-preferably-pil-or/9173430#9173430
"""

Regards
St?fan


From stefan at sun.ac.za  Thu Aug  9 12:18:42 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 9 Aug 2012 09:18:42 -0700
Subject: New core developer: Andreas Mueller
In-Reply-To: <CAEym_HoQMQ75Z8anKh-tJRHwQL1wGCe1DMhT6LgOkY2XtPvYPQ@mail.gmail.com>
References: <CAEym_HoQMQ75Z8anKh-tJRHwQL1wGCe1DMhT6LgOkY2XtPvYPQ@mail.gmail.com>
Message-ID: <CABDkGQ=xPKiR2xfw0tLXX02N=mAeJ4Sw9=mCPV0XeYd6G20XyQ@mail.gmail.com>

On Thu, Aug 9, 2012 at 8:20 AM, Tony Yu <tsyu80 at gmail.com> wrote:
> It's my pleasure to welcome Andreas Mueller to the scikits-image core
> development team. Andreas has made some valuable, high-quality code
> contributions to scikits-image, lately. In addition, he's been a great help
> in reviewing many of the recent pull requests; now he has the power of the
> green button (to merge those PRs).

Welcome to the team, Andy!  We're excited to have you.

St?fan


From tsyu80 at gmail.com  Thu Aug  9 11:20:46 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Thu, 9 Aug 2012 11:20:46 -0400
Subject: New core developer: Andreas Mueller
Message-ID: <CAEym_HoQMQ75Z8anKh-tJRHwQL1wGCe1DMhT6LgOkY2XtPvYPQ@mail.gmail.com>

Hi everyone,

It's my pleasure to welcome Andreas Mueller to the scikits-image core
development team. Andreas has made some valuable, high-quality code
contributions to scikits-image, lately. In addition, he's been a great help
in reviewing many of the recent pull requests; now he has the power of the
green button (to merge those PRs).

Andreas: I know you already have a pretty full plate, but I look forward to
many more contributions from you in the near future ;)

Cheers,
-Tony
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From amueller at ais.uni-bonn.de  Thu Aug  9 11:38:27 2012
From: amueller at ais.uni-bonn.de (Andreas =?utf-8?Q?M=C3=BCller?=)
Date: Thu, 9 Aug 2012 17:38:27 +0200 (CEST)
Subject: New core developer: Andreas Mueller
In-Reply-To: <CAEym_HoQMQ75Z8anKh-tJRHwQL1wGCe1DMhT6LgOkY2XtPvYPQ@mail.gmail.com>
Message-ID: <607195165.13937.1344526707279.JavaMail.root@ais.uni-bonn.de>

Hey everyone.
Thanks Tony. I'm happy to be on board :)

Looking forward to help out in this awesome project!

Cheers,
Andy

----- Urspr?ngliche Mail -----
Von: "Tony Yu" <tsyu80 at gmail.com>
An: scikits-image at googlegroups.com
Gesendet: Donnerstag, 9. August 2012 16:20:46
Betreff: New core developer: Andreas Mueller


Hi everyone, 

It's my pleasure to welcome Andreas Mueller to the scikits-image core development team. Andreas has made some valuable, high-quality code contributions to scikits-image, lately. In addition, he's been a great help in reviewing many of the recent pull requests; now he has the power of the green button (to merge those PRs). 


Andreas: I know you already have a pretty full plate, but I look forward to many more contributions from you in the near future ;) 


Cheers, 
-Tony


From hannesschoenberger at gmail.com  Fri Aug 10 01:26:40 2012
From: hannesschoenberger at gmail.com (=?UTF-8?Q?Johannes_Sch=C3=B6nberger?=)
Date: Thu, 9 Aug 2012 22:26:40 -0700 (PDT)
Subject: EuroSciPy sprint
In-Reply-To: <CABDkGQk5s+SGHcE9QYDbeXLff4-O=A6hoQx6gHRwDXqZEExipw@mail.gmail.com>
References: <CABDkGQk5s+SGHcE9QYDbeXLff4-O=A6hoQx6gHRwDXqZEExipw@mail.gmail.com>
Message-ID: <30b15b0d-83d9-491a-ac97-b9762e2eb8f4@googlegroups.com>

Hi,

would love to join you but unfortunately I am not at EuroScipy.

The anti-aliasing was on my agenda for the next weeks, but if you want to 
do it now - here is a good paper I found 
recently: http://free.pages.at/easyfilter/bresenham.html



Am Donnerstag, 9. August 2012 07:31:58 UTC+2 schrieb Stefan van der Walt:
>
> Hi, everyone 
>
> We'll be sprinting at EuroSciPy, and would like to solicit ideas. 
> Currently, the sprint description reads as follows.  I'd love to hear 
> other suggestions! 
>
> """ 
>
> scikits-image is a collection of algorithms for image processing. See 
> http://skimage.org for more detail. 
>
> Ideas for the sprint: 
>
> - Add text, anti-aliasing to the draw module 
> - Integrate Tony's visualization tools 
> - Add binary features (BRIEF, BRISK, FREAK) 
> - Update the user guide 
> - Better video loading 
> - Hough transform parameter space explorer 
>
> Outstanding challenges: 
>
> - Blurring kernel estimation: http://bit.ly/Nril3u 
> - 
> http://stackoverflow.com/questions/10196198/how-to-remove-convexity-defects-in-sudoku-square/11366549#11366549 
>
> And write up this one as an example: 
>
> - 
> http://stackoverflow.com/questions/8686926/python-image-processing-help-needed-for-corner-detection-in-preferably-pil-or/9173430#9173430 
> """ 
>
> Regards 
> St?fan 
>
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From witzjean at gmail.com  Fri Aug 10 01:46:20 2012
From: witzjean at gmail.com (jeff witz)
Date: Thu, 9 Aug 2012 22:46:20 -0700 (PDT)
Subject: EuroSciPy sprint
In-Reply-To: <CABDkGQk5s+SGHcE9QYDbeXLff4-O=A6hoQx6gHRwDXqZEExipw@mail.gmail.com>
References: <CABDkGQk5s+SGHcE9QYDbeXLff4-O=A6hoQx6gHRwDXqZEExipw@mail.gmail.com>
Message-ID: <2e40d44d-3ce2-4a29-8b93-b2d3aafc5c83@googlegroups.com>

Hello,

May one or two examples of Image Registration could be a good idea ? 

Le jeudi 9 ao?t 2012 07:31:58 UTC+2, Stefan van der Walt a ?crit :
>
> Hi, everyone 
>
> We'll be sprinting at EuroSciPy, and would like to solicit ideas. 
> Currently, the sprint description reads as follows.  I'd love to hear 
> other suggestions! 
>
> """ 
>
> scikits-image is a collection of algorithms for image processing. See 
> http://skimage.org for more detail. 
>
> Ideas for the sprint: 
>
> - Add text, anti-aliasing to the draw module 
> - Integrate Tony's visualization tools 
> - Add binary features (BRIEF, BRISK, FREAK) 
> - Update the user guide 
> - Better video loading 
> - Hough transform parameter space explorer 
>
> Outstanding challenges: 
>
> - Blurring kernel estimation: http://bit.ly/Nril3u 
> - 
> http://stackoverflow.com/questions/10196198/how-to-remove-convexity-defects-in-sudoku-square/11366549#11366549 
>
> And write up this one as an example: 
>
> - 
> http://stackoverflow.com/questions/8686926/python-image-processing-help-needed-for-corner-detection-in-preferably-pil-or/9173430#9173430 
> """ 
>
> Regards 
> St?fan 
>
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From hannesschoenberger at gmail.com  Fri Aug 10 02:35:47 2012
From: hannesschoenberger at gmail.com (=?UTF-8?Q?Johannes_Sch=C3=B6nberger?=)
Date: Thu, 9 Aug 2012 23:35:47 -0700 (PDT)
Subject: EuroSciPy sprint
In-Reply-To: <30b15b0d-83d9-491a-ac97-b9762e2eb8f4@googlegroups.com>
References: <CABDkGQk5s+SGHcE9QYDbeXLff4-O=A6hoQx6gHRwDXqZEExipw@mail.gmail.com>
 <30b15b0d-83d9-491a-ac97-b9762e2eb8f4@googlegroups.com>
Message-ID: <c7084a78-820a-4a50-9816-0594736417c0@googlegroups.com>

I misread something here... you were talking about anti-aliasing. Forget 
what I've written.

Am Freitag, 10. August 2012 07:26:40 UTC+2 schrieb Johannes Sch?nberger:
>
> Hi,
>
> would love to join you but unfortunately I am not at EuroScipy.
>
> The anti-aliasing was on my agenda for the next weeks, but if you want to 
> do it now - here is a good paper I found recently: 
> http://free.pages.at/easyfilter/bresenham.html
>
>
>
> Am Donnerstag, 9. August 2012 07:31:58 UTC+2 schrieb Stefan van der Walt:
>>
>> Hi, everyone 
>>
>> We'll be sprinting at EuroSciPy, and would like to solicit ideas. 
>> Currently, the sprint description reads as follows.  I'd love to hear 
>> other suggestions! 
>>
>> """ 
>>
>> scikits-image is a collection of algorithms for image processing. See 
>> http://skimage.org for more detail. 
>>
>> Ideas for the sprint: 
>>
>> - Add text, anti-aliasing to the draw module 
>> - Integrate Tony's visualization tools 
>> - Add binary features (BRIEF, BRISK, FREAK) 
>> - Update the user guide 
>> - Better video loading 
>> - Hough transform parameter space explorer 
>>
>> Outstanding challenges: 
>>
>> - Blurring kernel estimation: http://bit.ly/Nril3u 
>> - 
>> http://stackoverflow.com/questions/10196198/how-to-remove-convexity-defects-in-sudoku-square/11366549#11366549 
>>
>> And write up this one as an example: 
>>
>> - 
>> http://stackoverflow.com/questions/8686926/python-image-processing-help-needed-for-corner-detection-in-preferably-pil-or/9173430#9173430 
>> """ 
>>
>> Regards 
>> St?fan 
>>
>
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From tsyu80 at gmail.com  Fri Aug 10 00:05:26 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Fri, 10 Aug 2012 00:05:26 -0400
Subject: EuroSciPy sprint
In-Reply-To: <CABDkGQk5s+SGHcE9QYDbeXLff4-O=A6hoQx6gHRwDXqZEExipw@mail.gmail.com>
References: <CABDkGQk5s+SGHcE9QYDbeXLff4-O=A6hoQx6gHRwDXqZEExipw@mail.gmail.com>
Message-ID: <CAEym_HoK=og_YuHGFoMO_ZH54QrEeqU5=nYtGOsov+NvLk-fmA@mail.gmail.com>

On Thu, Aug 9, 2012 at 1:31 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> Hi, everyone
>
> We'll be sprinting at EuroSciPy, and would like to solicit ideas.
> Currently, the sprint description reads as follows.  I'd love to hear
> other suggestions!
>
> """
>
> scikits-image is a collection of algorithms for image processing. See
> http://skimage.org for more detail.
>
> Ideas for the sprint:
>
> - Add text, anti-aliasing to the draw module
> - Integrate Tony's visualization tools
> - Add binary features (BRIEF, BRISK, FREAK)
> - Update the user guide
> - Better video loading
> - Hough transform parameter space explorer
>
> Outstanding challenges:
>
> - Blurring kernel estimation: http://bit.ly/Nril3u
> -
> http://stackoverflow.com/questions/10196198/how-to-remove-convexity-defects-in-sudoku-square/11366549#11366549
>
> And write up this one as an example:
>
> -
> http://stackoverflow.com/questions/8686926/python-image-processing-help-needed-for-corner-detection-in-preferably-pil-or/9173430#9173430
> """
>
> Regards
> St?fan
>


It's depressing to see so many suggestions repeated from our last sprint.
That said, we did get a number of great contributions (many weren't on our
original list).

It sounds like there might be a *3rd* implementation of a an extensible
image viewer, so I won't be offended if you punt on the Qt-MPL viewer PR.
If you do tackle it, I think a good exercise would be to have someone
implement a new plugin for the viewer. (Maybe something as simple as
adapting parts of skivi.)

In case there are people at the sprint looking for simple problems to
tackle, I've also added a number of issues labeled quickfix, that *should*
in theory be fairly easy to implement. (Although the decision on the
correct implementation may or may not be so easy, but that's why it's nice
to have people in one room).

To get specific on updating the User Guide: I think a "Getting Started"
page would be great. Something that takes the user through a common
workflow; e.g.:

1) load an image
2) try using a feature detector or transform.
3) realize that it didn't perform ideally. Now try smoothing or denoising
(or something else).
4) successfully find feature.
5) save feature as some sort of data file.

One more item to the list:
- `imread_collection` should work for any plugin that implements `imread`.
(I guess I'll add this as an issue).

In regards to the Hough transform parameter space explorer, I have a
not-so-elegant implementation here:
https://github.com/tonysyu/scikits-image/blob/qtmpl-houghplugin/viewer_examples/plugins/hough_transform_simple.py

Cheers,
-Tony
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From stefan at sun.ac.za  Sun Aug 12 21:26:30 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 12 Aug 2012 18:26:30 -0700
Subject: Geometric transformations
Message-ID: <CABDkGQnFRu9n8961MSWsPTJizY=qXEyJd1xt1yWVYKyDEEvEoA@mail.gmail.com>

Hi everyone,

For those of you who work with warping and registration, check out the
freshly merged:

https://github.com/scikits-image/scikits-image/pull/197

This PR went through a long discussion, and I'm very happy with the result!

