From stefanv at berkeley.edu  Mon Apr  4 22:47:25 2016
From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Mon, 4 Apr 2016 19:47:25 -0700
Subject: New core team member
Message-ID: <CABDkGQ=Y5eLBNoN6kVHt8ZQxORX4PU0FBSG27QWQB4fS3828zg@mail.gmail.com>

Dear scikit-image community

It is my pleasure to welcome Egor Panfilov (@soupault) to the core
team!  As you may have seen on GitHub, Egor has been hard at working
triaging, reviewing, and contributing.

Thank you for your hard work so far, Egor, and we look forward to your
future contributions!

Best regards
St?fan


From multicolor.mood at gmail.com  Tue Apr  5 14:41:12 2016
From: multicolor.mood at gmail.com (Egor Panfilov)
Date: Tue, 5 Apr 2016 11:41:12 -0700 (PDT)
Subject: New core team member
In-Reply-To: <CABDkGQ=Y5eLBNoN6kVHt8ZQxORX4PU0FBSG27QWQB4fS3828zg@mail.gmail.com>
References: <CABDkGQ=Y5eLBNoN6kVHt8ZQxORX4PU0FBSG27QWQB4fS3828zg@mail.gmail.com>
Message-ID: <5e6f8cf1-f12e-43fd-b3b4-0fc4fd31475f@googlegroups.com>

Thank you very much, lady and gentlemen! ;)
It is a great pleasure for me to work with you side by side on such a 
strong project!

Kind regards,
Egor Panfilov
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From emmanuelle.gouillart at nsup.org  Tue Apr  5 09:16:47 2016
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Tue, 5 Apr 2016 15:16:47 +0200
Subject: New core team member
In-Reply-To: <CA+JHcKR7X=EJmOS=jJ72kddNuzSXEEXrEZReSjEnjptKUrx+3g@mail.gmail.com>
References: <CABDkGQ=Y5eLBNoN6kVHt8ZQxORX4PU0FBSG27QWQB4fS3828zg@mail.gmail.com>
 <CA+JHcKR7X=EJmOS=jJ72kddNuzSXEEXrEZReSjEnjptKUrx+3g@mail.gmail.com>
Message-ID: <20160405131647.GC2726200@phare.normalesup.org>

Welcome Egor! It's awesome to see the core team grow thanks to dedicated
and enthusiastic new members like you!

Emma

On Tue, Apr 05, 2016 at 06:04:30PM +1000, Juan Nunez-Iglesias wrote:
> Welcome, Egor! And I'll reiterate St??fan's statement: thank you very much for
> all your hard work on github so far! It's been impressive. =D

> On Tue, Apr 5, 2016 at 12:47 PM, St??fan van der Walt <stefanv at berkeley.edu>
> wrote:

>     Dear scikit-image community

>     It is my pleasure to welcome Egor Panfilov (@soupault) to the core
>     team!?? As you may have seen on GitHub, Egor has been hard at working
>     triaging, reviewing, and contributing.

>     Thank you for your hard work so far, Egor, and we look forward to your
>     future contributions!

>     Best regards
>     St??fan


From jni.soma at gmail.com  Tue Apr  5 04:04:30 2016
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Tue, 5 Apr 2016 18:04:30 +1000
Subject: New core team member
In-Reply-To: <CABDkGQ=Y5eLBNoN6kVHt8ZQxORX4PU0FBSG27QWQB4fS3828zg@mail.gmail.com>
References: <CABDkGQ=Y5eLBNoN6kVHt8ZQxORX4PU0FBSG27QWQB4fS3828zg@mail.gmail.com>
Message-ID: <CA+JHcKR7X=EJmOS=jJ72kddNuzSXEEXrEZReSjEnjptKUrx+3g@mail.gmail.com>

Welcome, Egor! And I'll reiterate St?fan's statement: thank you very much
for all your hard work on github so far! It's been impressive. =D

On Tue, Apr 5, 2016 at 12:47 PM, St?fan van der Walt <stefanv at berkeley.edu>
wrote:

> Dear scikit-image community
>
> It is my pleasure to welcome Egor Panfilov (@soupault) to the core
> team!  As you may have seen on GitHub, Egor has been hard at working
> triaging, reviewing, and contributing.
>
> Thank you for your hard work so far, Egor, and we look forward to your
> future contributions!
>
> Best regards
> St?fan
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> To post to this group, send an email to scikit-image at googlegroups.com.
> To view this discussion on the web, visit
> https://groups.google.com/d/msgid/scikit-image/CABDkGQ%3DY5eLBNoN6kVHt8ZQxORX4PU0FBSG27QWQB4fS3828zg%40mail.gmail.com
> .
> For more options, visit https://groups.google.com/d/optout.
>
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From arokem at gmail.com  Sat Apr  9 18:32:01 2016
From: arokem at gmail.com (Ariel Rokem)
Date: Sat, 9 Apr 2016 15:32:01 -0700
Subject: [JOB] Fwd: [Comp-neuro] Image Analysis Job Opportunity at Salk Institute
Message-ID: <CA+X4w0wn-LiQ0PX0tp32Q4wgC8jBJXw1uhCN82Mts_AH6s+NDA@mail.gmail.com>

Forgive cross-posting. This might be of interest to denizens of this list.

---------- Forwarded message ----------
From: Uri Manor <umanor at salk.edu>
Date: Fri, Apr 8, 2016 at 3:56 PM
Subject: [Comp-neuro] Image Analysis Job Opportunity at Salk Institute
To: "comp-neuro at neuroinf.org" <comp-neuro at neuroinf.org>


Hi everyone,
Please spread the word far and wide! Thanks!

WAITT ADVANCED BIOPHOTONICS CORE Job Opportunity ? Image Analysis Scientist

The Waitt Advanced Biophotonics Center has been established at the Salk
Institute for Biological Studies as a state-of-the-art research hub to
provide advanced and emerging imaging modalities to enable unprecedented
insights into the inner workings of cells, tissues and organisms. We are
seeking a highly motivated and experienced candidate in the field of
computational image analysis to serve as an Image Analysis Scientist for
the Biophotonics Core Facility.

The Image Analysis Scientist will have a principal responsibility to
collaborate with the other light and electron microscopy researchers in the
Biophotonics Core and the Salk Institute to provide specific expertise for
developing custom computer algorithms for complex and novel analyses of raw
imaging data, computer data management and developing algorithms for
microscopy operations. The Image Analysis Scientist will also develop and
publish novel imaging and image analysis techniques in collaboration
with the Core Director and Salk faculty. The Image Analysis Scientist will
apply existing image processing software to 2D and 3D images and videos,
and will also integrate data across different platforms (e.g. correlative
EM). Finally, under the supervision and training of the Core Director, the
Image Analysis Scientist will become familiar with the microscopes used in
the facility, and develop expertise in using the equipment to acquire
imaging data optimized for image analysis. Along with the Core Director,
the Image Analysis Scientist will train Salk scientists on how to properly
acquire high quality quantitative microscopy image data. This is a
multi-faceted job that involves the following components:

? Image Processing & Data Analysis - With the support of the Core Director,
the incumbent will participate in the collaborative development of custom
image data analysis and algorithm solutions.

? Research Design & Participation - aiding Director and independently
assisting users in design of imaging experiments. Educate facility users in
the use of facility instrumentation and methods used therein for optimal
acquisition of imaging data.

? Data Collection & Presentation - collecting and managing data and helping
to prepare data for publication & presentation.

? User Training - guide and assist Salk researchers in the use of existing
image acquisition and processing software.

To Apply: Send CV to umanor at salk.edu or http://www.salk.edu/about/careers/ (Job
# F142)


Uri Manor, Ph.D.
DIRECTOR
WAITT ADVANCED BIOPHOTONICS CORE
PH (858) 453-4100 x2119
*M *(314) 406-7618
E umanor at salk.edu <tberggren at salk.edu>
W http://bpho.salk.edu <tberggren at salk.edu>






Salk Institute for Biological Studies
10010 N Torrey Pines Rd ? La Jolla, CA 92037
WWW.SALK.EDU <http://www.salk.edu>





_______________________________________________
Comp-neuro mailing list
Comp-neuro at neuroinf.org
http://www.neuroinf.org/mailman/listinfo/comp-neuro
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From gustavo.goretkin at gmail.com  Mon Apr 11 03:07:55 2016
From: gustavo.goretkin at gmail.com (Gustavo Goretkin)
Date: Mon, 11 Apr 2016 00:07:55 -0700 (PDT)
Subject: suppress UserWarning
Message-ID: <a2ba7174-fb12-4a7a-aef0-85dcbc50136f@googlegroups.com>

I'm on skimage.__version__ '0.12.3' and I see warnings like

`UserWarning: test.png is a low contrast image`

and it gets printed every time, not just once. How can I suppress this 
warning? I am not even sure if skimage is responsible for printing this.