St?fan


From hannesschoenberger at gmail.com  Mon Aug 13 03:53:57 2012
From: hannesschoenberger at gmail.com (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Mon, 13 Aug 2012 09:53:57 +0200
Subject: Geometric transformations
In-Reply-To: <CABDkGQnFRu9n8961MSWsPTJizY=qXEyJd1xt1yWVYKyDEEvEoA@mail.gmail.com>
References: <CABDkGQnFRu9n8961MSWsPTJizY=qXEyJd1xt1yWVYKyDEEvEoA@mail.gmail.com>
Message-ID: <D8DB1E9E-6C4D-4E75-8412-0E506BA4AD81@gmail.com>

Hi St?fan,

I just noticed the documentation on skimage.org is based on one of the old builds of this branch. Maybe you can update this as the API looked different at that point.

Johannes Sch?nberger

Am 13.08.2012 um 03:26 schrieb St?fan van der Walt <stefan at sun.ac.za>:

> Hi everyone,
> 
> For those of you who work with warping and registration, check out the
> freshly merged:
> 
> https://github.com/scikits-image/scikits-image/pull/197
> 
> This PR went through a long discussion, and I'm very happy with the result!
> 
> St?fan



From stefan at sun.ac.za  Mon Aug 13 19:49:03 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 13 Aug 2012 16:49:03 -0700
Subject: Geometric transformations
In-Reply-To: <D8DB1E9E-6C4D-4E75-8412-0E506BA4AD81@gmail.com>
References: <CABDkGQnFRu9n8961MSWsPTJizY=qXEyJd1xt1yWVYKyDEEvEoA@mail.gmail.com>
 <D8DB1E9E-6C4D-4E75-8412-0E506BA4AD81@gmail.com>
Message-ID: <CABDkGQm0Ltpy9rpokK8=NR5qUWwO9RKx=w180OiCEHhThSOQUA@mail.gmail.com>

On Mon, Aug 13, 2012 at 12:53 AM, Johannes Sch?nberger
<hannesschoenberger at gmail.com> wrote:
> I just noticed the documentation on skimage.org is based on one of the old builds of this branch. Maybe you can update this as the API looked different at that point.

Thanks, that should be fixed now.

St?fan


From stefan at sun.ac.za  Mon Aug 13 22:52:20 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 13 Aug 2012 19:52:20 -0700
Subject: EuroSciPy sprint
In-Reply-To: <2e40d44d-3ce2-4a29-8b93-b2d3aafc5c83@googlegroups.com>
References: <CABDkGQk5s+SGHcE9QYDbeXLff4-O=A6hoQx6gHRwDXqZEExipw@mail.gmail.com>
 <2e40d44d-3ce2-4a29-8b93-b2d3aafc5c83@googlegroups.com>
Message-ID: <CABDkGQmY3ik=sw1EBnvjw-MScPSgnfEE7if9AT_DxUiuD1+8Yw@mail.gmail.com>

Hi Jeff

On Thu, Aug 9, 2012 at 10:46 PM, jeff witz <witzjean at gmail.com> wrote:
> May one or two examples of Image Registration could be a good idea ?

We don't currently have any image registration implemented.  With the
new geometric transforms merged, we can easily do feature based
registration, but dense registration is not covered.  I am very
interested in having this capability in skimage, and there has been
some work along those lines with Nathan Faggian in

https://github.com/pyimreg/imreg

If we can find a volunteer to do the work, I'd gladly help to guide the effort.

St?fan


From stefan at sun.ac.za  Mon Aug 13 22:56:56 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 13 Aug 2012 19:56:56 -0700
Subject: EuroSciPy sprint
In-Reply-To: <30b15b0d-83d9-491a-ac97-b9762e2eb8f4@googlegroups.com>
References: <CABDkGQk5s+SGHcE9QYDbeXLff4-O=A6hoQx6gHRwDXqZEExipw@mail.gmail.com>
 <30b15b0d-83d9-491a-ac97-b9762e2eb8f4@googlegroups.com>
Message-ID: <CABDkGQnv7AFRJSsiYvVnzG0rmmQzhd2sRuPSnXW0ywcKNWx++w@mail.gmail.com>

On Thu, Aug 9, 2012 at 10:26 PM, Johannes Sch?nberger
<hannesschoenberger at gmail.com> wrote:
> The anti-aliasing was on my agenda for the next weeks, but if you want to do
> it now - here is a good paper I found recently:
> http://free.pages.at/easyfilter/bresenham.html

This reminds me--we don't have bezier and/or nurbs in the drawing
module yet!  Unfortunately, I only have GPL code for Nurbs, but it
should be trivial to re-implement from scratch.  Anyone up for the
challenge?

St?fan


From hannesschoenberger at gmail.com  Tue Aug 14 02:03:32 2012
From: hannesschoenberger at gmail.com (=?UTF-8?Q?Johannes_Sch=C3=B6nberger?=)
Date: Mon, 13 Aug 2012 23:03:32 -0700 (PDT)
Subject: EuroSciPy sprint
In-Reply-To: <CABDkGQnv7AFRJSsiYvVnzG0rmmQzhd2sRuPSnXW0ywcKNWx++w@mail.gmail.com>
References: <CABDkGQk5s+SGHcE9QYDbeXLff4-O=A6hoQx6gHRwDXqZEExipw@mail.gmail.com>
 <30b15b0d-83d9-491a-ac97-b9762e2eb8f4@googlegroups.com>
 <CABDkGQnv7AFRJSsiYvVnzG0rmmQzhd2sRuPSnXW0ywcKNWx++w@mail.gmail.com>
Message-ID: <4d540b59-739b-4508-b87c-ec80b53b1b46@googlegroups.com>

If you haven't already done so, also have a look at the linked PDF document 
on this site.
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From bdholt1 at gmail.com  Tue Aug 14 06:09:32 2012
From: bdholt1 at gmail.com (Brian Holt)
Date: Tue, 14 Aug 2012 11:09:32 +0100
Subject: EuroSciPy sprint
In-Reply-To: <E4FDEF12-911A-4C0A-AABF-64D3488D5052@gmail.com>
References: <51034041.930.1344937228517.JavaMail.root@ais.uni-bonn.de>
	<E4FDEF12-911A-4C0A-AABF-64D3488D5052@gmail.com>
Message-ID: <CAFkP-qyvTAuJVBd49d8_89VU1sG8r5rEBor+j9X9VUH0X+0pEg@mail.gmail.com>

> You also mention camera transforms - my plan for autumn is to implement
camera calibration for skimage. As preparation for this, I am currently
contributing some features which are essential for this task.

I've implemented a camera class that might be of use as a starting point...
I needed to be able to register depth and RGB images coming from a Kinect

Brian

On 14 August 2012 11:03, Johannes Sch?nberger
<hannesschoenberger at gmail.com>wrote:

> Hi Andreas,
>
> Adding more feature descriptors would be great. Here is a good comparison?
> http://computer-vision-talks.com/2011/08/feature-descriptor-comparison-report/
>
> You also mention camera transforms - my plan for autumn is to implement
> camera calibration for skimage. As preparation for this, I am currently
> contributing some features which are essential for this task.
>
> Johannes Sch?nberger
>
> Am 14.08.2012 um 11:40 schrieb Andreas M?ller <amueller at ais.uni-bonn.de>:
>
> > Hey Everybody.
> > Just as a side node: If we had something like BRIEF, we could start with
> some serious vision applications.
> > With key point matching we can do stitching, getting camera transforms
> etc.
> > Using dense features, together with LBP and hog we can get
> state-of-the-art recognition.
> > Together with the segmentation algorithms, we can do semantic
> segmentation.
> >
> > So if we have a key-point descriptor like BRIEF, this enables us to cover
> > quite a lot of the popular computer vision applications.
> >
> > Just saying ;)
> >
> > LBP can also be used but I think BRIEF works better for natural images...
> >
> > Cheers,
> > Andy
> >
> >
> > ----- Urspr?ngliche Mail -----
> > Von: "St?fan van der Walt" <stefan at sun.ac.za>
> > An: scikits-image at googlegroups.com
> > Gesendet: Donnerstag, 9. August 2012 06:31:58
> > Betreff: EuroSciPy sprint
> >
> > Hi, everyone
> >
> > We'll be sprinting at EuroSciPy, and would like to solicit ideas.
> > Currently, the sprint description reads as follows.  I'd love to hear
> > other suggestions!
> >
> > """
> >
> > scikits-image is a collection of algorithms for image processing. See
> > http://skimage.org for more detail.
> >
> > Ideas for the sprint:
> >
> > - Add text, anti-aliasing to the draw module
> > - Integrate Tony's visualization tools
> > - Add binary features (BRIEF, BRISK, FREAK)
> > - Update the user guide
> > - Better video loading
> > - Hough transform parameter space explorer
> >
> > Outstanding challenges:
> >
> > - Blurring kernel estimation: http://bit.ly/Nril3u
> > -
> http://stackoverflow.com/questions/10196198/how-to-remove-convexity-defects-in-sudoku-square/11366549#11366549
> >
> > And write up this one as an example:
> >
> > -
> http://stackoverflow.com/questions/8686926/python-image-processing-help-needed-for-corner-detection-in-preferably-pil-or/9173430#9173430
> > """
> >
> > Regards
> > St?fan
>
>
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From bdholt1 at gmail.com  Tue Aug 14 06:19:38 2012
From: bdholt1 at gmail.com (Brian Holt)
Date: Tue, 14 Aug 2012 11:19:38 +0100
Subject: EuroSciPy sprint
In-Reply-To: <E1F58576-7E1F-4B62-9E61-E8CD66FC6C00@gmail.com>
References: <51034041.930.1344937228517.JavaMail.root@ais.uni-bonn.de>
	<E4FDEF12-911A-4C0A-AABF-64D3488D5052@gmail.com>
	<CAFkP-qyvTAuJVBd49d8_89VU1sG8r5rEBor+j9X9VUH0X+0pEg@mail.gmail.com>
	<E1F58576-7E1F-4B62-9E61-E8CD66FC6C00@gmail.com>
Message-ID: <CAFkP-qy4w5P0dYOt376fQL5M08prNZO7od2c-X3y1nsP9K++1Q@mail.gmail.com>

https://gist.github.com/3348000

Like I say, hopefully it might provide a starting point...

Brian
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From amueller at ais.uni-bonn.de  Tue Aug 14 05:40:28 2012
From: amueller at ais.uni-bonn.de (Andreas =?utf-8?Q?M=C3=BCller?=)
Date: Tue, 14 Aug 2012 11:40:28 +0200 (CEST)
Subject: EuroSciPy sprint
In-Reply-To: <CABDkGQk5s+SGHcE9QYDbeXLff4-O=A6hoQx6gHRwDXqZEExipw@mail.gmail.com>
Message-ID: <51034041.930.1344937228517.JavaMail.root@ais.uni-bonn.de>

Hey Everybody.
Just as a side node: If we had something like BRIEF, we could start with some serious vision applications.
With key point matching we can do stitching, getting camera transforms etc.
Using dense features, together with LBP and hog we can get state-of-the-art recognition.
Together with the segmentation algorithms, we can do semantic segmentation.

So if we have a key-point descriptor like BRIEF, this enables us to cover
quite a lot of the popular computer vision applications.

Just saying ;)

LBP can also be used but I think BRIEF works better for natural images...

Cheers,
Andy


----- Urspr?ngliche Mail -----
Von: "St?fan van der Walt" <stefan at sun.ac.za>
An: scikits-image at googlegroups.com
Gesendet: Donnerstag, 9. August 2012 06:31:58
Betreff: EuroSciPy sprint

Hi, everyone

We'll be sprinting at EuroSciPy, and would like to solicit ideas.
Currently, the sprint description reads as follows.  I'd love to hear
other suggestions!

"""

scikits-image is a collection of algorithms for image processing. See
http://skimage.org for more detail.

Ideas for the sprint:

- Add text, anti-aliasing to the draw module
- Integrate Tony's visualization tools
- Add binary features (BRIEF, BRISK, FREAK)
- Update the user guide
- Better video loading
- Hough transform parameter space explorer

Outstanding challenges:

- Blurring kernel estimation: http://bit.ly/Nril3u
- http://stackoverflow.com/questions/10196198/how-to-remove-convexity-defects-in-sudoku-square/11366549#11366549

And write up this one as an example:

- http://stackoverflow.com/questions/8686926/python-image-processing-help-needed-for-corner-detection-in-preferably-pil-or/9173430#9173430
"""

Regards
St?fan


From hannesschoenberger at gmail.com  Tue Aug 14 06:03:08 2012
From: hannesschoenberger at gmail.com (=?windows-1252?Q?Johannes_Sch=F6nberger?=)
Date: Tue, 14 Aug 2012 12:03:08 +0200
Subject: EuroSciPy sprint
In-Reply-To: <51034041.930.1344937228517.JavaMail.root@ais.uni-bonn.de>
References: <51034041.930.1344937228517.JavaMail.root@ais.uni-bonn.de>
Message-ID: <E4FDEF12-911A-4C0A-AABF-64D3488D5052@gmail.com>

Hi Andreas,

Adding more feature descriptors would be great. Here is a good comparison? http://computer-vision-talks.com/2011/08/feature-descriptor-comparison-report/

You also mention camera transforms - my plan for autumn is to implement camera calibration for skimage. As preparation for this, I am currently contributing some features which are essential for this task.