Thanks,
Gustavo



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From gustavo.goretkin at gmail.com  Mon Apr 11 03:30:43 2016
From: gustavo.goretkin at gmail.com (Gustavo Goretkin)
Date: Mon, 11 Apr 2016 00:30:43 -0700 (PDT)
Subject: suppress UserWarning
In-Reply-To: <a2ba7174-fb12-4a7a-aef0-85dcbc50136f@googlegroups.com>
References: <a2ba7174-fb12-4a7a-aef0-85dcbc50136f@googlegroups.com>
Message-ID: <1faa281a-86ab-4e02-b4b8-e4ef53c89787@googlegroups.com>

I should be clear, that the warning message changes each time, because the 
file name is different each time, so the warning module doesn't know it's 
the same warning
https://github.com/scikit-image/scikit-image/blob/bfb6175485afc929ba2ee6f1ba73013f8fa98731/skimage/io/_io.py#L132

For anyone else searching, these warnings are using the general python 
`warnings` module, and that this works to suppress the warning.

                with warnings.catch_warnings():
                    warnings.simplefilter("ignore")
                    skimage.io.imsave


On Monday, April 11, 2016 at 3:07:55 AM UTC-4, Gustavo Goretkin wrote:
>
> I'm on skimage.__version__ '0.12.3' and I see warnings like
>
> `UserWarning: test.png is a low contrast image`
>
> and it gets printed every time, not just once. How can I suppress this 
> warning? I am not even sure if skimage is responsible for printing this.
>
> Thanks,
> Gustavo
>
>
>
>
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From stefanv at berkeley.edu  Wed Apr 13 13:49:00 2016
From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Wed, 13 Apr 2016 10:49:00 -0700
Subject: Please share your use cases
In-Reply-To: <CABDkGQnDMxk87RmvA3e32XBUGLBKOHgS7OD1v5DkFO6hpbZn=A@mail.gmail.com>
References: <CABDkGQn3MncBAF3w-oDxE23p_GkX90AtK1Y_O3+O1muLLOtq3A@mail.gmail.com>
	<CABDkGQmFfrbRQrQgqLSWm-Y2gXVoWPaEAkYpoWutDRKhPO6YkQ@mail.gmail.com>
	<CABDkGQnDMxk87RmvA3e32XBUGLBKOHgS7OD1v5DkFO6hpbZn=A@mail.gmail.com>
Message-ID: <CABDkGQkQgf7sGpd0agAReX5MHiNUx6zohsRuoXEuzS1Gq_rQiw@mail.gmail.com>

Hi, everyone

I am giving a talk on scikit-image soon, and would like to highlight how it
is being used in practice.

Please share your own applications with links to images or plots, or let me
know if you spot someone else doing something cool!

Thanks,
St?fan
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From stefanv at berkeley.edu  Thu Apr 14 04:08:30 2016
From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Thu, 14 Apr 2016 01:08:30 -0700
Subject: Fwd: [Scikit-learn-general] Binary wheel packages for Linux are coming
In-Reply-To: <CAFvE7K4ni-TE5EM2QxaKtcidLoaS1H-6Xt91uGf5_5PMVNUAcg@mail.gmail.com>
References: <CAFvE7K7cRrjcx9ccZ+FzonfMbMxavCcNaVbn2bUu2mXw2+DacA@mail.gmail.com>
 <CAFvE7K4ni-TE5EM2QxaKtcidLoaS1H-6Xt91uGf5_5PMVNUAcg@mail.gmail.com>
Message-ID: <CABDkGQ=4oB=krOz1u+epgFTz3ArB1hkpDq1dpB6hxoehyQho1A@mail.gmail.com>

Hi everyone

Please see Olivier's email below.  The same holds for scikit-image, so

pip install scikit-image

should now do a binary install on (many) Linux systems.

Please thank Nathaniel Smith (who wrote the manylinux PEP and worked
on pypi/pip integration), Robbert McGibbon (who wrote the tools to
include libraries in the wheels), Matthew Brett (who set up build
infrastructure & tested), and Olivier (who patched pypi/pip and
tested).

Best regards
St?fan



---------- Forwarded message ----------
From: Olivier Grisel
Date: 13 April 2016 at 14:52
Subject: Re: [Scikit-learn-general] Binary wheel packages for Linux are coming


OpenBLAS 0.2.18 has been released yesterday with many fixes several
bugs found via testing the scipy stack on:

https://build.openblas.net/

Matthew Brett did a full-rebuild of BLAS dependent projects (including
numpy, scipy and scikit-learn) and the resulting wheels are being
uploaded to PyPI.

On most Linux distros you can now already do:

python -m pip install --upgrade pip  # to upgrade to 8.1 or later
python -m pip install numpy scipy scikit-learn

And get the stack installed with an optimized BLAS/LAPACK without
having to compile anything.

Next I will work on updating our CI configuration to build and test
those wheels on our master branch and for future release tags.

Best,

--
Olivier

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From jalopcar at gmail.com  Thu Apr 14 11:42:00 2016
From: jalopcar at gmail.com (Jaime Lopez Carvajal)
Date: Thu, 14 Apr 2016 08:42:00 -0700 (PDT)
Subject: profile_line
Message-ID: <a3d9784e-0c57-4233-8ac0-d778229a6f9b@googlegroups.com>

HI friends,

I am having problems with *profile_line function*, because I want to get 
gray values following some coordinates, but it is given to me wrong gray 
values
that does not exist in the original image, like 128, 126 or 64.

image = np.array([[170, 170,  70,  70,  70,  70,  70,  70,  70,  70],
       [170, 170,  70,  70,  70,  70,  70,  70,  90,  70],
       [170, 170, 170,  70,  70,  70,  70,  70,  70,  70],
       [170, 170, 170,  70,  70,  70,  70,  70,  70,  70],
       [170, 170, 170,  70,  70,  70,  70,  70,  70,  70],
       [170, 170, 170, 170,  70,  70,  70,  70,  70,  70],
       [110, 170, 170, 170,  70,  70,  70,  70,  70,  70],
       [ 50, 170, 170, 170,  70,  70,  70,  70,  70,  10],
       [ 50,  50, 170, 170,  70,  70,  70,  70,  10,  10],
       [ 50, 110, 110, 110,  70,  70,  70,  70,  10,  10]], dtype=uint8)


coords = np.array([[70,  0],

       [70,  0],
       [71,  1],
       [71,  2],
       [72,  3],
       [72,  4],
       [73,  4],
       [74,  5],
       [74,  6],
       [75,  7],
       [75,  8],
       [76,  8],
       [77,  9]])


gray_values = profile_line(image,(0,0),(7,9)).astype(int)

gray_values

array([170, 170, 128, 126,  70,  70,  70,  70,  70,  70,  70,  64,  10])


but the correct values would be:

gray_values

array([170, 170, 170, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70])


Do you know why this is happening? Any suggestion?


Thanks in advance, Jaime

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From jalopcar at gmail.com  Thu Apr 14 11:54:02 2016
From: jalopcar at gmail.com (Jaime Lopez Carvajal)
Date: Thu, 14 Apr 2016 08:54:02 -0700 (PDT)
Subject: profile_line
In-Reply-To: <a3d9784e-0c57-4233-8ac0-d778229a6f9b@googlegroups.com>
References: <a3d9784e-0c57-4233-8ac0-d778229a6f9b@googlegroups.com>
Message-ID: <28bd27cf-0761-4f73-89f9-61db6668e90f@googlegroups.com>

Sorry, the correct coordinates are:
coords = np.array([[0, 0],

       [0, 0],
       [1, 1],
       [1, 2],
       [2, 3],
       [2, 3],
       [3, 4],
       [4, 5],
       [4, 6],
       [5, 6],
       [5, 7],
       [6, 8],
       [7, 9]])


On Thursday, April 14, 2016 at 11:42:01 AM UTC-4, Jaime Lopez Carvajal 
wrote:
>
> HI friends,
>
> I am having problems with *profile_line function*, because I want to get 
> gray values following some coordinates, but it is given to me wrong gray 
> values
> that does not exist in the original image, like 128, 126 or 64.
>
> image = np.array([[170, 170,  70,  70,  70,  70,  70,  70,  70,  70],
>        [170, 170,  70,  70,  70,  70,  70,  70,  90,  70],
>        [170, 170, 170,  70,  70,  70,  70,  70,  70,  70],
>        [170, 170, 170,  70,  70,  70,  70,  70,  70,  70],
>        [170, 170, 170,  70,  70,  70,  70,  70,  70,  70],
>        [170, 170, 170, 170,  70,  70,  70,  70,  70,  70],
>        [110, 170, 170, 170,  70,  70,  70,  70,  70,  70],
>        [ 50, 170, 170, 170,  70,  70,  70,  70,  70,  10],
>        [ 50,  50, 170, 170,  70,  70,  70,  70,  10,  10],
>        [ 50, 110, 110, 110,  70,  70,  70,  70,  10,  10]], dtype=uint8)
>
>
> coords = np.array([[70,  0],
>
>        [70,  0],
>        [71,  1],
>        [71,  2],
>        [72,  3],
>        [72,  4],
>        [73,  4],
>        [74,  5],
>        [74,  6],
>        [75,  7],
>        [75,  8],
>        [76,  8],
>        [77,  9]])
>
>
> gray_values = profile_line(image,(0,0),(7,9)).astype(int)
>
> gray_values
>
> array([170, 170, 128, 126,  70,  70,  70,  70,  70,  70,  70,  64,  10])
>
>
> but the correct values would be:
>
> gray_values
>
> array([170, 170, 170, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70])
>
>
> Do you know why this is happening? Any suggestion?
>
>
> Thanks in advance, Jaime
>
>
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From jalopcar at gmail.com  Thu Apr 14 19:43:51 2016
From: jalopcar at gmail.com (Jaime Lopez Carvajal)
Date: Thu, 14 Apr 2016 16:43:51 -0700 (PDT)
Subject: profile_line
In-Reply-To: <CA+JHcKTAGPyED06WUJPwyrFgR3A1MP4NMA7nnuKXLG_k70w6oQ@mail.gmail.com>
References: <a3d9784e-0c57-4233-8ac0-d778229a6f9b@googlegroups.com> <28bd27cf-0761-4f73-89f9-61db6668e90f@googlegroups.com>
 <CA+JHcKTAGPyED06WUJPwyrFgR3A1MP4NMA7nnuKXLG_k70w6oQ@mail.gmail.com>
Message-ID: <e9e7fcae-270b-44cf-8f48-e80964d8c84e@googlegroups.com>

Hi Juan,

Thanks, now I understand how it works.
Do you know how can I get the gray values without interpolation, just the 
raw gray values taken from original image?

Thanks in advance, Jaime

On Thursday, April 14, 2016 at 6:41:43 PM UTC-4, Juan Nunez-Iglesias wrote:
>
> No, those aren't the correct coordinates. ;)
>
> profile_line ensures that the coordinates are spaced 1 pixel apart, and 
> then performs interpolation (the "order" argument to the function) to find 
> the values.
>
> On Fri, Apr 15, 2016 at 1:54 AM, Jaime Lopez Carvajal <jalo... at gmail.com 
> <javascript:>> wrote:
>
>> Sorry, the correct coordinates are:
>> coords = np.array([[0, 0],
>>
>>        [0, 0],
>>        [1, 1],
>>        [1, 2],
>>        [2, 3],
>>        [2, 3],
>>        [3, 4],
>>        [4, 5],
>>        [4, 6],
>>        [5, 6],
>>        [5, 7],
>>        [6, 8],
>>        [7, 9]])
>>
>>
>> On Thursday, April 14, 2016 at 11:42:01 AM UTC-4, Jaime Lopez Carvajal 
>> wrote:
>>>
>>> HI friends,
>>>
>>> I am having problems with *profile_line function*, because I want to 
>>> get gray values following some coordinates, but it is given to me wrong 
>>> gray values
>>> that does not exist in the original image, like 128, 126 or 64.
>>>
>>> image = np.array([[170, 170,  70,  70,  70,  70,  70,  70,  70,  70],
>>>        [170, 170,  70,  70,  70,  70,  70,  70,  90,  70],
>>>        [170, 170, 170,  70,  70,  70,  70,  70,  70,  70],
>>>        [170, 170, 170,  70,  70,  70,  70,  70,  70,  70],
>>>        [170, 170, 170,  70,  70,  70,  70,  70,  70,  70],
>>>        [170, 170, 170, 170,  70,  70,  70,  70,  70,  70],
>>>        [110, 170, 170, 170,  70,  70,  70,  70,  70,  70],
>>>        [ 50, 170, 170, 170,  70,  70,  70,  70,  70,  10],
>>>        [ 50,  50, 170, 170,  70,  70,  70,  70,  10,  10],
>>>        [ 50, 110, 110, 110,  70,  70,  70,  70,  10,  10]], dtype=uint8)
>>>
>>>
>>> coords = np.array([[70,  0],
>>>
>>>        [70,  0],
>>>        [71,  1],
>>>        [71,  2],
>>>        [72,  3],
>>>        [72,  4],
>>>        [73,  4],
>>>        [74,  5],
>>>        [74,  6],
>>>        [75,  7],
>>>        [75,  8],
>>>        [76,  8],
>>>        [77,  9]])
>>>
>>>
>>> gray_values = profile_line(image,(0,0),(7,9)).astype(int)
>>>
>>> gray_values
>>>
>>> array([170, 170, 128, 126,  70,  70,  70,  70,  70,  70,  70,  64,  10])
>>>
>>>
>>> but the correct values would be:
>>>
>>> gray_values
>>>
>>> array([170, 170, 170, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70])
>>>
>>>
>>> Do you know why this is happening? Any suggestion?
>>>
>>>
>>> Thanks in advance, Jaime
>>>
>>> -- 
>> You received this message because you are subscribed to the Google Groups 
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an 
>> email to scikit-image... at googlegroups.com <javascript:>.
>> To post to this group, send email to scikit... at googlegroups.com 
>> <javascript:>.
>> To view this discussion on the web, visit 
>> https://groups.google.com/d/msgid/scikit-image/28bd27cf-0761-4f73-89f9-61db6668e90f%40googlegroups.com 
>> <https://groups.google.com/d/msgid/scikit-image/28bd27cf-0761-4f73-89f9-61db6668e90f%40googlegroups.com?utm_medium=email&utm_source=footer>
>> .
>>
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>
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From jalopcar at gmail.com  Fri Apr 15 08:33:57 2016
From: jalopcar at gmail.com (Jaime Lopez Carvajal)
Date: Fri, 15 Apr 2016 05:33:57 -0700 (PDT)
Subject: profile_line
In-Reply-To: <CA+JHcKQ-LUkG8d9qSvLSZ1n6Y=z3kpqjEJe6xb9qpTK+Ah0hkA@mail.gmail.com>
References: <a3d9784e-0c57-4233-8ac0-d778229a6f9b@googlegroups.com>
 <28bd27cf-0761-4f73-89f9-61db6668e90f@googlegroups.com> <CA+JHcKTAGPyED06WUJPwyrFgR3A1MP4NMA7nnuKXLG_k70w6oQ@mail.gmail.com>
 <e9e7fcae-270b-44cf-8f48-e80964d8c84e@googlegroups.com>
 <CA+JHcKQ-LUkG8d9qSvLSZ1n6Y=z3kpqjEJe6xb9qpTK+Ah0hkA@mail.gmail.com>
Message-ID: <ab517ed1-625c-4893-bb00-d2d02a8e260d@googlegroups.com>

Hi Juan,

Yeah, that is what I needed, no interpolation, so I will set it to 0.