Johannes Sch?nberger

Am 14.08.2012 um 11:40 schrieb Andreas M?ller <amueller at ais.uni-bonn.de>:

> Hey Everybody.
> Just as a side node: If we had something like BRIEF, we could start with some serious vision applications.
> With key point matching we can do stitching, getting camera transforms etc.
> Using dense features, together with LBP and hog we can get state-of-the-art recognition.
> Together with the segmentation algorithms, we can do semantic segmentation.
> 
> So if we have a key-point descriptor like BRIEF, this enables us to cover
> quite a lot of the popular computer vision applications.
> 
> Just saying ;)
> 
> LBP can also be used but I think BRIEF works better for natural images...
> 
> Cheers,
> Andy
> 
> 
> ----- Urspr?ngliche Mail -----
> Von: "St?fan van der Walt" <stefan at sun.ac.za>
> An: scikits-image at googlegroups.com
> Gesendet: Donnerstag, 9. August 2012 06:31:58
> Betreff: EuroSciPy sprint
> 
> Hi, everyone
> 
> We'll be sprinting at EuroSciPy, and would like to solicit ideas.
> Currently, the sprint description reads as follows.  I'd love to hear
> other suggestions!
> 
> """
> 
> scikits-image is a collection of algorithms for image processing. See
> http://skimage.org for more detail.
> 
> Ideas for the sprint:
> 
> - Add text, anti-aliasing to the draw module
> - Integrate Tony's visualization tools
> - Add binary features (BRIEF, BRISK, FREAK)
> - Update the user guide
> - Better video loading
> - Hough transform parameter space explorer
> 
> Outstanding challenges:
> 
> - Blurring kernel estimation: http://bit.ly/Nril3u
> - http://stackoverflow.com/questions/10196198/how-to-remove-convexity-defects-in-sudoku-square/11366549#11366549
> 
> And write up this one as an example:
> 
> - http://stackoverflow.com/questions/8686926/python-image-processing-help-needed-for-corner-detection-in-preferably-pil-or/9173430#9173430
> """
> 
> Regards
> St?fan



From hannesschoenberger at gmail.com  Tue Aug 14 06:14:02 2012
From: hannesschoenberger at gmail.com (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Tue, 14 Aug 2012 12:14:02 +0200
Subject: EuroSciPy sprint
In-Reply-To: <CAFkP-qyvTAuJVBd49d8_89VU1sG8r5rEBor+j9X9VUH0X+0pEg@mail.gmail.com>
References: <51034041.930.1344937228517.JavaMail.root@ais.uni-bonn.de> <E4FDEF12-911A-4C0A-AABF-64D3488D5052@gmail.com> <CAFkP-qyvTAuJVBd49d8_89VU1sG8r5rEBor+j9X9VUH0X+0pEg@mail.gmail.com>
Message-ID: <E1F58576-7E1F-4B62-9E61-E8CD66FC6C00@gmail.com>

Could you paste the code somewhere or send it to me via EMail? Would be great.


From amueller at ais.uni-bonn.de  Tue Aug 14 06:20:30 2012
From: amueller at ais.uni-bonn.de (Andreas =?utf-8?Q?M=C3=BCller?=)
Date: Tue, 14 Aug 2012 12:20:30 +0200 (CEST)
Subject: EuroSciPy sprint
In-Reply-To: <E4FDEF12-911A-4C0A-AABF-64D3488D5052@gmail.com>
Message-ID: <2003951478.1201.1344939630131.JavaMail.root@ais.uni-bonn.de>

Hi Johannes.
Thanks for the link. That's a very interesting comparison, though I'm actually more into recognition.
What would be your favorite new descriptor be?

Btw, if you have some time, would you mind having a look at my PR at
https://github.com/scikits-image/scikits-image/pull/206

It's a bit longish and I think Tony and Stefan are a bit short on time.

Cheers,
Andy


----- Urspr?ngliche Mail -----
Von: "Johannes Sch?nberger" <hannesschoenberger at gmail.com>
An: scikits-image at googlegroups.com
Gesendet: Dienstag, 14. August 2012 11:03:08
Betreff: Re: EuroSciPy sprint

Hi Andreas,

Adding more feature descriptors would be great. Here is a good comparison? http://computer-vision-talks.com/2011/08/feature-descriptor-comparison-report/

You also mention camera transforms - my plan for autumn is to implement camera calibration for skimage. As preparation for this, I am currently contributing some features which are essential for this task.

Johannes Sch?nberger

Am 14.08.2012 um 11:40 schrieb Andreas M?ller <amueller at ais.uni-bonn.de>:

> Hey Everybody.
> Just as a side node: If we had something like BRIEF, we could start with some serious vision applications.
> With key point matching we can do stitching, getting camera transforms etc.
> Using dense features, together with LBP and hog we can get state-of-the-art recognition.
> Together with the segmentation algorithms, we can do semantic segmentation.
> 
> So if we have a key-point descriptor like BRIEF, this enables us to cover
> quite a lot of the popular computer vision applications.
> 
> Just saying ;)
> 
> LBP can also be used but I think BRIEF works better for natural images...
> 
> Cheers,
> Andy
> 
> 
> ----- Urspr?ngliche Mail -----
> Von: "St?fan van der Walt" <stefan at sun.ac.za>
> An: scikits-image at googlegroups.com
> Gesendet: Donnerstag, 9. August 2012 06:31:58
> Betreff: EuroSciPy sprint
> 
> Hi, everyone
> 
> We'll be sprinting at EuroSciPy, and would like to solicit ideas.
> Currently, the sprint description reads as follows.  I'd love to hear
> other suggestions!
> 
> """
> 
> scikits-image is a collection of algorithms for image processing. See
> http://skimage.org for more detail.
> 
> Ideas for the sprint:
> 
> - Add text, anti-aliasing to the draw module
> - Integrate Tony's visualization tools
> - Add binary features (BRIEF, BRISK, FREAK)
> - Update the user guide
> - Better video loading
> - Hough transform parameter space explorer
> 
> Outstanding challenges:
> 
> - Blurring kernel estimation: http://bit.ly/Nril3u
> - http://stackoverflow.com/questions/10196198/how-to-remove-convexity-defects-in-sudoku-square/11366549#11366549
> 
> And write up this one as an example:
> 
> - http://stackoverflow.com/questions/8686926/python-image-processing-help-needed-for-corner-detection-in-preferably-pil-or/9173430#9173430
> """
> 
> Regards
> St?fan



From stefan at sun.ac.za  Tue Aug 14 22:17:43 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 14 Aug 2012 19:17:43 -0700
Subject: Alpha-expansion, alpha-beta swaps and patents
In-Reply-To: <1068916926.5041.1344972709624.JavaMail.root@ais.uni-bonn.de>
References: <18727247.5040.1344972530039.JavaMail.root@ais.uni-bonn.de> <1068916926.5041.1344972709624.JavaMail.root@ais.uni-bonn.de>
Message-ID: <CABDkGQkkmoZqW5aDXHq1P_SWjd9B3nsoXkv+0zve41YKU34-iA@mail.gmail.com>

Hi Andy

On Tue, Aug 14, 2012 at 12:31 PM, Andreas M?ller
<amueller at ais.uni-bonn.de> wrote:
> To restart a conversation we had before on SIFT:
> Do we want patented algorithms in sklearn?

While there's nothing stopping us from implementing patented
algorithms, I do not like the implications.  It means we have to start
advertising to users that there are specific functions that they
cannot use without carefully examining the conditions.  I'd much
prefer for the whole package to be freely usable.

I get very unhappy when I see patents on algorithms such as SIFT,
built on top of (or at least inspired by) an entire volume of
non-patented research.  Fortunately, there are often
work-arounds--e.g., I believe the STAR (CenSurE) features used in
OpenCV (BSD-licensed!) are not patented, and work as well as or better
than SIFT.  So I suggest we implement that instead:

http://pr.willowgarage.com/wiki/Star_Detector

St?fan


From amueller at ais.uni-bonn.de  Tue Aug 14 15:31:49 2012
From: amueller at ais.uni-bonn.de (Andreas =?utf-8?Q?M=C3=BCller?=)
Date: Tue, 14 Aug 2012 21:31:49 +0200 (CEST)
Subject: Alpha-expansion, alpha-beta swaps and patents
In-Reply-To: <18727247.5040.1344972530039.JavaMail.root@ais.uni-bonn.de>
Message-ID: <1068916926.5041.1344972709624.JavaMail.root@ais.uni-bonn.de>

Hi everybody.
To restart a conversation we had before on SIFT:
Do we want patented algorithms in sklearn?
I just found out that alpha-expansion and alpha-beta swaps are patented,
which makes me very unhappy.

What do patents mean:
We can implement patented algorithms and distribute them under BSD license.
If someone uses the software for commercial purposes, they can be sued by the patent holder.


If we choose to include patented algorithms, we can include them with a warning.
Then there is no problem in having SIFT or including graph cuts with alpha expansion.

Cheers,
Andy


From amueller at ais.uni-bonn.de  Wed Aug 15 02:34:35 2012
From: amueller at ais.uni-bonn.de (Andreas Mueller)
Date: Wed, 15 Aug 2012 07:34:35 +0100
Subject: Alpha-expansion, alpha-beta swaps and patents
In-Reply-To: <CABDkGQkkmoZqW5aDXHq1P_SWjd9B3nsoXkv+0zve41YKU34-iA@mail.gmail.com>
References: <18727247.5040.1344972530039.JavaMail.root@ais.uni-bonn.de> <1068916926.5041.1344972709624.JavaMail.root@ais.uni-bonn.de> <CABDkGQkkmoZqW5aDXHq1P_SWjd9B3nsoXkv+0zve41YKU34-iA@mail.gmail.com>
Message-ID: <502B42FB.10503@ais.uni-bonn.de>

Hi Stefan.
I fully agree with you. This is why I advertised BRIEF
earlier. The thing is: it might prove very
hard to find a replacement for alpha expansion.

I'll be in Vienna next week and I'll talk to Vladimir Kolmogorov
and see if I can get his TRW-S code, but that probably
belongs to microsoft. And I'm not sure it is humanly
possible to reimplement Vladimirs algorithms ;)

Just to recall why I want a graph cut method:
That basically is state of the art in small baseline stereo,
optical flow, multi-class image segmentation, interactive
segmentation, ...

Cheers,
Andy


On 08/15/2012 03:17 AM, St??????fan van der Walt wrote:
> Hi Andy
>
> On Tue, Aug 14, 2012 at 12:31 PM, Andreas M??????ller
> <amueller at ais.uni-bonn.de> wrote:
>> To restart a conversation we had before on SIFT:
>> Do we want patented algorithms in sklearn?
> While there's nothing stopping us from implementing patented
> algorithms, I do not like the implications.  It means we have to start
> advertising to users that there are specific functions that they
> cannot use without carefully examining the conditions.  I'd much
> prefer for the whole package to be freely usable.
>
> I get very unhappy when I see patents on algorithms such as SIFT,
> built on top of (or at least inspired by) an entire volume of
> non-patented research.  Fortunately, there are often
> work-arounds--e.g., I believe the STAR (CenSurE) features used in
> OpenCV (BSD-licensed!) are not patented, and work as well as or better
> than SIFT.  So I suggest we implement that instead:
>
> http://pr.willowgarage.com/wiki/Star_Detector
>
> St??????fan



From stefan at sun.ac.za  Thu Aug 16 17:53:00 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 16 Aug 2012 14:53:00 -0700
Subject: EuroSciPy sprint
In-Reply-To: <2003951478.1201.1344939630131.JavaMail.root@ais.uni-bonn.de>
References: <E4FDEF12-911A-4C0A-AABF-64D3488D5052@gmail.com> <2003951478.1201.1344939630131.JavaMail.root@ais.uni-bonn.de>
Message-ID: <CABDkGQkB_0dNk5M+HaLqCvMrc6sMn5Ukvs6WHiqUCGgdLe4k9w@mail.gmail.com>

Thanks for all the suggestions.  Here then is the latest sprint summary:


SPRINT: scikits-image

What?
scikits-image is a collection of algorithms for image processing. See
http://scikits-image.org/ for more detail.

When?
Both on Mon Aug 27 and Tue Aug 28

Whom to contact?
St?fan van der Walt (stefan at sun.ac.za)

Tasks

There are a few outstanding issues that can be fixed easily:
https://github.com/scikits-image/scikits-image/issues?labels=quickfix

Ideas for the sprint:

- Add text, anti-aliasing to the draw module
- Add Bezier curves to the draw module (see the PDF linked from
http://free.pages.at/easyfilter/bresenham.html)
- Integrate Tony's visualization tools, and use them to write  a
plugin, or fine-tune the existing Hough parameter space explorer
- Add binary features (BRIEF, BRISK, FREAK, LAZY)
  http://computer-vision-talks.com/2011/08/feature-descriptor-comparison-report/
- Camera calibration
  Start from https://gist.github.com/3348000 and
http://bazaar.launchpad.net/~astraw/pinpoint/dev/files/
- Better video loading
- Update the user guide
  We need a ?Getting started? section, guiding a user through a
typical workflow:
  1. Load an image
  2. Try using a feature detector or transform.
  3. Realize that it didn't perform ideally. Now try smoothing or
denoising (or something else).
  4. Successfully find feature.
  5. Save feature as some sort of data file.
- Add imread_collection to all imread plugins.