Thanks, Jaime

On Friday, April 15, 2016 at 1:14:22 AM UTC-4, Juan Nunez-Iglesias wrote:
>
> Hey Jaime,
>
> Yes, if you set the interpolation order equal to 0, that resolves to 
> nearest neighbor interpolation, so it will pick the value from the nearest 
> pixel. The coordinates will still be fractional so that distances are 
> preserved, though. I hope that's still useful to you! =)
>
> Juan.
>
> On Fri, Apr 15, 2016 at 9:43 AM, Jaime Lopez Carvajal <jalo... at gmail.com 
> <javascript:>> wrote:
>
>> Hi Juan,
>>
>> Thanks, now I understand how it works.
>> Do you know how can I get the gray values without interpolation, just the 
>> raw gray values taken from original image?
>>
>> Thanks in advance, Jaime
>>
>> On Thursday, April 14, 2016 at 6:41:43 PM UTC-4, Juan Nunez-Iglesias 
>> wrote:
>>>
>>> No, those aren't the correct coordinates. ;)
>>>
>>> profile_line ensures that the coordinates are spaced 1 pixel apart, and 
>>> then performs interpolation (the "order" argument to the function) to find 
>>> the values.
>>>
>>> On Fri, Apr 15, 2016 at 1:54 AM, Jaime Lopez Carvajal <jalo... at gmail.com
>>> > wrote:
>>>
>>>> Sorry, the correct coordinates are:
>>>> coords = np.array([[0, 0],
>>>>
>>>>        [0, 0],
>>>>        [1, 1],
>>>>        [1, 2],
>>>>        [2, 3],
>>>>        [2, 3],
>>>>        [3, 4],
>>>>        [4, 5],
>>>>        [4, 6],
>>>>        [5, 6],
>>>>        [5, 7],
>>>>        [6, 8],
>>>>        [7, 9]])
>>>>
>>>>
>>>> On Thursday, April 14, 2016 at 11:42:01 AM UTC-4, Jaime Lopez Carvajal 
>>>> wrote:
>>>>>
>>>>> HI friends,
>>>>>
>>>>> I am having problems with *profile_line function*, because I want to 
>>>>> get gray values following some coordinates, but it is given to me wrong 
>>>>> gray values
>>>>> that does not exist in the original image, like 128, 126 or 64.
>>>>>
>>>>> image = np.array([[170, 170,  70,  70,  70,  70,  70,  70,  70,  70],
>>>>>        [170, 170,  70,  70,  70,  70,  70,  70,  90,  70],
>>>>>        [170, 170, 170,  70,  70,  70,  70,  70,  70,  70],
>>>>>        [170, 170, 170,  70,  70,  70,  70,  70,  70,  70],
>>>>>        [170, 170, 170,  70,  70,  70,  70,  70,  70,  70],
>>>>>        [170, 170, 170, 170,  70,  70,  70,  70,  70,  70],
>>>>>        [110, 170, 170, 170,  70,  70,  70,  70,  70,  70],
>>>>>        [ 50, 170, 170, 170,  70,  70,  70,  70,  70,  10],
>>>>>        [ 50,  50, 170, 170,  70,  70,  70,  70,  10,  10],
>>>>>        [ 50, 110, 110, 110,  70,  70,  70,  70,  10,  10]], dtype=uint8)
>>>>>
>>>>>
>>>>> coords = np.array([[70,  0],
>>>>>
>>>>>        [70,  0],
>>>>>        [71,  1],
>>>>>        [71,  2],
>>>>>        [72,  3],
>>>>>        [72,  4],
>>>>>        [73,  4],
>>>>>        [74,  5],
>>>>>        [74,  6],
>>>>>        [75,  7],
>>>>>        [75,  8],
>>>>>        [76,  8],
>>>>>        [77,  9]])
>>>>>
>>>>>
>>>>> gray_values = profile_line(image,(0,0),(7,9)).astype(int)
>>>>>
>>>>> gray_values
>>>>>
>>>>> array([170, 170, 128, 126,  70,  70,  70,  70,  70,  70,  70,  64,  10])
>>>>>
>>>>>
>>>>> but the correct values would be:
>>>>>
>>>>> gray_values
>>>>>
>>>>> array([170, 170, 170, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70])
>>>>>
>>>>>
>>>>> Do you know why this is happening? Any suggestion?
>>>>>
>>>>>
>>>>> Thanks in advance, Jaime
>>>>>
>>>>> -- 
>>>> You received this message because you are subscribed to the Google 
>>>> Groups "scikit-image" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send 
>>>> an email to scikit-image... at googlegroups.com.
>>>> To post to this group, send email to scikit... at googlegroups.com.
>>>> To view this discussion on the web, visit 
>>>> https://groups.google.com/d/msgid/scikit-image/28bd27cf-0761-4f73-89f9-61db6668e90f%40googlegroups.com 
>>>> <https://groups.google.com/d/msgid/scikit-image/28bd27cf-0761-4f73-89f9-61db6668e90f%40googlegroups.com?utm_medium=email&utm_source=footer>
>>>> .
>>>>
>>>> For more options, visit https://groups.google.com/d/optout.
>>>>
>>>
>>> -- 
>> You received this message because you are subscribed to the Google Groups 
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an 
>> email to scikit-image... at googlegroups.com <javascript:>.
>> To post to this group, send email to scikit... at googlegroups.com 
>> <javascript:>.
>> To view this discussion on the web, visit 
>> https://groups.google.com/d/msgid/scikit-image/e9e7fcae-270b-44cf-8f48-e80964d8c84e%40googlegroups.com 
>> <https://groups.google.com/d/msgid/scikit-image/e9e7fcae-270b-44cf-8f48-e80964d8c84e%40googlegroups.com?utm_medium=email&utm_source=footer>
>> .
>>
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>
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From jni.soma at gmail.com  Thu Apr 14 18:41:22 2016
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Fri, 15 Apr 2016 08:41:22 +1000
Subject: profile_line
In-Reply-To: <28bd27cf-0761-4f73-89f9-61db6668e90f@googlegroups.com>
References: <a3d9784e-0c57-4233-8ac0-d778229a6f9b@googlegroups.com> <28bd27cf-0761-4f73-89f9-61db6668e90f@googlegroups.com>
Message-ID: <CA+JHcKTAGPyED06WUJPwyrFgR3A1MP4NMA7nnuKXLG_k70w6oQ@mail.gmail.com>

No, those aren't the correct coordinates. ;)

profile_line ensures that the coordinates are spaced 1 pixel apart, and
then performs interpolation (the "order" argument to the function) to find
the values.

On Fri, Apr 15, 2016 at 1:54 AM, Jaime Lopez Carvajal <jalopcar at gmail.com>
wrote:

> Sorry, the correct coordinates are:
> coords = np.array([[0, 0],
>
>        [0, 0],
>        [1, 1],
>        [1, 2],
>        [2, 3],
>        [2, 3],
>        [3, 4],
>        [4, 5],
>        [4, 6],
>        [5, 6],
>        [5, 7],
>        [6, 8],
>        [7, 9]])
>
>
> On Thursday, April 14, 2016 at 11:42:01 AM UTC-4, Jaime Lopez Carvajal
> wrote:
>>
>> HI friends,
>>
>> I am having problems with *profile_line function*, because I want to get
>> gray values following some coordinates, but it is given to me wrong gray
>> values
>> that does not exist in the original image, like 128, 126 or 64.
>>
>> image = np.array([[170, 170,  70,  70,  70,  70,  70,  70,  70,  70],
>>        [170, 170,  70,  70,  70,  70,  70,  70,  90,  70],
>>        [170, 170, 170,  70,  70,  70,  70,  70,  70,  70],
>>        [170, 170, 170,  70,  70,  70,  70,  70,  70,  70],
>>        [170, 170, 170,  70,  70,  70,  70,  70,  70,  70],
>>        [170, 170, 170, 170,  70,  70,  70,  70,  70,  70],
>>        [110, 170, 170, 170,  70,  70,  70,  70,  70,  70],
>>        [ 50, 170, 170, 170,  70,  70,  70,  70,  70,  10],
>>        [ 50,  50, 170, 170,  70,  70,  70,  70,  10,  10],
>>        [ 50, 110, 110, 110,  70,  70,  70,  70,  10,  10]], dtype=uint8)
>>
>>
>> coords = np.array([[70,  0],
>>
>>        [70,  0],
>>        [71,  1],
>>        [71,  2],
>>        [72,  3],
>>        [72,  4],
>>        [73,  4],
>>        [74,  5],
>>        [74,  6],
>>        [75,  7],
>>        [75,  8],
>>        [76,  8],
>>        [77,  9]])
>>
>>
>> gray_values = profile_line(image,(0,0),(7,9)).astype(int)
>>
>> gray_values
>>
>> array([170, 170, 128, 126,  70,  70,  70,  70,  70,  70,  70,  64,  10])
>>
>>
>> but the correct values would be:
>>
>> gray_values
>>
>> array([170, 170, 170, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70])
>>
>>
>> Do you know why this is happening? Any suggestion?
>>
>>
>> Thanks in advance, Jaime
>>
>> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> To post to this group, send email to scikit-image at googlegroups.com.
> To view this discussion on the web, visit
> https://groups.google.com/d/msgid/scikit-image/28bd27cf-0761-4f73-89f9-61db6668e90f%40googlegroups.com
> <https://groups.google.com/d/msgid/scikit-image/28bd27cf-0761-4f73-89f9-61db6668e90f%40googlegroups.com?utm_medium=email&utm_source=footer>
> .
>
> For more options, visit https://groups.google.com/d/optout.
>
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From jni.soma at gmail.com  Fri Apr 15 01:14:01 2016
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Fri, 15 Apr 2016 15:14:01 +1000
Subject: profile_line
In-Reply-To: <e9e7fcae-270b-44cf-8f48-e80964d8c84e@googlegroups.com>
References: <a3d9784e-0c57-4233-8ac0-d778229a6f9b@googlegroups.com>
 <28bd27cf-0761-4f73-89f9-61db6668e90f@googlegroups.com> <CA+JHcKTAGPyED06WUJPwyrFgR3A1MP4NMA7nnuKXLG_k70w6oQ@mail.gmail.com>
 <e9e7fcae-270b-44cf-8f48-e80964d8c84e@googlegroups.com>
Message-ID: <CA+JHcKQ-LUkG8d9qSvLSZ1n6Y=z3kpqjEJe6xb9qpTK+Ah0hkA@mail.gmail.com>

Hey Jaime,

Yes, if you set the interpolation order equal to 0, that resolves to
nearest neighbor interpolation, so it will pick the value from the nearest
pixel. The coordinates will still be fractional so that distances are
preserved, though. I hope that's still useful to you! =)

Juan.