Outstanding challenges:

- Blurring kernel estimation (http://bit.ly/Nril3u)
- ?Sudoku challenge?
(http://stackoverflow.com/questions/10196198/how-to-remove-convexity-defects-in-sudoku-square/11366549#11366549)

Specific examples to be implemented:

- Corner detection
(http://stackoverflow.com/questions/8686926/python-image-processing-help-needed-for-corner-detection-in-preferably-pil-or/9173430#9173430)


From tsyu80 at gmail.com  Thu Aug 16 22:06:28 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Thu, 16 Aug 2012 22:06:28 -0400
Subject: Subpackage for utilities
Message-ID: <CAEym_HoyOusM09r0PBHf3dL-ijduJTjrnzdiOnOL0fxatkm7NA@mail.gmail.com>

In PR #239<https://github.com/scikits-image/scikits-image/pull/239#issuecomment-7792726>,
Johannes suggested a new `utils` module or subpackage, which I think this
is a great idea.

We currently have the `util` package, but I'm inclined to suggest a new
subpackage (not named `utils` to avoid confusion). It would be nice to
separate functions that would be useful to consumers of image processing
functions (e.g., the dtype conversion routines in `util`) from functions
that are useful to developers of image processing functions (e.g., the
`shape` module in the `util` package, which has `view_as_blocks` and
`view_as_windows`). I wouldn't be surprised if people think this is an
arbitrary (or false) distinction.

Regardless of whether there should be a new subpackage (or if it should be
put in `util`), there are a number of candidate functions that come to mind:

- rank order (`filter` package)
- heap (`graph` package)
- heap_* (`morphology` package) (*.pxi files?)
- integral images (`transform` package). (The transform package does make
sense for this, but keep in mind that this is used in other packages, e.g.,
`match_template` in the `feature` package.)

There are probably a number of others that I'm missing.

In the past, there have been discussions of dependency versions and adding
compatibility functions so that we can support older versions of numpy,
matplotlib, etc. A utility package would be good for those sorts of things.

-Tony
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From amueller at ais.uni-bonn.de  Fri Aug 17 03:05:12 2012
From: amueller at ais.uni-bonn.de (Andreas Mueller)
Date: Fri, 17 Aug 2012 08:05:12 +0100
Subject: Subpackage for utilities
In-Reply-To: <CAEym_HoyOusM09r0PBHf3dL-ijduJTjrnzdiOnOL0fxatkm7NA@mail.gmail.com>
References: <CAEym_HoyOusM09r0PBHf3dL-ijduJTjrnzdiOnOL0fxatkm7NA@mail.gmail.com>
Message-ID: <502DED28.5050509@ais.uni-bonn.de>

Hi Tony.
As I said, I think it is a great idea to collect the utility functions.
I'm undecided on whether it is a good idea to separate them from the
user utility functions.

To the candidates I'd like to add the union find that I reused in my 
segmentation PR.

Cheers,
Andy

On 08/17/2012 03:06 AM, Tony Yu wrote:
> In PR #239 
> <https://github.com/scikits-image/scikits-image/pull/239#issuecomment-7792726>, 
> Johannes suggested a new `utils` module or subpackage, which I think 
> this is a great idea.
>
> We currently have the `util` package, but I'm inclined to suggest a 
> new subpackage (not named `utils` to avoid confusion). It would be 
> nice to separate functions that would be useful to consumers of image 
> processing functions (e.g., the dtype conversion routines in `util`) 
> from functions that are useful to developers of image processing 
> functions (e.g., the `shape` module in the `util` package, which has 
> `view_as_blocks` and `view_as_windows`). I wouldn't be surprised if 
> people think this is an arbitrary (or false) distinction.
>
> Regardless of whether there should be a new subpackage (or if it 
> should be put in `util`), there are a number of candidate functions 
> that come to mind:
>
> - rank order (`filter` package)
> - heap (`graph` package)
> - heap_* (`morphology` package) (*.pxi files?)
> - integral images (`transform` package). (The transform package does 
> make sense for this, but keep in mind that this is used in other 
> packages, e.g., `match_template` in the `feature` package.)
>
> There are probably a number of others that I'm missing.
>
> In the past, there have been discussions of dependency versions and 
> adding compatibility functions so that we can support older versions 
> of numpy, matplotlib, etc. A utility package would be good for those 
> sorts of things.
>
> -Tony

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From hannesschoenberger at gmail.com  Sat Aug 18 03:03:44 2012
From: hannesschoenberger at gmail.com (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Sat, 18 Aug 2012 09:03:44 +0200
Subject: Subpackage for utilities
In-Reply-To: <502DED28.5050509@ais.uni-bonn.de>
References: <CAEym_HoyOusM09r0PBHf3dL-ijduJTjrnzdiOnOL0fxatkm7NA@mail.gmail.com> <502DED28.5050509@ais.uni-bonn.de>
Message-ID: <94222D1B-2E3D-4EBD-92B4-D1B5993B72BF@gmail.com>

Hi,

I would suggest to create a directory like `util/shared` and put all necessary `.py`, `.pxd` and `.pyx` files in there. As Tony said I would put all functions in there that are used from different packages and that might in future be of use for other code. (like integral images, pnpoly, bilinear interpolation etc.)

Johannes Sch?nberger


From stefan at sun.ac.za  Mon Aug 20 11:19:26 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 20 Aug 2012 08:19:26 -0700
Subject: Subpackage for utilities
In-Reply-To: <CAEym_HoyOusM09r0PBHf3dL-ijduJTjrnzdiOnOL0fxatkm7NA@mail.gmail.com>
References: <CAEym_HoyOusM09r0PBHf3dL-ijduJTjrnzdiOnOL0fxatkm7NA@mail.gmail.com>
Message-ID: <CABDkGQmxm6=onSLV5Wnafp02L5mLt5c_Qc2KOxF+aLiZ_TYT1w@mail.gmail.com>

Hi Tony

On Thu, Aug 16, 2012 at 7:06 PM, Tony Yu <tsyu80 at gmail.com> wrote:
> In PR #239, Johannes suggested a new `utils` module or subpackage, which I
> think this is a great idea.

+1

> We currently have the `util` package, but I'm inclined to suggest a new
> subpackage (not named `utils` to avoid confusion).

How about ``skimage._algorithms`` or, based upon another suggestion on
this thread, ``skimage._shared``?

St?fan


From stefan at sun.ac.za  Mon Aug 20 13:47:00 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 20 Aug 2012 10:47:00 -0700
Subject: Subpackage for utilities
In-Reply-To: <C46E9260-8A9A-4B80-815C-EA04179E5CEA@gmail.com>
References: <CAEym_HoyOusM09r0PBHf3dL-ijduJTjrnzdiOnOL0fxatkm7NA@mail.gmail.com>
 <CABDkGQmxm6=onSLV5Wnafp02L5mLt5c_Qc2KOxF+aLiZ_TYT1w@mail.gmail.com> <C46E9260-8A9A-4B80-815C-EA04179E5CEA@gmail.com>
Message-ID: <CABDkGQk09K+7nghb4YVUh-a0XTVVd=erY6hQm6iBYB6syZ5W4g@mail.gmail.com>

On Mon, Aug 20, 2012 at 10:09 AM, Johannes Sch?nberger
<hannesschoenberger at gmail.com> wrote:
>> How about ``skimage._algorithms`` or, based upon another suggestion on
>> this thread, ``skimage._shared``?
>
> ``skimage._shared`` sounds good. If you don't mind I'll add a pull request for this and add some of the important functions in there.

Thanks, please go ahead.

St?fan


From hannesschoenberger at gmail.com  Mon Aug 20 13:09:05 2012
From: hannesschoenberger at gmail.com (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Mon, 20 Aug 2012 19:09:05 +0200
Subject: Subpackage for utilities
In-Reply-To: <CABDkGQmxm6=onSLV5Wnafp02L5mLt5c_Qc2KOxF+aLiZ_TYT1w@mail.gmail.com>
References: <CAEym_HoyOusM09r0PBHf3dL-ijduJTjrnzdiOnOL0fxatkm7NA@mail.gmail.com> <CABDkGQmxm6=onSLV5Wnafp02L5mLt5c_Qc2KOxF+aLiZ_TYT1w@mail.gmail.com>
Message-ID: <C46E9260-8A9A-4B80-815C-EA04179E5CEA@gmail.com>

> How about ``skimage._algorithms`` or, based upon another suggestion on
> this thread, ``skimage._shared``?

``skimage._shared`` sounds good. If you don't mind I'll add a pull request for this and add some of the important functions in there.

Johannes


From emmanuelle.gouillart at nsup.org  Mon Aug 20 17:11:45 2012
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Mon, 20 Aug 2012 23:11:45 +0200
Subject: Multispectral random walker segmentation
In-Reply-To: <3632b7ed-0b4b-4889-959f-5cae47d80ae9@googlegroups.com>
References: <3632b7ed-0b4b-4889-959f-5cae47d80ae9@googlegroups.com>
Message-ID: <20120820211145.GB949@phare.normalesup.org>

Hi Josh,

extending the random walker algorithm to multichannel images sounds like
a very nice idea, and I'm sure that it would be useful for other people
(including myself!). 

In fact, I had started working on some improvements of the random walker
code but didn't go as far as proposing the pull request. I have a branch
for that on
https://github.com/emmanuelle/scikits.image/tree/fix_random_walker, maybe
you can include these changes when you contribute your changes?

Cheers,
Emmanuelle

On Mon, Aug 20, 2012 at 10:03:53AM -0700, Josh Warner wrote:
>    I have modified the existing random walker algorithm into a fully
>    backwards-compatible version which allows inclusion of multispectral data,
>    e.g. RGBA channels or different (registered) image modalities. ??????I really
>    liked the existing algorithm, so I just extended it rather than write one
>    from scratch for my own purposes. ??????The overhead is minimal; multispectral
>    processing is triggered if data is passed as an iterable of arrays rather
>    than just an array. ??????
>    This amounts to combining image gradients as sqrt(sum-of-squares) and
>    dividing by sqrt(#channels). ??????For obvious reasons, the several channels
>    must be pre-processed to have data on similar ranges by whitening or a
>    similar method. ??????Not usually a problem for RGB, but in medical imaging
>    this rears its head.
>    Would this be of interest to the community? ??????I'd be happy to contribute
>    the changes if there is interest.


From hannesschoenberger at gmail.com  Tue Aug 21 05:19:55 2012
From: hannesschoenberger at gmail.com (=?UTF-8?Q?Johannes_Sch=C3=B6nberger?=)
Date: Tue, 21 Aug 2012 02:19:55 -0700 (PDT)
Subject: Subpackage for utilities
In-Reply-To: <CABDkGQk09K+7nghb4YVUh-a0XTVVd=erY6hQm6iBYB6syZ5W4g@mail.gmail.com>
References: <CAEym_HoyOusM09r0PBHf3dL-ijduJTjrnzdiOnOL0fxatkm7NA@mail.gmail.com>
 <CABDkGQmxm6=onSLV5Wnafp02L5mLt5c_Qc2KOxF+aLiZ_TYT1w@mail.gmail.com> <C46E9260-8A9A-4B80-815C-EA04179E5CEA@gmail.com>
 <CABDkGQk09K+7nghb4YVUh-a0XTVVd=erY6hQm6iBYB6syZ5W4g@mail.gmail.com>
Message-ID: <2f5686a4-3961-4175-9c5b-85b52f72f90c@googlegroups.com>

Pull request has been added.

Am Montag, 20. August 2012 19:47:00 UTC+2 schrieb Stefan van der Walt:
>
> On Mon, Aug 20, 2012 at 10:09 AM, Johannes Sch?nberger 
> <hannessch... at gmail.com <javascript:>> wrote: 
> >> How about ``skimage._algorithms`` or, based upon another suggestion on 
> >> this thread, ``skimage._shared``? 
> > 
> > ``skimage._shared`` sounds good. If you don't mind I'll add a pull 
> request for this and add some of the important functions in there. 
>
> Thanks, please go ahead. 
>
> St?fan 
>
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From luca.fiaschi at gmail.com  Wed Aug 22 04:41:29 2012
From: luca.fiaschi at gmail.com (Luca Fiaschi)
Date: Wed, 22 Aug 2012 01:41:29 -0700 (PDT)
Subject: bug in regionprops underlying library qhull?
In-Reply-To: <9fec784a-35d4-4a3a-9de3-bf46b348bf67@googlegroups.com>
References: <9fec784a-35d4-4a3a-9de3-bf46b348bf67@googlegroups.com>
Message-ID: <8ac6fc2e-8f2f-47d1-bd89-e72a9c9df87c@googlegroups.com>

Hi,
I confirm the bug to be really in qhull.
I  substituted the computation of the convex hull in scipy (qhull) with 
another library (vigranumpy) and thins fix the problem.

If useful I might consider working on a cython implementation of the 2D 
convex hull algorithm and flash a pull request.
Best
Luca



Il giorno marted? 21 agosto 2012 12:40:39 UTC+2, Luca Fiaschi ha scritto:
>
> Hi all,
> I get a strange bug trying to uses regionprops on some images.
> Computing the hull of some objects result a internal error in the qhull 
> library:
> Below you can find the error and and the set of points which triggers it:
>
> Does anybody know how to fix it?
>
>
> [[  5.   12.5]
>  [  6.    6.5]
>  [  7.    4.5]
>  [  8.    4.5]
>  [  9.    4.5]
>  [ 10.    5.5]
>  [  7.    4.5]
>  [  7.    5.5]
>  [  6.    6.5]
>  [  6.    7.5]
>  [  6.    8.5]
>  [  6.    9.5]
>  [  6.   10.5]
>  [  6.   11.5]
>  [  5.   12.5]
>  [  5.   13.5]
>  [  5.   14.5]
>  [  5.   15.5]
>  [  5.   16.5]
>  [  5.   17.5]
>  [  5.   18.5]
>  [  5.   19.5]
>  [  5.   20.5]
>  [  5.   21.5]
>  [  5.   22.5]
>  [  5.   23.5]
>  [  5.   24.5]
>  [  6.   25.5]
>  [  5.   24.5]
>  [  6.   25.5]
>  [  7.   25.5]
>  [  8.   23.5]
>  [  9.   20.5]
>  [ 10.   16.5]
>  [  9.    4.5]
>  [ 10.    5.5]
>  [ 10.    6.5]
>  [ 10.    7.5]
>  [ 10.    8.5]
>  [ 10.    9.5]
>  [ 10.   10.5]
>  [ 10.   11.5]
>  [ 10.   12.5]
>  [ 10.   13.5]
>  [ 10.   14.5]
>  [ 10.   15.5]
>  [ 10.   16.5]
>  [  9.   17.5]
>  [  9.   18.5]
>  [  9.   19.5]
>  [  9.   20.5]
>  [  8.   21.5]
>  [  8.   22.5]
>  [  8.   23.5]
>  [  7.   24.5]
>  [  7.   25.5]
>  [  5.   13.5]
>  [  6.    7.5]
>  [  7.    5.5]
>  [  8.    5.5]
>  [  9.    5.5]
>  [ 10.    6.5]
>  [  7.    5.5]
>  [  7.    6.5]
>  [  6.    7.5]
>  [  6.    8.5]
>  [  6.    9.5]
>  [  6.   10.5]
>  [  6.   11.5]
>  [  6.   12.5]
>  [  5.   13.5]
>  [  5.   14.5]
>  [  5.   15.5]
>  [  5.   16.5]
>  [  5.   17.5]
>  [  5.   18.5]
>  [  5.   19.5]
>  [  5.   20.5]
>  [  5.   21.5]
>  [  5.   22.5]
>  [  5.   23.5]
>  [  5.   24.5]
>  [  5.   25.5]
>  [  6.   26.5]
>  [  5.   25.5]
>  [  6.   26.5]
>  [  7.   26.5]
>  [  8.   24.5]
>  [  9.   21.5]
>  [ 10.   17.5]
>  [  9.    5.5]
>  [ 10.    6.5]
>  [ 10.    7.5]
>  [ 10.    8.5]
>  [ 10.    9.5]
>  [ 10.   10.5]
>  [ 10.   11.5]
>  [ 10.   12.5]
>  [ 10.   13.5]
>  [ 10.   14.5]
>  [ 10.   15.5]
>  [ 10.   16.5]
>  [ 10.   17.5]
>  [  9.   18.5]
>  [  9.   19.5]
>  [  9.   20.5]
>  [  9.   21.5]
>  [  8.   22.5]
>  [  8.   23.5]
>  [  8.   24.5]
>  [  7.   25.5]
>  [  7.   26.5]
>  [  4.5  13. ]
>  [  5.5   7. ]
>  [  6.5   5. ]
>  [  7.5   5. ]
>  [  8.5   5. ]
>  [  9.5   6. ]
>  [  6.5   5. ]
>  [  6.5   6. ]
>  [  5.5   7. ]
>  [  5.5   8. ]
>  [  5.5   9. ]
>  [  5.5  10. ]
>  [  5.5  11. ]
>  [  5.5  12. ]
>  [  4.5  13. ]
>  [  4.5  14. ]
>  [  4.5  15. ]
>  [  4.5  16. ]
>  [  4.5  17. ]
>  [  4.5  18. ]
>  [  4.5  19. ]
>  [  4.5  20. ]
>  [  4.5  21. ]
>  [  4.5  22. ]
>  [  4.5  23. ]
>  [  4.5  24. ]
>  [  4.5  25. ]
>  [  5.5  26. ]
>  [  4.5  25. ]
>  [  5.5  26. ]
>  [  6.5  26. ]
>  [  7.5  24. ]
>  [  8.5  21. ]
>  [  9.5  17. ]
>  [  8.5   5. ]
>  [  9.5   6. ]
>  [  9.5   7. ]
>  [  9.5   8. ]
>  [  9.5   9. ]
>  [  9.5  10. ]
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>  [  9.5  12. ]
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>  [  7.5  22. ]
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>  [  6.5  25. ]
>  [  6.5  26. ]
>  [  5.5  13. ]
>  [  6.5   7. ]
>  [  7.5   5. ]
>  [  8.5   5. ]
>  [  9.5   5. ]
>  [ 10.5   6. ]
>  [  7.5   5. ]
>  [  7.5   6. ]
>  [  6.5   7. ]
>  [  6.5   8. ]
>  [  6.5   9. ]
>  [  6.5  10. ]
>  [  6.5  11. ]
>  [  6.5  12. ]
>  [  5.5  13. ]
>  [  5.5  14. ]
>  [  5.5  15. ]
>  [  5.5  16. ]
>  [  5.5  17. ]
>  [  5.5  18. ]
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>  [  5.5  20. ]
>  [  5.5  21. ]
>  [  5.5  22. ]
>  [  5.5  23. ]
>  [  5.5  24. ]
>  [  5.5  25. ]
>  [  6.5  26. ]
>  [  5.5  25. ]
>  [  6.5  26. ]
>  [  7.5  26. ]
>  [  8.5  24. ]
>  [  9.5  21. ]
>  [ 10.5  17. ]
>  [  9.5   5. ]
>  [ 10.5   6. ]
>  [ 10.5   7. ]
>  [ 10.5   8. ]
>  [ 10.5   9. ]
>  [ 10.5  10. ]
>  [ 10.5  11. ]
>  [ 10.5  12. ]
>  [ 10.5  13. ]
>  [ 10.5  14. ]
>  [ 10.5  15. ]
>  [ 10.5  16. ]
>  [ 10.5  17. ]
>  [  9.5  18. ]
>  [  9.5  19. ]
>  [  9.5  20. ]
>  [  9.5  21. ]
>  [  8.5  22. ]
>  [  8.5  23. ]
>  [  8.5  24. ]
>  [  7.5  25. ]
>  [  7.5  26. ]]
> QH6228 
> Qhull internal error (qh_findbestlower): all neighbors of facet 12 are 
> flipped or upper Delaunay.
> Please report this error to qhull_bug at qhull.org with the input and all of 
> the output.
> ERRONEOUS FACET:
> - f12
>     - flags: top simplicial upperDelaunay
>     - normal:    -0.965  -0.1942   0.1764
>     - offset:   6.243641
>     - vertices: p138(v7) p224(v3) p112(v0)
>     - neighboring facets: f6 f28 f13
>
> While executing:  | qhull d Qz Qbb Qt
> Options selected for Qhull 2010.1 2010/01/14:
>   run-id 1565793501  delaunay  Qz-infinity-point  Qbbound-last 
>  Qtriangulate
>   _pre-merge  _zero-centrum  Pgood  _max-width 22  Error-roundoff 3.7e-14
>   _one-merge 2.6e-13  _near-inside 1.3e-12  Visible-distance 7.4e-14
>   U-coplanar-distance 7.4e-14  Width-outside 1.5e-13  _wide-facet 4.4e-13
> Last point added to hull was p132.
>
> At error exit:
>
> Delaunay triangulation by the convex hull of 225 points in 3-d:
>
>   Number of input sites and at-infinity: 11
>   Number of nearly incident points: 9
>   Number of Delaunay regions: 0
>
> Statistics for:  | qhull d Qz Qbb Qt
>
>   Number of points processed: 11
>   Number of hyperplanes created: 31
>   Number of facets in hull: 18
>   Number of distance tests for qhull: 1324
>
>
> precision problems (corrected unless 'Q0' or an error)
>       8 coplanar points during partitioning
>
>
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From emmanuelle.gouillart at nsup.org  Thu Aug 23 08:49:06 2012
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Thu, 23 Aug 2012 14:49:06 +0200
Subject: EuroSciPy sprint
In-Reply-To: <CABDkGQkB_0dNk5M+HaLqCvMrc6sMn5Ukvs6WHiqUCGgdLe4k9w@mail.gmail.com>
References: <E4FDEF12-911A-4C0A-AABF-64D3488D5052@gmail.com>
 <2003951478.1201.1344939630131.JavaMail.root@ais.uni-bonn.de>
 <CABDkGQkB_0dNk5M+HaLqCvMrc6sMn5Ukvs6WHiqUCGgdLe4k9w@mail.gmail.com>
Message-ID: <20120823124906.GA5211@phare.normalesup.org>

Thank you St?fan, I just copied the summary on
https://github.com/scikits-image/scikits-image/wiki/Euroscipy-2012-sprint

Who is going to participate to the sprint, eventually? If you plan to
participate, please add you name on the wiki page.

Cheers,
Emmanuelle

On Thu, Aug 16, 2012 at 02:53:00PM -0700, St?fan van der Walt wrote:
> Thanks for all the suggestions.  Here then is the latest sprint summary:


> SPRINT: scikits-image

> What?
> scikits-image is a collection of algorithms for image processing. See
> http://scikits-image.org/ for more detail.

> When?
> Both on Mon Aug 27 and Tue Aug 28

> Whom to contact?
> St?fan van der Walt (stefan at sun.ac.za)

> Tasks

> There are a few outstanding issues that can be fixed easily:
> https://github.com/scikits-image/scikits-image/issues?labels=quickfix

> Ideas for the sprint:

> - Add text, anti-aliasing to the draw module
> - Add Bezier curves to the draw module (see the PDF linked from
> http://free.pages.at/easyfilter/bresenham.html)
> - Integrate Tony's visualization tools, and use them to write  a
> plugin, or fine-tune the existing Hough parameter space explorer
> - Add binary features (BRIEF, BRISK, FREAK, LAZY)
>   http://computer-vision-talks.com/2011/08/feature-descriptor-comparison-report/
> - Camera calibration
>   Start from https://gist.github.com/3348000 and
> http://bazaar.launchpad.net/~astraw/pinpoint/dev/files/
> - Better video loading
> - Update the user guide
>   We need a ?Getting started? section, guiding a user through a
> typical workflow:
>   1. Load an image
>   2. Try using a feature detector or transform.
>   3. Realize that it didn't perform ideally. Now try smoothing or
> denoising (or something else).
>   4. Successfully find feature.
>   5. Save feature as some sort of data file.
> - Add imread_collection to all imread plugins.

> Outstanding challenges:

> - Blurring kernel estimation (http://bit.ly/Nril3u)
> - ?Sudoku challenge?
> (http://stackoverflow.com/questions/10196198/how-to-remove-convexity-defects-in-sudoku-square/11366549#11366549)

> Specific examples to be implemented:

> - Corner detection
> (http://stackoverflow.com/questions/8686926/python-image-processing-help-needed-for-corner-detection-in-preferably-pil-or/9173430#9173430)


From silvertrumpet999 at gmail.com  Thu Aug 23 17:50:05 2012
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Thu, 23 Aug 2012 14:50:05 -0700 (PDT)
Subject: Multispectral random walker segmentation
In-Reply-To: <20120820211145.GB949@phare.normalesup.org>
References: <3632b7ed-0b4b-4889-959f-5cae47d80ae9@googlegroups.com>
 <20120820211145.GB949@phare.normalesup.org>
Message-ID: <8f5b3756-7912-4cdf-8aad-f8d47b0ecae6@googlegroups.com>

I'd be happy to include your suggested changes, if it's simpler to go that 
route than have two separate pull requests.  I don't want to step on any 
toes regarding attribution, though.  

Having the 'soft' probabilities available is definitely a useful 
improvement (cleanup, fuzzy post-processing), and I'm glad you implemented 
that!  