On Fri, Apr 15, 2016 at 9:43 AM, Jaime Lopez Carvajal <jalopcar at gmail.com>
wrote:

> Hi Juan,
>
> Thanks, now I understand how it works.
> Do you know how can I get the gray values without interpolation, just the
> raw gray values taken from original image?
>
> Thanks in advance, Jaime
>
> On Thursday, April 14, 2016 at 6:41:43 PM UTC-4, Juan Nunez-Iglesias wrote:
>>
>> No, those aren't the correct coordinates. ;)
>>
>> profile_line ensures that the coordinates are spaced 1 pixel apart, and
>> then performs interpolation (the "order" argument to the function) to find
>> the values.
>>
>> On Fri, Apr 15, 2016 at 1:54 AM, Jaime Lopez Carvajal <jalo... at gmail.com>
>> wrote:
>>
>>> Sorry, the correct coordinates are:
>>> coords = np.array([[0, 0],
>>>
>>>        [0, 0],
>>>        [1, 1],
>>>        [1, 2],
>>>        [2, 3],
>>>        [2, 3],
>>>        [3, 4],
>>>        [4, 5],
>>>        [4, 6],
>>>        [5, 6],
>>>        [5, 7],
>>>        [6, 8],
>>>        [7, 9]])
>>>
>>>
>>> On Thursday, April 14, 2016 at 11:42:01 AM UTC-4, Jaime Lopez Carvajal
>>> wrote:
>>>>
>>>> HI friends,
>>>>
>>>> I am having problems with *profile_line function*, because I want to
>>>> get gray values following some coordinates, but it is given to me wrong
>>>> gray values
>>>> that does not exist in the original image, like 128, 126 or 64.
>>>>
>>>> image = np.array([[170, 170,  70,  70,  70,  70,  70,  70,  70,  70],
>>>>        [170, 170,  70,  70,  70,  70,  70,  70,  90,  70],
>>>>        [170, 170, 170,  70,  70,  70,  70,  70,  70,  70],
>>>>        [170, 170, 170,  70,  70,  70,  70,  70,  70,  70],
>>>>        [170, 170, 170,  70,  70,  70,  70,  70,  70,  70],
>>>>        [170, 170, 170, 170,  70,  70,  70,  70,  70,  70],
>>>>        [110, 170, 170, 170,  70,  70,  70,  70,  70,  70],
>>>>        [ 50, 170, 170, 170,  70,  70,  70,  70,  70,  10],
>>>>        [ 50,  50, 170, 170,  70,  70,  70,  70,  10,  10],
>>>>        [ 50, 110, 110, 110,  70,  70,  70,  70,  10,  10]], dtype=uint8)
>>>>
>>>>
>>>> coords = np.array([[70,  0],
>>>>
>>>>        [70,  0],
>>>>        [71,  1],
>>>>        [71,  2],
>>>>        [72,  3],
>>>>        [72,  4],
>>>>        [73,  4],
>>>>        [74,  5],
>>>>        [74,  6],
>>>>        [75,  7],
>>>>        [75,  8],
>>>>        [76,  8],
>>>>        [77,  9]])
>>>>
>>>>
>>>> gray_values = profile_line(image,(0,0),(7,9)).astype(int)
>>>>
>>>> gray_values
>>>>
>>>> array([170, 170, 128, 126,  70,  70,  70,  70,  70,  70,  70,  64,  10])
>>>>
>>>>
>>>> but the correct values would be:
>>>>
>>>> gray_values
>>>>
>>>> array([170, 170, 170, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70])
>>>>
>>>>
>>>> Do you know why this is happening? Any suggestion?
>>>>
>>>>
>>>> Thanks in advance, Jaime
>>>>
>>>> --
>>> You received this message because you are subscribed to the Google
>>> Groups "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to scikit-image... at googlegroups.com.
>>> To post to this group, send email to scikit... at googlegroups.com.
>>> To view this discussion on the web, visit
>>> https://groups.google.com/d/msgid/scikit-image/28bd27cf-0761-4f73-89f9-61db6668e90f%40googlegroups.com
>>> <https://groups.google.com/d/msgid/scikit-image/28bd27cf-0761-4f73-89f9-61db6668e90f%40googlegroups.com?utm_medium=email&utm_source=footer>
>>> .
>>>
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>
>> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> To post to this group, send email to scikit-image at googlegroups.com.
> To view this discussion on the web, visit
> https://groups.google.com/d/msgid/scikit-image/e9e7fcae-270b-44cf-8f48-e80964d8c84e%40googlegroups.com
> <https://groups.google.com/d/msgid/scikit-image/e9e7fcae-270b-44cf-8f48-e80964d8c84e%40googlegroups.com?utm_medium=email&utm_source=footer>
> .
>
> For more options, visit https://groups.google.com/d/optout.
>
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From kanohen at gmail.com  Sat Apr 16 13:05:17 2016
From: kanohen at gmail.com (potato_head)
Date: Sat, 16 Apr 2016 10:05:17 -0700 (PDT)
Subject: Evaluating the predictive accuracy of the NB model
Message-ID: <acb93ac9-a262-40f0-ac4d-3d710a4c0053@googlegroups.com>



Please guys,

What am I doing wrong with using scikitlearn from nltk to check the 
accuracy of the naive bayes classifier?


...readFile definition not needed #divide the data into training and testing sets
data = readFile('Data_test/')
training_set = list_nltk[:2000000]
testing_set = list_nltk[2000000:]
#applied Bag of words as a way to select and extract feature
count_vect = CountVectorizer()
X_train_counts = count_vect.fit_transform(training_set.split('\n'))
#apply tfd
tf_transformer = TfidfTransformer(use_idf=False).fit(X_train_counts)
X_train_tf = tf_transformer.transform(X_train_counts)
#Train the data
clf = MultinomialNB().fit(X_train_tf, training_set.split('\n'))
#now test the accuracy of the naive bayes classifier
test_data_features = count_vect.transform(testing_set)
X_new_tfidf = tf_transformer.transform(test_data_features)

predicted = clf.predict(X_new_tfidf)print "%.3f" % nltk.classify.accuracy(clf, predicted)


The problem is when I print the nltk.classify.accuracy, it takes forever 
and I am suspecting this is because I have done something wrong but since I 
get no error, I can't figure out what it is that is wrong. I would really 
appreciate any pointer.
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From stefanv at berkeley.edu  Sat Apr 16 14:31:29 2016
From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Sat, 16 Apr 2016 11:31:29 -0700
Subject: Evaluating the predictive accuracy of the NB model
In-Reply-To: <acb93ac9-a262-40f0-ac4d-3d710a4c0053@googlegroups.com>
References: <acb93ac9-a262-40f0-ac4d-3d710a4c0053@googlegroups.com>
Message-ID: <CABDkGQkvgn1Y0QJs_yG_nn-OjLUjKcuNLXnuUQCcOYVbA+CsHw@mail.gmail.com>

Sorry, wrong mailing list.

On 16 April 2016 at 10:05, potato_head <kanohen at gmail.com> wrote:
> Please guys,
>
> What am I doing wrong with using scikitlearn from nltk to check the accuracy
> of the naive bayes classifier?
>
>
> ...readFile definition not needed
> #divide the data into training and testing sets
> data = readFile('Data_test/')
> training_set = list_nltk[:2000000]
> testing_set = list_nltk[2000000:]
>
> #applied Bag of words as a way to select and extract feature
> count_vect = CountVectorizer()
> X_train_counts = count_vect.fit_transform(training_set.split('\n'))
>
> #apply tfd
> tf_transformer = TfidfTransformer(use_idf=False).fit(X_train_counts)
> X_train_tf = tf_transformer.transform(X_train_counts)
>
> #Train the data
> clf = MultinomialNB().fit(X_train_tf, training_set.split('\n'))
>
> #now test the accuracy of the naive bayes classifier
> test_data_features = count_vect.transform(testing_set)
> X_new_tfidf = tf_transformer.transform(test_data_features)
>
> predicted = clf.predict(X_new_tfidf)
> print "%.3f" % nltk.classify.accuracy(clf, predicted)
>
>
> The problem is when I print the nltk.classify.accuracy, it takes forever and
> I am suspecting this is because I have done something wrong but since I get
> no error, I can't figure out what it is that is wrong. I would really
> appreciate any pointer.
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> To post to this group, send email to scikit-image at googlegroups.com.
> To view this discussion on the web, visit
> https://groups.google.com/d/msgid/scikit-image/acb93ac9-a262-40f0-ac4d-3d710a4c0053%40googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.


From stefanv at berkeley.edu  Mon Apr 18 16:03:38 2016
From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Mon, 18 Apr 2016 13:03:38 -0700
Subject: skimage.io.Image??
In-Reply-To: <CAFFEDuk8tXLyGSzJ-zPsEzpZ2qR1+1kifM0D5idJS_HECgaxwQ@mail.gmail.com>
References: <CAFFEDuk8tXLyGSzJ-zPsEzpZ2qR1+1kifM0D5idJS_HECgaxwQ@mail.gmail.com>
Message-ID: <CABDkGQnWpbHb3sDSQZBkfzr+VTDb8xzZmNVjPHj7_hpq7GzNvA@mail.gmail.com>

Hey Fernando (& skimage list, CC'd)

On 18 April 2016 at 01:43, Fernando Perez <fperez at lbl.gov> wrote:
> Quick question, where did this go?
>
> http://scikit-image.org/docs/0.11.x/api/skimage.io.html#image
>
> It's not there in 0.12 and newer, and nowhere do the docs indicate that it
> was removed, moved or otherwise tell me what I should do:
>
> http://scikit-image.org/docs/dev/api_changes.html#version-0-12

This was an oversight; we have a two release deprecation policy (with
inline warnings + mentions in the docs) which was not followed in this
case.  The internal API change was documented in the v0.9 api_changes
document, but unfortunately not the rest.