Josh


On Monday, August 20, 2012 4:11:45 PM UTC-5, Emmanuelle Gouillart wrote:
>
> Hi Josh, 
>
> extending the random walker algorithm to multichannel images sounds like 
> a very nice idea, and I'm sure that it would be useful for other people 
> (including myself!). 
>
> In fact, I had started working on some improvements of the random walker 
> code but didn't go as far as proposing the pull request. I have a branch 
> for that on 
> https://github.com/emmanuelle/scikits.image/tree/fix_random_walker, maybe 
> you can include these changes when you contribute your changes? 
>
> Cheers, 
> Emmanuelle 
>
> On Mon, Aug 20, 2012 at 10:03:53AM -0700, Josh Warner wrote: 
> >    I have modified the existing random walker algorithm into a fully 
> >    backwards-compatible version which allows inclusion of multispectral 
> data, 
> >    e.g. RGBA channels or different (registered) image modalities. ???I 
> really 
> >    liked the existing algorithm, so I just extended it rather than write 
> one 
> >    from scratch for my own purposes. ???The overhead is minimal; 
> multispectral 
> >    processing is triggered if data is passed as an iterable of arrays 
> rather 
> >    than just an array. ??? 
> >    This amounts to combining image gradients as sqrt(sum-of-squares) and 
> >    dividing by sqrt(#channels). ???For obvious reasons, the several 
> channels 
> >    must be pre-processed to have data on similar ranges by whitening or 
> a 
> >    similar method. ???Not usually a problem for RGB, but in medical 
> imaging 
> >    this rears its head. 
> >    Would this be of interest to the community? ???I'd be happy to 
> contribute 
> >    the changes if there is interest. 
>
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From stefan at sun.ac.za  Fri Aug 24 07:43:43 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Fri, 24 Aug 2012 04:43:43 -0700
Subject: bug in regionprops underlying library qhull?
In-Reply-To: <8ac6fc2e-8f2f-47d1-bd89-e72a9c9df87c@googlegroups.com>
References: <9fec784a-35d4-4a3a-9de3-bf46b348bf67@googlegroups.com> <8ac6fc2e-8f2f-47d1-bd89-e72a9c9df87c@googlegroups.com>
Message-ID: <CABDkGQnBcEGFLeuMj2umdUx4YaWQ7HSstcXp-F=JherrZLhN=g@mail.gmail.com>

Hi Luca

On Wed, Aug 22, 2012 at 1:41 AM, Luca Fiaschi <luca.fiaschi at gmail.com> wrote:
> I confirm the bug to be really in qhull.
> I  substituted the computation of the convex hull in scipy (qhull) with
> another library (vigranumpy) and thins fix the problem.

Strange, do you know if the points are pathological for some reason?
Perhaps we can pre-filter them to prevent any crashes.  Where did you
get these coordinates from?

St?fan


From stefan at sun.ac.za  Fri Aug 24 08:22:07 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Fri, 24 Aug 2012 05:22:07 -0700
Subject: Questions about hog.py file
In-Reply-To: <220a3aab-fd52-4d4d-a33d-ed7c717bf77c@googlegroups.com>
References: <220a3aab-fd52-4d4d-a33d-ed7c717bf77c@googlegroups.com>
Message-ID: <CABDkGQmhBmzX=t-MKSga-e5-zo-hP3zT44sQpyfGqWo6Qf_3MQ@mail.gmail.com>

On Mon, Aug 6, 2012 at 6:31 AM, Omar Trinidad Guti?rrez M?ndez
<omar.vpa at gmail.com> wrote:
>  I am reading the source code of the file hog.py, I found the next line of
> code:
>
> n_cellsx = int(np.floor(sx // cx))
>
> I don't know why they join the NumPy function floor and the // operator. Is
> there any reason to do this? I can't see. I feel that is doing the same
> thing twice.

I never followed up on this; has the issue been addressed by the
latest HoG fixes?

St?fan


From stefan at sun.ac.za  Fri Aug 24 08:24:02 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Fri, 24 Aug 2012 05:24:02 -0700
Subject: Bundling scikits-image using pyinstaller
In-Reply-To: <fbbdefc6-6cfb-4eac-9a68-2c96bfbe0d33@googlegroups.com>
References: <3dfeb136-ad04-4de2-93b2-be5210808d4e@googlegroups.com>
 <CABDkGQ=oDCB11oTQs1tS2bwGXis6ubjPJZ2+ruh6_hgxMVxhMQ@mail.gmail.com> <fbbdefc6-6cfb-4eac-9a68-2c96bfbe0d33@googlegroups.com>
Message-ID: <CABDkGQkxdY3+kb4tSz4mv2Htwc+fAz8on7-qyRBYSphzoWf-bA@mail.gmail.com>

Hi Nicklas,

On Tue, Jul 31, 2012 at 2:16 AM, Nicklas Nordenmark
<nordenmark at gmail.com> wrote:
> From the Pyinstaller manual
> (http://www.pyinstaller.org/export/develop/project/doc/Manual.html?format=raw):
>
>> In most sophisticated apps, it becomes necessary to figure out (at
>> runtime) whether you're running "live" or "frozen". For example, you might
>> have a configuration file that (running "live") you locate based on a
>> module's __file__ attribute. That won't work once the code is packaged up.
>> You'll probably want to look for it based on sys.executable instead.

Would you be interested in preparing a pull-request to handle this issue?

Regards
St?fan


From stefan at sun.ac.za  Fri Aug 24 08:55:55 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Fri, 24 Aug 2012 05:55:55 -0700
Subject: Qt-MPL image viewer
In-Reply-To: <CAEym_HrvrzWgSeYroP9MU3S9xj-io257=jCOsuRs58y64-Jc3g@mail.gmail.com>
References: <CAEym_HrvrzWgSeYroP9MU3S9xj-io257=jCOsuRs58y64-Jc3g@mail.gmail.com>
Message-ID: <CABDkGQ=xG0xoMUZDBsSyfNJCHuHXZoJPyRwB0Eus2=0j16WjMA@mail.gmail.com>

Hi Tony

On Sat, Jul 28, 2012 at 7:08 AM, Tony Yu <tsyu80 at gmail.com> wrote:
> So I've been hacking on a new implementation of an
> image-viewer/interactive-image-processor. See PR 229:
>
>     https://github.com/scikits-image/scikits-image/pull/229

This is great!  I've played around with the PR, and I love the
simplicity of the API.  It's now been merged into master.

> P.S. Stefan: In a separate branch, I've added the Hough Transform plugin you
> so desired.

Ah, neat!  I'm going to try that right now.

St?fan


From stefan at sun.ac.za  Sat Aug 25 14:09:38 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sat, 25 Aug 2012 11:09:38 -0700
Subject: Cython version to build master
In-Reply-To: <50390BBD.9080603@ais.uni-bonn.de>
References: <503904C7.90209@ais.uni-bonn.de>
	<5039093B.7000207@ais.uni-bonn.de>
	<CAEym_HqEuLR7y=akrfV=VVD4v0jAf6BxgVXo06KtyHGShASAMA@mail.gmail.com>
	<50390BBD.9080603@ais.uni-bonn.de>
Message-ID: <CABDkGQmUyFKxx_RNc65Dm-qiU++p-yBkVAu4qKK6-pyiZPduoQ@mail.gmail.com>

Fixed.. Thanks, Tony!
On Aug 25, 2012 8:06 PM, "Andreas Mueller" <amueller at ais.uni-bonn.de> wrote:

>  On 08/25/2012 07:27 PM, Tony Yu wrote:
>
>
>
> On Sat, Aug 25, 2012 at 1:19 PM, Andreas Mueller <amueller at ais.uni-bonn.de
> > wrote:
>
>> I just saw the commit with the change in the docs.
>> Is this because of the memory views? Can someone point me to the
>> discussion?
>> Not being able to build scikits-image on current Ubuntu seems a bit
>> annoying to me.
>>
>>
>  Argh. I didn't realize this. I think it would probably be a good policy
> if the current Ubuntu version sets a *maximum* version on our dependencies.
>
>  -T
>
>  Yeah, I think that is a good idea.
> I think Ubuntu and Debian are used by many researchers and as long as it
> doesn't
> hold us back, I think it is a good idea to support some versions back -
> and definitely the current.
>
>
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From tsyu80 at gmail.com  Sat Aug 25 13:20:08 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Sat, 25 Aug 2012 13:20:08 -0400
Subject: Cython version to build master
In-Reply-To: <503904C7.90209@ais.uni-bonn.de>
References: <503904C7.90209@ais.uni-bonn.de>
Message-ID: <CAEym_HohbOV1=FDr1WpzkkE559+qsn1EeW+u8e51ODXHzJZ2tg@mail.gmail.com>

On Sat, Aug 25, 2012 at 1:00 PM, Andreas Mueller
<amueller at ais.uni-bonn.de>wrote:

> Hi everybody.
> I haven't kept track of all of the many PRs this last weeks, but I noticed
> today
> that I can't build master. There is an error in "skimage/morphology/_**
> greyreconstruct.pyx".
> I guess that is because I use Cython 0.15.1.
> Is that correct? Do we only support Cython 0.16 now?
>
> Cheers,
> Andy
>
>

Hi Andy,

This is my fault. I should have asked the list first: I bumped up the
Cython version to use typed
memoryviews<http://docs.cython.org/src/userguide/memoryviews.html>
.

My rationale was that we should be pretty conservative with older,
more-entrenched packages like numpy and matplotlib, but less conservative
with something that's rapidly evolving, like Cython.

I'm fine with converting morphological reconstruction to support Cython
0.15 if there's push back.

Cheers,
-Tony
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From tsyu80 at gmail.com  Sat Aug 25 13:27:02 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Sat, 25 Aug 2012 13:27:02 -0400
Subject: Cython version to build master
In-Reply-To: <5039093B.7000207@ais.uni-bonn.de>
References: <503904C7.90209@ais.uni-bonn.de> <5039093B.7000207@ais.uni-bonn.de>
Message-ID: <CAEym_HqEuLR7y=akrfV=VVD4v0jAf6BxgVXo06KtyHGShASAMA@mail.gmail.com>

On Sat, Aug 25, 2012 at 1:19 PM, Andreas Mueller
<amueller at ais.uni-bonn.de>wrote:

> I just saw the commit with the change in the docs.
> Is this because of the memory views? Can someone point me to the
> discussion?
> Not being able to build scikits-image on current Ubuntu seems a bit
> annoying to me.
>
>
Argh. I didn't realize this. I think it would probably be a good policy if
the current Ubuntu version sets a *maximum* version on our dependencies.

-T


>
> On 08/25/2012 07:00 PM, Andreas Mueller wrote:
>
>> Hi everybody.
>> I haven't kept track of all of the many PRs this last weeks, but I
>> noticed today
>> that I can't build master. There is an error in "skimage/morphology/_**
>> greyreconstruct.pyx".
>> I guess that is because I use Cython 0.15.1.
>> Is that correct? Do we only support Cython 0.16 now?
>>
>> Cheers,
>> Andy
>>
>>
>
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From amueller at ais.uni-bonn.de  Sat Aug 25 13:00:55 2012
From: amueller at ais.uni-bonn.de (Andreas Mueller)
Date: Sat, 25 Aug 2012 19:00:55 +0200
Subject: Cython version to build master
Message-ID: <503904C7.90209@ais.uni-bonn.de>

Hi everybody.
I haven't kept track of all of the many PRs this last weeks, but I 
noticed today
that I can't build master. There is an error in 
"skimage/morphology/_greyreconstruct.pyx".
I guess that is because I use Cython 0.15.1.
Is that correct? Do we only support Cython 0.16 now?

Cheers,
Andy



From amueller at ais.uni-bonn.de  Sat Aug 25 13:19:55 2012
From: amueller at ais.uni-bonn.de (Andreas Mueller)
Date: Sat, 25 Aug 2012 19:19:55 +0200
Subject: Cython version to build master
In-Reply-To: <503904C7.90209@ais.uni-bonn.de>
References: <503904C7.90209@ais.uni-bonn.de>
Message-ID: <5039093B.7000207@ais.uni-bonn.de>

I just saw the commit with the change in the docs.
Is this because of the memory views? Can someone point me to the discussion?
Not being able to build scikits-image on current Ubuntu seems a bit 
annoying to me.


On 08/25/2012 07:00 PM, Andreas Mueller wrote:
> Hi everybody.
> I haven't kept track of all of the many PRs this last weeks, but I 
> noticed today
> that I can't build master. There is an error in 
> "skimage/morphology/_greyreconstruct.pyx".
> I guess that is because I use Cython 0.15.1.
> Is that correct? Do we only support Cython 0.16 now?
>
> Cheers,
> Andy
>



From amueller at ais.uni-bonn.de  Sat Aug 25 13:30:37 2012
From: amueller at ais.uni-bonn.de (Andreas Mueller)
Date: Sat, 25 Aug 2012 19:30:37 +0200
Subject: Cython version to build master
In-Reply-To: <CAEym_HqEuLR7y=akrfV=VVD4v0jAf6BxgVXo06KtyHGShASAMA@mail.gmail.com>
References: <503904C7.90209@ais.uni-bonn.de> <5039093B.7000207@ais.uni-bonn.de> <CAEym_HqEuLR7y=akrfV=VVD4v0jAf6BxgVXo06KtyHGShASAMA@mail.gmail.com>
Message-ID: <50390BBD.9080603@ais.uni-bonn.de>

On 08/25/2012 07:27 PM, Tony Yu wrote:
>
>
> On Sat, Aug 25, 2012 at 1:19 PM, Andreas Mueller 
> <amueller at ais.uni-bonn.de <mailto:amueller at ais.uni-bonn.de>> wrote:
>
>     I just saw the commit with the change in the docs.
>     Is this because of the memory views? Can someone point me to the
>     discussion?
>     Not being able to build scikits-image on current Ubuntu seems a
>     bit annoying to me.
>
>
> Argh. I didn't realize this. I think it would probably be a good 
> policy if the current Ubuntu version sets a *maximum* version on our 
> dependencies.
>
> -T
>
Yeah, I think that is a good idea.
I think Ubuntu and Debian are used by many researchers and as long as it 
doesn't
hold us back, I think it is a good idea to support some versions back - 
and definitely the current.

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From stefan at sun.ac.za  Sun Aug 26 09:22:11 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 26 Aug 2012 06:22:11 -0700
Subject: Sprint
In-Reply-To: <681D2C8C-55A2-4E75-8B57-07E5439D8FBE@inria.fr>
References: <681D2C8C-55A2-4E75-8B57-07E5439D8FBE@inria.fr>
Message-ID: <CABDkGQn8MNmfCKTBtURe01mdn4pqHC4nGXym8NJ9ob+kxwAO5A@mail.gmail.com>

Thanks, Nicolas--this is going to help a lot!

Forwarding to the list as well.

Regards
St?fan

On Sun, Aug 26, 2012 at 6:20 AM, Nicolas Rougier
<Nicolas.Rougier at inria.fr> wrote:
>
> Hi,
>
>
> I've tried to post to the mailing list but for some reason my message did not appear (feel free to forward this one to the list).
>
> For text, there are the freetype-py bindings available from http://code.google.com/p/freetype-py/
>
> Be sure to check the example directory that explain how to render text once you've chosen a font file.
> By default, I generally use the Bitstream Vera family that might be BSD compatible (but I'm not so sure).
>
> Also, there is a nice article on text rendering: http://www.antigrain.com/research/font_rasterization/
> The "agg_trick.py" demo does just that.
>
> In the end, you get a RGBA array with the text within so it should be easy to add it to an image.
>
>
>
> Also, I read you need bezier curves and I recently translated the bezier curve code from the antigrain library:
>
> http://www.antigrain.com/research/adaptive_bezier/index.html
>
>
> You can find at http://code.google.com/p/gl-agg/source/browse/python/gl-curve.py two functions:
>
> curve3_bezier( P1, P2, P3 ) and curve4_bezier( P1, P2, P3, P4) that takes respectively 3 and 4 points as input and will give you back a list of points. If you draw straight lines between those points, then you're done with bezier.
>
>
>
>
> Nicolas
>
>


From stefan at sun.ac.za  Sun Aug 26 09:29:25 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 26 Aug 2012 06:29:25 -0700
Subject: Fwd: Sprint
In-Reply-To: <53B1990C-3245-4095-A876-5099C450C9BC@inria.fr>
References: <681D2C8C-55A2-4E75-8B57-07E5439D8FBE@inria.fr>
 <CABDkGQn8MNmfCKTBtURe01mdn4pqHC4nGXym8NJ9ob+kxwAO5A@mail.gmail.com> <53B1990C-3245-4095-A876-5099C450C9BC@inria.fr>
Message-ID: <CABDkGQmzayhFiJGKYAM2HbH6w+oAZtr02+QK9q8v4jfkJFHWWg@mail.gmail.com>

Andreas, look at these nifty super-pixels :)

---------- Forwarded message ----------
From: Nicolas Rougier
Date: Sun, Aug 26, 2012 at 6:26 AM
Subject: Re: Sprint

Cool.

Also, I forgot a probably useless filter based on voronoi cells. Just don't
know if it might be of some interest or not for scikit-image:
Code at: https://github.com/rougier/gallery (showcase/showcase-9.py)


Nicolas
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From amueller at ais.uni-bonn.de  Sun Aug 26 09:31:26 2012
From: amueller at ais.uni-bonn.de (Andreas Mueller)
Date: Sun, 26 Aug 2012 15:31:26 +0200
Subject: Fwd: Sprint
In-Reply-To: <CABDkGQmzayhFiJGKYAM2HbH6w+oAZtr02+QK9q8v4jfkJFHWWg@mail.gmail.com>
References: <681D2C8C-55A2-4E75-8B57-07E5439D8FBE@inria.fr> <CABDkGQn8MNmfCKTBtURe01mdn4pqHC4nGXym8NJ9ob+kxwAO5A@mail.gmail.com> <53B1990C-3245-4095-A876-5099C450C9BC@inria.fr> <CABDkGQmzayhFiJGKYAM2HbH6w+oAZtr02+QK9q8v4jfkJFHWWg@mail.gmail.com>
Message-ID: <503A252E.7070709@ais.uni-bonn.de>

Nice. I guess they work a lot like SLIC, only they put more emphasis on 
the (x,y) space.


On 08/26/2012 03:29 PM, St??????fan van der Walt wrote:
> Andreas, look at these nifty super-pixels :)
>
> ---------- Forwarded message ----------
> From: *Nicolas Rougier*
> Date: Sun, Aug 26, 2012 at 6:26 AM
> Subject: Re: Sprint
>
> Cool.
>
> Also, I forgot a probably useless filter based on voronoi cells. Just 
> don't know if it might be of some interest or not for scikit-image:
> Code at: https://github.com/rougier/gallery (showcase/showcase-9.py)
>
>
> Nicolas

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From luca.fiaschi at gmail.com  Mon Aug 27 05:17:56 2012
From: luca.fiaschi at gmail.com (Luca Fiaschi)
Date: Mon, 27 Aug 2012 02:17:56 -0700 (PDT)
Subject: bug in regionprops underlying library qhull?
In-Reply-To: <CABDkGQnBcEGFLeuMj2umdUx4YaWQ7HSstcXp-F=JherrZLhN=g@mail.gmail.com>
References: <9fec784a-35d4-4a3a-9de3-bf46b348bf67@googlegroups.com> <8ac6fc2e-8f2f-47d1-bd89-e72a9c9df87c@googlegroups.com>
 <CABDkGQnBcEGFLeuMj2umdUx4YaWQ7HSstcXp-F=JherrZLhN=g@mail.gmail.com>
Message-ID: <28085f79-ee9e-4958-921d-979ff1da814d@googlegroups.com>


Hi Stefan,
I do not know well the algorithm that qhul implements, and it is lucky to 
be more complicated than what is needed in this case since it seems to work 
in higher dimensions than 2D. Nevertheless, I do not see any reason why the 
points should be pathological:

here my modifications:

--- a/skimage/morphology/convex_hull.py
+++ b/skimage/morphology/convex_hull.py
@@ -51,9 +51,15 @@ def convex_hull_image(image):
                           'scipy >= 0.9.')
 
     # Find the convex hull
-    chull = Delaunay(coords).convex_hull
-    v = coords[np.unique(chull)]
 
+    #chull = Delaunay(coords).convex_hull
+    #v1 = coords[np.unique(chull)]
+    import vigra
+    
v=vigra.geometry.convexHull(np.copy(coords).astype(np.float32)).view(np.ndarray)
+    #print v1
+    #print v2
+    #raise



As you can see I just exchanged the computation from scipy with that of 
another library to which I personally had contributed implementing the 
standard monotone chain convex hull algorithm.
Everything seems fine now.





Il giorno venerd? 24 agosto 2012 13:43:43 UTC+2, Stefan van der Walt ha 
scritto:
>
> Hi Luca 
>
> On Wed, Aug 22, 2012 at 1:41 AM, Luca Fiaschi <luca.f... at gmail.com<javascript:>> 
> wrote: 
> > I confirm the bug to be really in qhull. 
> > I  substituted the computation of the convex hull in scipy (qhull) with 
> > another library (vigranumpy) and thins fix the problem. 
>
> Strange, do you know if the points are pathological for some reason? 
> Perhaps we can pre-filter them to prevent any crashes.  Where did you 
> get these coordinates from? 
>
> St?fan 
>
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From silvertrumpet999 at gmail.com  Mon Aug 27 17:18:22 2012
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Mon, 27 Aug 2012 14:18:22 -0700 (PDT)
Subject: Multispectral random walker segmentation
In-Reply-To: <20120827125511.GA4067@phare.normalesup.org>
References: <3632b7ed-0b4b-4889-959f-5cae47d80ae9@googlegroups.com>
 <20120820211145.GB949@phare.normalesup.org>
 <8f5b3756-7912-4cdf-8aad-f8d47b0ecae6@googlegroups.com>
 <20120827125511.GA4067@phare.normalesup.org>
Message-ID: <aca261ce-91c7-4b7e-aea8-f53fba0ecf61@googlegroups.com>

Pull request is up!  I also fixed a bug in the fallback call of _solve_cg() 
if pyamg is not installed.  Comments appreciated.

Josh


On Monday, August 27, 2012 7:55:11 AM UTC-5, Emmanuelle Gouillart wrote:
>
> Hi Josh, 
>
> my changes have been merged, so if you pull from github they are in 
> the master branch now, you can add your changes and make a pull request! 
>
> Cheers, 
> Emmanuelle 
>
> On Thu, Aug 23, 2012 at 02:50:05PM -0700, Josh Warner wrote: 
> >    I'd be happy to include your suggested changes, if it's simpler to go 
> that 
> >    route than have two separate pull requests. ???I don't want to step 
> on any 
> >    toes regarding attribution, though. ??? 
> >    Having the 'soft' probabilities available is definitely a useful 
> >    improvement (cleanup, fuzzy post-processing), and I'm glad you 
> implemented 
> >    that! ??? 
> >    Josh 
>
> >    On Monday, August 20, 2012 4:11:45 PM UTC-5, Emmanuelle Gouillart 
> wrote: 
>
> >      Hi Josh, 
>
> >      extending the random walker algorithm to multichannel images sounds 
> like 
> >      a very nice idea, and I'm sure that it would be useful for other 
> people 
> >      (including myself!). 
>
> >      In fact, I had started working on some improvements of the random 
> walker 
> >      code but didn't go as far as proposing the pull request. I have a 
> branch 
> >      for that on 
> >      [1]
> https://github.com/emmanuelle/scikits.image/tree/fix_random_walker, 
> >      maybe 
> >      you can include these changes when you contribute your changes? 
>
> >      Cheers, 
> >      Emmanuelle 
>
> >      On Mon, Aug 20, 2012 at 10:03:53AM -0700, Josh Warner wrote: 
> >      > ??? ???I have modified the existing random walker algorithm into 
> a fully 
> >      > ??? ???backwards-compatible version which allows inclusion of 
> >      multispectral data, 
> >      > ??? ???e.g. RGBA channels or different (registered) image 
> modalities. ???I 
> >      really 
> >      > ??? ???liked the existing algorithm, so I just extended it rather 
> than 
> >      write one 
> >      > ??? ???from scratch for my own purposes. ???The overhead is 
> minimal; 
> >      multispectral 
> >      > ??? ???processing is triggered if data is passed as an iterable 
> of arrays 
> >      rather 
> >      > ??? ???than just an array. ??? 
> >      > ??? ???This amounts to combining image gradients as 
> sqrt(sum-of-squares) 
> >      and 
> >      > ??? ???dividing by sqrt(#channels). ???For obvious reasons, the 
> several 
> >      channels 
> >      > ??? ???must be pre-processed to have data on similar ranges by 
> whitening 
> >      or a 
> >      > ??? ???similar method. ???Not usually a problem for RGB, but in 
> medical 
> >      imaging 
> >      > ??? ???this rears its head. 
> >      > ??? ???Would this be of interest to the community? ???I'd be 
> happy to 
> >      contribute 
> >      > ??? ???the changes if there is interest. 
>
> > References 
>
> >    Visible links 
> >    1. https://github.com/emmanuelle/scikits.image/tree/fix_random_walker 
>
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From emmanuelle.gouillart at nsup.org  Mon Aug 27 08:55:11 2012
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Mon, 27 Aug 2012 14:55:11 +0200
Subject: Multispectral random walker segmentation
In-Reply-To: <8f5b3756-7912-4cdf-8aad-f8d47b0ecae6@googlegroups.com>
References: <3632b7ed-0b4b-4889-959f-5cae47d80ae9@googlegroups.com>
 <20120820211145.GB949@phare.normalesup.org>
 <8f5b3756-7912-4cdf-8aad-f8d47b0ecae6@googlegroups.com>
Message-ID: <20120827125511.GA4067@phare.normalesup.org>

Hi Josh,

my changes have been merged, so if you pull from github they are in
the master branch now, you can add your changes and make a pull request!

Cheers,
Emmanuelle

On Thu, Aug 23, 2012 at 02:50:05PM -0700, Josh Warner wrote:
>    I'd be happy to include your suggested changes, if it's simpler to go that
>    route than have two separate pull requests. ??????I don't want to step on any
>    toes regarding attribution, though. ??????
>    Having the 'soft' probabilities available is definitely a useful
>    improvement (cleanup, fuzzy post-processing), and I'm glad you implemented
>    that! ??????
>    Josh

>    On Monday, August 20, 2012 4:11:45 PM UTC-5, Emmanuelle Gouillart wrote:

>      Hi Josh,

>      extending the random walker algorithm to multichannel images sounds like
>      a very nice idea, and I'm sure that it would be useful for other people
>      (including myself!).

>      In fact, I had started working on some improvements of the random walker
>      code but didn't go as far as proposing the pull request. I have a branch
>      for that on
>      [1]https://github.com/emmanuelle/scikits.image/tree/fix_random_walker,
>      maybe
>      you can include these changes when you contribute your changes?