> We have an example in IPython that uses it:
> https://github.com/ipython/ipywidgets/blob/master/docs/source/examples/Image%20Processing.ipynb

I spoke to Brian several months ago to fix the issue after this came
to our attention, but I guess the changes have not made their way
through to ipywidgets.

> Any help appreciated (and you shouldn't remove classes like this from the
> API without deprecation period, warning or mention in the docs :)

Of course, you are right, this type of thing should never, ever
happen--I apologize for the confusion and wasted time.

The Image class, just like most other numpy subclasses, turned out to
be a mistake.  It wouldn't carry through the whole pipeline, and ended
up causing more confusion than what it helped.

I've factored out the source and attached it here, in case that is of some help:

from image import Image
from skimage import data
cat = data.chelsea()
Image(cat)

St?fan
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From wwjd228 at gmail.com  Mon Apr 18 23:36:52 2016
From: wwjd228 at gmail.com (Jungle Chan)
Date: Mon, 18 Apr 2016 20:36:52 -0700 (PDT)
Subject: the spatial aspect ratio in gabor kernel
Message-ID: <178327ed-ea83-4021-bbd8-1ce11a97b16d@googlegroups.com>

There is no parameter "gama(the spatial aspect ratio)" in gabor kernel, may 
I modify for it?
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From emmanuelle.gouillart at nsup.org  Mon Apr 18 16:23:58 2016
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Mon, 18 Apr 2016 22:23:58 +0200
Subject: skimage.io.Image??
In-Reply-To: <CABDkGQnWpbHb3sDSQZBkfzr+VTDb8xzZmNVjPHj7_hpq7GzNvA@mail.gmail.com>
References: <CAFFEDuk8tXLyGSzJ-zPsEzpZ2qR1+1kifM0D5idJS_HECgaxwQ@mail.gmail.com>
 <CABDkGQnWpbHb3sDSQZBkfzr+VTDb8xzZmNVjPHj7_hpq7GzNvA@mail.gmail.com>
Message-ID: <20160418202358.GB866404@phare.normalesup.org>

Oops sorry Fernando, and thanks St??fan for sharing a healthy reminder
that the deprecation policy is very useful, and should be enforced with
care. 

On Mon, Apr 18, 2016 at 01:03:38PM -0700, St??fan van der Walt wrote:
> Hey Fernando (& skimage list, CC'd)

> On 18 April 2016 at 01:43, Fernando Perez <fperez at lbl.gov> wrote:
> > Quick question, where did this go?

> > http://scikit-image.org/docs/0.11.x/api/skimage.io.html#image

> > It's not there in 0.12 and newer, and nowhere do the docs indicate that it
> > was removed, moved or otherwise tell me what I should do:

> > http://scikit-image.org/docs/dev/api_changes.html#version-0-12

> This was an oversight; we have a two release deprecation policy (with
> inline warnings + mentions in the docs) which was not followed in this
> case.  The internal API change was documented in the v0.9 api_changes
> document, but unfortunately not the rest.

> > We have an example in IPython that uses it:
> > https://github.com/ipython/ipywidgets/blob/master/docs/source/examples/Image%20Processing.ipynb

> I spoke to Brian several months ago to fix the issue after this came
> to our attention, but I guess the changes have not made their way
> through to ipywidgets.

> > Any help appreciated (and you shouldn't remove classes like this from the
> > API without deprecation period, warning or mention in the docs :)

> Of course, you are right, this type of thing should never, ever
> happen--I apologize for the confusion and wasted time.

> The Image class, just like most other numpy subclasses, turned out to
> be a mistake.  It wouldn't carry through the whole pipeline, and ended
> up causing more confusion than what it helped.

> I've factored out the source and attached it here, in case that is of some help:

> from image import Image
> from skimage import data
> cat = data.chelsea()
> Image(cat)

> St??fan


From amiksvi at gmail.com  Wed Apr 20 04:40:25 2016
From: amiksvi at gmail.com (amiksvi at gmail.com)
Date: Wed, 20 Apr 2016 01:40:25 -0700 (PDT)
Subject: Maximum Area Convex Subset (MACS)
Message-ID: <72770f60-a235-49c3-b635-be80d75b21fd@googlegroups.com>

Hello,

Let's assume I have an image with 0's as background B and a connected set S 
made of 1. Is there an easy way with scikit-image to find the maximum (in 
terms of area) subset of S that is convex. This question is also described 
here:

- 
http://math.stackexchange.com/questions/455687/find-the-maximum-convex-area
- 
http://stackoverflow.com/questions/17943482/find-the-maximum-convex-area/17967201#17967201

I was wondering if there was an algorithm already implemented in the 
library to easily do that. Otherwise I guess I'll have to implement it by 
myself as described in the links above.

Many thanks,
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From jalopcar at gmail.com  Mon Apr 25 16:30:21 2016
From: jalopcar at gmail.com (Jaime Lopez Carvajal)
Date: Mon, 25 Apr 2016 13:30:21 -0700 (PDT)
Subject: maximum square inside a contour
Message-ID: <e02b1a11-2b3f-47a8-8e22-387f8cc4e298@googlegroups.com>

Hi friends,

Someone knows how can I find a maximum square inside a contour, giving as 
parameter the centroid point? 
I need whole square area fall inside the contour. Any advice?

Thanks in advance, Jaime?
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From stefanv at berkeley.edu  Mon Apr 25 19:24:53 2016
From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Mon, 25 Apr 2016 23:24:53 +0000
Subject: ANN: Tutorial at SciPy 2016
Message-ID: <CABDkGQnR+FBRStYwpsntKJhoT=dXJP-z7GUZCSjEHYgv=xBR6w@mail.gmail.com>

Hi everyone

A quick announcement: we'll be giving a scikit-image tutorial at SciPy 2016
this year!  So far on the team we have Juan, myself, and Andreas Mueller
for machine learning advice.

If any of you would like to be involved in preparing and/or delivering
material, please let me know.

Best regards
Stefan
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From stefanv at berkeley.edu  Mon Apr 25 19:29:03 2016
From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Mon, 25 Apr 2016 23:29:03 +0000
Subject: Opinion poll: feedback URL upon import
Message-ID: <CABDkGQ=WbpDLxo4pu-UQFTM=eAVzv+76yKLnbAo6awgNWAqW8A@mail.gmail.com>

Hi all,

It has been difficult to discover use cases of scikit-image out in the wild
(even though I know they are plentiful, and users would excitedly tell me
about them at conferences once the topic is broached).

So, I was wondering if it would be considered bad form to print a message
upon importing scikit-image, something along the lines of:

"Thank you for using scikit-image v0.12! Please help us by telling us about
your use-case at http://scikit-image.org/feedback?v=0.12.3"

Thanks for your feedback,

St?fan
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From emmanuelle.gouillart at nsup.org  Mon Apr 25 17:46:14 2016
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Mon, 25 Apr 2016 23:46:14 +0200
Subject: maximum square inside a contour
In-Reply-To: <e02b1a11-2b3f-47a8-8e22-387f8cc4e298@googlegroups.com>
References: <e02b1a11-2b3f-47a8-8e22-387f8cc4e298@googlegroups.com>
Message-ID: <20160425214614.GA57801@phare.normalesup.org>

Hi Jaime,

I don't have a good solution to your problem, which seems a tricky one
from a theoretical point of view
https://en.wikipedia.org/wiki/Inscribed_square_problem
(however we can be relieved since a solution always exists for a polygon
:-)

However, if you have a 2D contour (are you in 2D?), then the square can
be parametrized by an angle and a radius (if you know its radius). A
brute-force search would do, since it's easy to find an upper boundary
for the radius (take the bounding box of scipy.ndimage). You just need
a function that tells you whether one edge of a square lies within the
contour, maybe you can do this by rasterizing the edge using
skimage.draw? 

Only small bits here, if I have better ideas I'll get back to you.

Cheers,
Emma

On Mon, Apr 25, 2016 at 01:30:21PM -0700, Jaime Lopez Carvajal wrote:
> Hi friends,

> Someone knows how can I find a maximum square inside a contour, giving as
> parameter the centroid point???
> I need whole square area fall inside the contour. Any advice?

> Thanks in advance, Jaime


From r.t.wilson.bak at googlemail.com  Tue Apr 26 06:10:34 2016
From: r.t.wilson.bak at googlemail.com (Robin Wilson)
Date: Tue, 26 Apr 2016 03:10:34 -0700 (PDT)
Subject: Opinion poll: feedback URL upon import
In-Reply-To: <D8144ED0-C052-4A55-AF46-7E772BB224B8@googlemail.com>
References: <CABDkGQ=WbpDLxo4pu-UQFTM=eAVzv+76yKLnbAo6awgNWAqW8A@mail.gmail.com> <20160426064948.GB940933@phare.normalesup.org>
 <D8144ED0-C052-4A55-AF46-7E772BB224B8@googlemail.com>
Message-ID: <55d7ee35-aae3-458f-8245-1d35756dd0ce@googlegroups.com>

I agree with the others: please don't do this!