>      Cheers,
>      Emmanuelle

>      On Mon, Aug 20, 2012 at 10:03:53AM -0700, Josh Warner wrote:
>      > ?????? ??????I have modified the existing random walker algorithm into a fully
>      > ?????? ??????backwards-compatible version which allows inclusion of
>      multispectral data,
>      > ?????? ??????e.g. RGBA channels or different (registered) image modalities. ??????I
>      really
>      > ?????? ??????liked the existing algorithm, so I just extended it rather than
>      write one
>      > ?????? ??????from scratch for my own purposes. ??????The overhead is minimal;
>      multispectral
>      > ?????? ??????processing is triggered if data is passed as an iterable of arrays
>      rather
>      > ?????? ??????than just an array. ??????
>      > ?????? ??????This amounts to combining image gradients as sqrt(sum-of-squares)
>      and
>      > ?????? ??????dividing by sqrt(#channels). ??????For obvious reasons, the several
>      channels
>      > ?????? ??????must be pre-processed to have data on similar ranges by whitening
>      or a
>      > ?????? ??????similar method. ??????Not usually a problem for RGB, but in medical
>      imaging
>      > ?????? ??????this rears its head.
>      > ?????? ??????Would this be of interest to the community? ??????I'd be happy to
>      contribute
>      > ?????? ??????the changes if there is interest.

> References

>    Visible links
>    1. https://github.com/emmanuelle/scikits.image/tree/fix_random_walker


From emmanuelle.gouillart at nsup.org  Mon Aug 27 09:43:56 2012
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Mon, 27 Aug 2012 15:43:56 +0200
Subject: inconsistency between label and regionprops
Message-ID: <20120827134356.GC4067@phare.normalesup.org>

	Hello,

	regionsprops only measures the properties of region labeled with
strictly positive labels (since it uses ndimage.find_objects). However,
when using skimage's label with the background keyword argument, the
background pixels are labeled with -1, so that there is one foreground
region labeled with the label 0. This region will not be taken into
account by regionprops.

	This behaviour can be fixed easily in regionprops, but wouldn't
it be better to label background pixels with 0?

	Cheers,
	Emmanuelle



From emmanuelle.gouillart at nsup.org  Mon Aug 27 17:27:31 2012
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Mon, 27 Aug 2012 23:27:31 +0200
Subject: Multispectral random walker segmentation
In-Reply-To: <aca261ce-91c7-4b7e-aea8-f53fba0ecf61@googlegroups.com>
References: <3632b7ed-0b4b-4889-959f-5cae47d80ae9@googlegroups.com>
 <20120820211145.GB949@phare.normalesup.org>
 <8f5b3756-7912-4cdf-8aad-f8d47b0ecae6@googlegroups.com>
 <20120827125511.GA4067@phare.normalesup.org>
 <aca261ce-91c7-4b7e-aea8-f53fba0ecf61@googlegroups.com>
Message-ID: <20120827212731.GA19434@phare.normalesup.org>

Wow, that was quick :-), thanks!

I'll have a look tomorrow, I'm just back from Brussels and Euroscipy!

Emmanuelle

On Mon, Aug 27, 2012 at 02:18:22PM -0700, Josh Warner wrote:
>    Pull request is up! ??????I also fixed a bug in the fallback call of
>    _solve_cg() if pyamg is not installed. ??????Comments appreciated.
>    Josh
>    On Monday, August 27, 2012 7:55:11 AM UTC-5, Emmanuelle Gouillart wrote:

>      Hi Josh,

>      my changes have been merged, so if you pull from github they are in
>      the master branch now, you can add your changes and make a pull request!

>      Cheers,
>      Emmanuelle

>      On Thu, Aug 23, 2012 at 02:50:05PM -0700, Josh Warner wrote:
>      > ?????? ??????I'd be happy to include your suggested changes, if it's simpler to
>      go that
>      > ?????? ??????route than have two separate pull requests. ??????I don't want to step
>      on any
>      > ?????? ??????toes regarding attribution, though. ??????
>      > ?????? ??????Having the 'soft' probabilities available is definitely a useful
>      > ?????? ??????improvement (cleanup, fuzzy post-processing), and I'm glad you
>      implemented
>      > ?????? ??????that! ??????
>      > ?????? ??????Josh

>      > ?????? ??????On Monday, August 20, 2012 4:11:45 PM UTC-5, Emmanuelle Gouillart
>      wrote:

>      > ?????? ?????? ??????Hi Josh,

>      > ?????? ?????? ??????extending the random walker algorithm to multichannel images
>      sounds like
>      > ?????? ?????? ??????a very nice idea, and I'm sure that it would be useful for other
>      people
>      > ?????? ?????? ??????(including myself!).

>      > ?????? ?????? ??????In fact, I had started working on some improvements of the random
>      walker
>      > ?????? ?????? ??????code but didn't go as far as proposing the pull request. I have a
>      branch
>      > ?????? ?????? ??????for that on
>      > ?????? ??????
>      ??????[1][1]https://github.com/emmanuelle/scikits.image/tree/fix_random_walker,
>      > ?????? ?????? ??????maybe
>      > ?????? ?????? ??????you can include these changes when you contribute your changes?

>      > ?????? ?????? ??????Cheers,
>      > ?????? ?????? ??????Emmanuelle

>      > ?????? ?????? ??????On Mon, Aug 20, 2012 at 10:03:53AM -0700, Josh Warner wrote:
>      > ?????? ?????? ??????> ?????? ??????I have modified the existing random walker algorithm
>      into a fully
>      > ?????? ?????? ??????> ?????? ??????backwards-compatible version which allows inclusion of
>      > ?????? ?????? ??????multispectral data,
>      > ?????? ?????? ??????> ?????? ??????e.g. RGBA channels or different (registered) image
>      modalities. ??????I
>      > ?????? ?????? ??????really
>      > ?????? ?????? ??????> ?????? ??????liked the existing algorithm, so I just extended it
>      rather than
>      > ?????? ?????? ??????write one
>      > ?????? ?????? ??????> ?????? ??????from scratch for my own purposes. ??????The overhead is
>      minimal;
>      > ?????? ?????? ??????multispectral
>      > ?????? ?????? ??????> ?????? ??????processing is triggered if data is passed as an iterable
>      of arrays
>      > ?????? ?????? ??????rather
>      > ?????? ?????? ??????> ?????? ??????than just an array. ??????
>      > ?????? ?????? ??????> ?????? ??????This amounts to combining image gradients as
>      sqrt(sum-of-squares)
>      > ?????? ?????? ??????and
>      > ?????? ?????? ??????> ?????? ??????dividing by sqrt(#channels). ??????For obvious reasons, the
>      several
>      > ?????? ?????? ??????channels
>      > ?????? ?????? ??????> ?????? ??????must be pre-processed to have data on similar ranges by
>      whitening
>      > ?????? ?????? ??????or a
>      > ?????? ?????? ??????> ?????? ??????similar method. ??????Not usually a problem for RGB, but in
>      medical
>      > ?????? ?????? ??????imaging
>      > ?????? ?????? ??????> ?????? ??????this rears its head.
>      > ?????? ?????? ??????> ?????? ??????Would this be of interest to the community? ??????I'd be
>      happy to
>      > ?????? ?????? ??????contribute
>      > ?????? ?????? ??????> ?????? ??????the changes if there is interest.

>      > References

>      > ?????? ??????Visible links
>      > ?????? ??????1.
>      [2]https://github.com/emmanuelle/scikits.image/tree/fix_random_walker

> References

>    Visible links
>    1. https://github.com/emmanuelle/scikits.image/tree/fix_random_walker
>    2. https://github.com/emmanuelle/scikits.image/tree/fix_random_walker


From stefan at sun.ac.za  Wed Aug 29 09:56:18 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 29 Aug 2012 06:56:18 -0700
Subject: Funding proposal
Message-ID: <CABDkGQkMzYGQzV0HZehD2kd8mfZ0dJ=NwX6ZTyq=9_=V-zkuaw@mail.gmail.com>

Hi everyone

There is an opportunity to apply for some funding, and I'd like to
know who'd be interested to co-author the grant.  I started a Google
document for this purpose, so let me know and I will add you.

Here's to a healthy and well-funded skimage!

St?fan


From amueller at ais.uni-bonn.de  Wed Aug 29 16:51:42 2012
From: amueller at ais.uni-bonn.de (Andreas Mueller)
Date: Wed, 29 Aug 2012 22:51:42 +0200
Subject: Funding proposal
In-Reply-To: <CABDkGQkMzYGQzV0HZehD2kd8mfZ0dJ=NwX6ZTyq=9_=V-zkuaw@mail.gmail.com>
References: <CABDkGQkMzYGQzV0HZehD2kd8mfZ0dJ=NwX6ZTyq=9_=V-zkuaw@mail.gmail.com>
Message-ID: <503E80DE.9020407@ais.uni-bonn.de>

Hi Stefan.
In principle I'd be interested and if you don't find any one else, I can 
volunteer.
The only issue is that I am super swamped. But for funding skimage, I'm sure
I could make some room ;)

Cheers,
Andy


On 08/29/2012 03:56 PM, St??????fan van der Walt wrote:
> Hi everyone
>
> There is an opportunity to apply for some funding, and I'd like to
> know who'd be interested to co-author the grant.  I started a Google
> document for this purpose, so let me know and I will add you.
>
> Here's to a healthy and well-funded skimage!
>
> St??????fan



From stefan at sun.ac.za  Thu Aug 30 18:12:18 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 30 Aug 2012 15:12:18 -0700
Subject: Timing comparisons between mahotas & scikits-image
In-Reply-To: <1778077.rfoaDOHWWB@peterrabbit>
References: <1778077.rfoaDOHWWB@peterrabbit>
Message-ID: <CABDkGQmLT0Z150Txkm6R5Rp=VOWcZag06N9vpowGOLUGeE_9qQ@mail.gmail.com>

On Aug 30, 2012 7:05 PM, "Luis Pedro Coelho" <luis at luispedro.org> wrote:
> I attach the script that generates these (against github skimage). If you
> think that I have used skimage incorrectly, please let me know.

Thanks for these timings, Luis. We'll work on improving the execution speed
for the time of publication!

For anyone interested in a bounty...let me know :)

Cheers
St?fan
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From luis at luispedro.org  Thu Aug 30 12:46:46 2012
From: luis at luispedro.org (Luis Pedro Coelho)
Date: Thu, 30 Aug 2012 17:46:46 +0100
Subject: Timing comparisons between mahotas & scikits-image
Message-ID: <1778077.rfoaDOHWWB@peterrabbit>

Hello,

In the context of my previous email to pythonvision

https://groups.google.com/d/topic/pythonvision/SSCF4LUlRKQ/discussion

I made a timing comparison between mahotas & scikits-image.

operation   | mahotas  | pymorph  | skimage
------------+----------+----------+---------
erode       |    10.80 |    14.33 |    80.17
dilate      |    11.44 |     8.93 |    41.59
open        |    22.45 |    23.20 |    80.18
center mass |     7.05 |       NA |       NA
sobel       |    75.03 |       NA |   105.72
cwatershed  |   201.03 | 56586.50 |   290.41
daubechies  |    19.05 |       NA |       NA
haralick    |   306.48 |       NA |  7391.37

(Best viewed with fixed-width fonts)

The unit of measurement is the time it takes to run ``numpy.max(image)`` 
Mahotas is always faster than skimage (although pymorph is better for certain 
morphological basic operations). I used GCLM in skimage to stand for Haralick, 
which is a rough approximation.

I attach the script that generates these (against github skimage). If you 
think that I have used skimage incorrectly, please let me know.

Best,
-- 
Luis Pedro Coelho | Institute for Molecular Medicine | http://luispedro.org
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From stefan at sun.ac.za  Fri Aug 31 09:58:30 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Fri, 31 Aug 2012 06:58:30 -0700
Subject: Geometric transformations
In-Reply-To: <94c74137-0a17-49af-8748-a0a63932fa1b@googlegroups.com>
References: <CABDkGQnFRu9n8961MSWsPTJizY=qXEyJd1xt1yWVYKyDEEvEoA@mail.gmail.com>
	<D8DB1E9E-6C4D-4E75-8412-0E506BA4AD81@gmail.com>
	<CABDkGQm0Ltpy9rpokK8=NR5qUWwO9RKx=w180OiCEHhThSOQUA@mail.gmail.com>
	<94c74137-0a17-49af-8748-a0a63932fa1b@googlegroups.com>
Message-ID: <CABDkGQmm7sKDqY9y7jTfX5iDuaCSofOTeNvpU_DXhkuaUr5hAA@mail.gmail.com>

Hi Tim
On Aug 31, 2012 3:48 PM, "Tim Sheerman-Chase" <timsc60 at googlemail.com>
wrote:
>
> Hi all,
>
> I just implemented a stand alone piecewise affine image warp function. A
friend pointed me at this project and said you might be interested. I
noticed this thread on the recently merged geometric transforms. It seems
to include an affine transform function. I wondered if it would be worth
extending the new affine transform in scikits-image to also handle
piecewise affine?
>
> https://github.com/TimSC/image-piecewise-affine
>
> Any thoughts?

Thanks for getting in touch; we are definitely interested! I think you'll
find it easy to integrate your code with our warp module.. All you need to
specify is a coordinate transformation.

Would you like to have a look at our code as well? We'd gladly work with
you to get this integrated.

Regards
St?fan
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From timsc60 at googlemail.com  Fri Aug 31 14:24:39 2012
From: timsc60 at googlemail.com (Tim Sheerman-Chase)
Date: Fri, 31 Aug 2012 11:24:39 -0700 (PDT)
Subject: Geometric transformations
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St?fan,

I found scikits-image is using quite a different approach than my version 
but I think I have it mostly working now!

https://github.com/scikits-image/scikits-image/pull/286 

Regards,
Tim
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