However, being more obvious about wanting feedback, via the website, 
mailing list, in conference presentations etc, is definitely a good idea.

Robin

On Tuesday, 26 April 2016 08:05:42 UTC+1, Christoph wrote:
>
> Hi,
>
> I agree with Emma, as a scikit-image user, I would find it annoying.
> Especially if it catches on and many other Python packages start doing the 
> same.
>
> It?s probably very rare, but if people check the text output of their 
> library or application and use scikit-image somewhere, this could even 
> break their test build.
>
> In Astropy there has also been some discussion about how to get feedback 
> from users. There the discussion was more along the lines of wanting to 
> collect info which platform, versions are in use, and which sub-packages 
> and functions in the Astropy package are used. I.e. there was discussion 
> about adding some code to send such usage stats info to a server, like many 
> apps do. This didn?t happen, I think the idea has been dropped.
>
> It would be very nice and important to get more feedback from users!
>
> But it seems to me that asking for it on the website like Emma proposes or 
> in conversations and presentations might be the safer way.
>
> Christoph
>
>
>
> On 26 Apr 2016, at 08:49, Emmanuelle Gouillart <emmanuelle... at nsup.org 
> <javascript:>> wrote:
>
> Hi St?fan
>
> I'm quite against it, since it's a feature that would push scikit-image
> to be more an application and less a self-standing library: we would like
> any other package to be able to import skimage in their code without
> bothering about such messages. Indeed, such a message at import is only
> useful/relevant for people that use scikit-image deliberately and as an
> important part of their workflow, not so much for people that import
> skimage in another projects, or that just use a couple of functions of
> scikit-image (but it's not the core part of their workflow). I consider
> it important for scikit-image to be a versatile block of the ecosystem,
> and not only an application at the end of the "food chain". 
>
> We could advertise the feedback form in a different way, for example by
> making it very visible on the website. With 20000 unique visitors coming
> to the website every month, I hope that we could get some feedback... 
>
> Best,
> Emma
>
> On Mon, Apr 25, 2016 at 11:29:03PM +0000, St?fan van der Walt wrote:
>
> Hi all,
>
>
> It has been difficult to discover use cases of scikit-image out in the wild
> (even though I know they are plentiful, and users would excitedly tell me 
> about
> them at conferences once the topic is broached).
>
>
> So, I was wondering if it would be considered bad form to print a message 
> upon
> importing scikit-image, something along the lines of:
>
>
> "Thank you for using scikit-image v0.12! Please help us by telling us about
> your use-case at http://scikit-image.org/feedback?v=0.12.3"
>
>
> Thanks for your feedback,
>
>
> St?fan
>
>
> -- 
> You received this message because you are subscribed to the Google Groups 
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an 
> email to scikit-image... at googlegroups.com <javascript:>.
> To post to this group, send an email to scikit... at googlegroups.com 
> <javascript:>.
> To view this discussion on the web, visit 
> https://groups.google.com/d/msgid/scikit-image/20160426064948.GB940933%40phare.normalesup.org
> .
> For more options, visit https://groups.google.com/d/optout.
>
>
>
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From jalopcar at gmail.com  Tue Apr 26 07:40:13 2016
From: jalopcar at gmail.com (Jaime Lopez Carvajal)
Date: Tue, 26 Apr 2016 04:40:13 -0700 (PDT)
Subject: maximum square inside a contour
In-Reply-To: <20160426063933.GA940933@phare.normalesup.org>
References: <e02b1a11-2b3f-47a8-8e22-387f8cc4e298@googlegroups.com>
 <20160425214614.GA57801@phare.normalesup.org>
 <20160426063933.GA940933@phare.normalesup.org>
Message-ID: <9dcafe96-3fcd-45e4-9351-f1a5b2f1aaca@googlegroups.com>

Hi Emma,

Yeah, I know the square's centroid, and I am working in 2D.
I need my square fall inside the contour's region, 
and also the square must be not rotated, just like the green square in the 
image.

Thanks, Jaime

On Tuesday, April 26, 2016 at 2:39:34 AM UTC-4, Emmanuelle Gouillart wrote:
>
> I meant "parametrized by an angle and a radius, if you know its 
> centroid". 
>
> In the image you sent, the edges of the square are parallel to the edges 
> of the images. Are you only considering such squares, or do you also 
> allow a rotation of the square? 
>
> Best, 
> Emma 
>
> On Mon, Apr 25, 2016 at 11:46:14PM +0200, Emmanuelle Gouillart wrote: 
> > Hi Jaime, 
>
> > I don't have a good solution to your problem, which seems a tricky one 
> > from a theoretical point of view 
> > https://en.wikipedia.org/wiki/Inscribed_square_problem 
> > (however we can be relieved since a solution always exists for a polygon 
> > :-) 
>
> > However, if you have a 2D contour (are you in 2D?), then the square can 
> > be parametrized by an angle and a radius (if you know its radius). A 
> > brute-force search would do, since it's easy to find an upper boundary 
> > for the radius (take the bounding box of scipy.ndimage). You just need 
> > a function that tells you whether one edge of a square lies within the 
> > contour, maybe you can do this by rasterizing the edge using 
> > skimage.draw? 
>
> > Only small bits here, if I have better ideas I'll get back to you. 
>
> > Cheers, 
> > Emma 
>
> > On Mon, Apr 25, 2016 at 01:30:21PM -0700, Jaime Lopez Carvajal wrote: 
> > > Hi friends, 
>
> > > Someone knows how can I find a maximum square inside a contour, giving 
> as 
> > > parameter the centroid point?  
> > > I need whole square area fall inside the contour. Any advice? 
>
> > > Thanks in advance, Jaime 
>
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From emmanuelle.gouillart at nsup.org  Tue Apr 26 02:39:33 2016
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Tue, 26 Apr 2016 08:39:33 +0200
Subject: maximum square inside a contour
In-Reply-To: <20160425214614.GA57801@phare.normalesup.org>
References: <e02b1a11-2b3f-47a8-8e22-387f8cc4e298@googlegroups.com>
 <20160425214614.GA57801@phare.normalesup.org>
Message-ID: <20160426063933.GA940933@phare.normalesup.org>

I meant "parametrized by an angle and a radius, if you know its
centroid".

In the image you sent, the edges of the square are parallel to the edges
of the images. Are you only considering such squares, or do you also
allow a rotation of the square?

Best,
Emma

On Mon, Apr 25, 2016 at 11:46:14PM +0200, Emmanuelle Gouillart wrote:
> Hi Jaime,

> I don't have a good solution to your problem, which seems a tricky one
> from a theoretical point of view
> https://en.wikipedia.org/wiki/Inscribed_square_problem
> (however we can be relieved since a solution always exists for a polygon
> :-)

> However, if you have a 2D contour (are you in 2D?), then the square can
> be parametrized by an angle and a radius (if you know its radius). A
> brute-force search would do, since it's easy to find an upper boundary
> for the radius (take the bounding box of scipy.ndimage). You just need
> a function that tells you whether one edge of a square lies within the
> contour, maybe you can do this by rasterizing the edge using
> skimage.draw? 

> Only small bits here, if I have better ideas I'll get back to you.

> Cheers,
> Emma

> On Mon, Apr 25, 2016 at 01:30:21PM -0700, Jaime Lopez Carvajal wrote:
> > Hi friends,

> > Someone knows how can I find a maximum square inside a contour, giving as
> > parameter the centroid point???
> > I need whole square area fall inside the contour. Any advice?

> > Thanks in advance, Jaime


From emmanuelle.gouillart at nsup.org  Tue Apr 26 02:49:48 2016
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Tue, 26 Apr 2016 08:49:48 +0200
Subject: Opinion poll: feedback URL upon import
In-Reply-To: <CABDkGQ=WbpDLxo4pu-UQFTM=eAVzv+76yKLnbAo6awgNWAqW8A@mail.gmail.com>
References: <CABDkGQ=WbpDLxo4pu-UQFTM=eAVzv+76yKLnbAo6awgNWAqW8A@mail.gmail.com>
Message-ID: <20160426064948.GB940933@phare.normalesup.org>

Hi St??fan

I'm quite against it, since it's a feature that would push scikit-image
to be more an application and less a self-standing library: we would like
any other package to be able to import skimage in their code without
bothering about such messages. Indeed, such a message at import is only
useful/relevant for people that use scikit-image deliberately and as an
important part of their workflow, not so much for people that import
skimage in another projects, or that just use a couple of functions of
scikit-image (but it's not the core part of their workflow). I consider
it important for scikit-image to be a versatile block of the ecosystem,
and not only an application at the end of the "food chain". 

We could advertise the feedback form in a different way, for example by
making it very visible on the website. With 20000 unique visitors coming
to the website every month, I hope that we could get some feedback... 

Best,
Emma

On Mon, Apr 25, 2016 at 11:29:03PM +0000, St??fan van der Walt wrote:
> Hi all,

> It has been difficult to discover use cases of scikit-image out in the wild
> (even though I know they are plentiful, and users would excitedly tell me about
> them at conferences once the topic is broached).

> So, I was wondering if it would be considered bad form to print a message upon
> importing scikit-image, something along the lines of:

> "Thank you for using scikit-image v0.12! Please help us by telling us about
> your use-case at http://scikit-image.org/feedback?v=0.12.3"

> Thanks for your feedback,

> St??fan


From deil.christoph at googlemail.com  Tue Apr 26 03:05:39 2016
From: deil.christoph at googlemail.com (Christoph Deil)
Date: Tue, 26 Apr 2016 09:05:39 +0200
Subject: Opinion poll: feedback URL upon import
In-Reply-To: <20160426064948.GB940933@phare.normalesup.org>
References: <CABDkGQ=WbpDLxo4pu-UQFTM=eAVzv+76yKLnbAo6awgNWAqW8A@mail.gmail.com> <20160426064948.GB940933@phare.normalesup.org>
Message-ID: <D8144ED0-C052-4A55-AF46-7E772BB224B8@googlemail.com>

Hi,

I agree with Emma, as a scikit-image user, I would find it annoying.
Especially if it catches on and many other Python packages start doing the same.

It?s probably very rare, but if people check the text output of their library or application and use scikit-image somewhere, this could even break their test build.

In Astropy there has also been some discussion about how to get feedback from users. There the discussion was more along the lines of wanting to collect info which platform, versions are in use, and which sub-packages and functions in the Astropy package are used. I.e. there was discussion about adding some code to send such usage stats info to a server, like many apps do. This didn?t happen, I think the idea has been dropped.

It would be very nice and important to get more feedback from users!

But it seems to me that asking for it on the website like Emma proposes or in conversations and presentations might be the safer way.

Christoph



> On 26 Apr 2016, at 08:49, Emmanuelle Gouillart <emmanuelle.gouillart at nsup.org> wrote:
> 
> Hi St?fan
> 
> I'm quite against it, since it's a feature that would push scikit-image
> to be more an application and less a self-standing library: we would like
> any other package to be able to import skimage in their code without
> bothering about such messages. Indeed, such a message at import is only
> useful/relevant for people that use scikit-image deliberately and as an
> important part of their workflow, not so much for people that import
> skimage in another projects, or that just use a couple of functions of
> scikit-image (but it's not the core part of their workflow). I consider
> it important for scikit-image to be a versatile block of the ecosystem,
> and not only an application at the end of the "food chain". 
> 
> We could advertise the feedback form in a different way, for example by
> making it very visible on the website. With 20000 unique visitors coming
> to the website every month, I hope that we could get some feedback... 
> 
> Best,
> Emma
> 
> On Mon, Apr 25, 2016 at 11:29:03PM +0000, St?fan van der Walt wrote:
>> Hi all,
> 
>> It has been difficult to discover use cases of scikit-image out in the wild
>> (even though I know they are plentiful, and users would excitedly tell me about
>> them at conferences once the topic is broached).
> 
>> So, I was wondering if it would be considered bad form to print a message upon
>> importing scikit-image, something along the lines of:
> 
>> "Thank you for using scikit-image v0.12! Please help us by telling us about
>> your use-case at http://scikit-image.org/feedback?v=0.12.3"
> 
>> Thanks for your feedback,
> 
>> St?fan
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> To post to this group, send an email to scikit-image at googlegroups.com <mailto:scikit-image at googlegroups.com>.
> To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/20160426064948.GB940933%40phare.normalesup.org <https://groups.google.com/d/msgid/scikit-image/20160426064948.GB940933%40phare.normalesup.org>.
> For more options, visit https://groups.google.com/d/optout <https://groups.google.com/d/optout>.

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From kevin.keraudren at googlemail.com  Tue Apr 26 07:49:15 2016
From: kevin.keraudren at googlemail.com (Kevin Keraudren)
Date: Tue, 26 Apr 2016 12:49:15 +0100
Subject: Opinion poll: feedback URL upon import
In-Reply-To: <CAB=suEkN-VdjQ=Z6=RXKnMX2mwotjqVJ2X3HO1ihRH8k-iDQ8w@mail.gmail.com>
References: <CABDkGQ=WbpDLxo4pu-UQFTM=eAVzv+76yKLnbAo6awgNWAqW8A@mail.gmail.com>
	<20160426064948.GB940933@phare.normalesup.org>
	<D8144ED0-C052-4A55-AF46-7E772BB224B8@googlemail.com>
	<55d7ee35-aae3-458f-8245-1d35756dd0ce@googlegroups.com>
	<CAB=suEkN-VdjQ=Z6=RXKnMX2mwotjqVJ2X3HO1ihRH8k-iDQ8w@mail.gmail.com>
Message-ID: <CADe6jSp756gGkgXYhdjvGzzD2q3g2-y9+iK+SEWQpOetq1pWaQ@mail.gmail.com>

Noisy output at import is bad. In addition to the suggestions previously
made, what about also mentioning the feedback url in the main docstring of
skimage, something like here:
https://github.com/scikit-image/scikit-image/blob/master/skimage/__init__.py#L9

On Tue, Apr 26, 2016 at 12:40 PM, Jaidev Deshpande <
deshpande.jaidev at gmail.com> wrote:

>
>
> On Tue, Apr 26, 2016 at 3:40 PM, 'Robin Wilson' via scikit-image <
> scikit-image at googlegroups.com> wrote:
>
>> I agree with the others: please don't do this!
>>
>> However, being more obvious about wanting feedback, via the website,
>> mailing list, in conference presentations etc, is definitely a good idea.
>>
>> Robin
>>
>> On Tuesday, 26 April 2016 08:05:42 UTC+1, Christoph wrote:
>>>
>>> Hi,
>>>
>>> I agree with Emma, as a scikit-image user, I would find it annoying.
>>> Especially if it catches on and many other Python packages start doing
>>> the same.
>>>
>>> It?s probably very rare, but if people check the text output of their
>>> library or application and use scikit-image somewhere, this could even
>>> break their test build.
>>>
>>> In Astropy there has also been some discussion about how to get feedback
>>> from users. There the discussion was more along the lines of wanting to
>>> collect info which platform, versions are in use, and which sub-packages
>>> and functions in the Astropy package are used. I.e. there was discussion
>>> about adding some code to send such usage stats info to a server, like many
>>> apps do. This didn?t happen, I think the idea has been dropped.
>>>
>>> It would be very nice and important to get more feedback from users!
>>>
>>> But it seems to me that asking for it on the website like Emma proposes
>>> or in conversations and presentations might be the safer way.
>>>
>>> Christoph
>>>
>>>
>>>
>>> On 26 Apr 2016, at 08:49, Emmanuelle Gouillart <emmanuelle... at nsup.org>
>>> wrote:
>>>
>>> Hi St?fan
>>>
>>> I'm quite against it, since it's a feature that would push scikit-image
>>> to be more an application and less a self-standing library: we would like
>>> any other package to be able to import skimage in their code without
>>> bothering about such messages. Indeed, such a message at import is only
>>> useful/relevant for people that use scikit-image deliberately and as an
>>> important part of their workflow, not so much for people that import
>>> skimage in another projects, or that just use a couple of functions of
>>> scikit-image (but it's not the core part of their workflow). I consider
>>> it important for scikit-image to be a versatile block of the ecosystem,
>>> and not only an application at the end of the "food chain".
>>>
>>> We could advertise the feedback form in a different way, for example by
>>> making it very visible on the website. With 20000 unique visitors coming
>>> to the website every month, I hope that we could get some feedback...
>>>
>>> Best,
>>> Emma
>>>
>>> On Mon, Apr 25, 2016 at 11:29:03PM +0000, St?fan van der Walt wrote:
>>>
>>> Hi all,
>>>
>>>
>>> It has been difficult to discover use cases of scikit-image out in the
>>> wild
>>> (even though I know they are plentiful, and users would excitedly tell
>>> me about
>>> them at conferences once the topic is broached).
>>>
>>>
>>> So, I was wondering if it would be considered bad form to print a
>>> message upon
>>> importing scikit-image, something along the lines of:
>>>
>>>
>>> "Thank you for using scikit-image v0.12! Please help us by telling us
>>> about
>>> your use-case at http://scikit-image.org/feedback?v=0.12.3"
>>>
>>>
>>> Thanks for your feedback,
>>>
>>>
>>> St?fan
>>>
>>>
>>> --
>>> You received this message because you are subscribed to the Google
>>> Groups "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to scikit-image... at googlegroups.com.
>>> To post to this group, send an email to scikit... at googlegroups.com.
>>> To view this discussion on the web, visit
>>> https://groups.google.com/d/msgid/scikit-image/20160426064948.GB940933%40phare.normalesup.org
>>> .
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>>
>>> --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> To post to this group, send email to scikit-image at googlegroups.com.
>> To view this discussion on the web, visit
>> https://groups.google.com/d/msgid/scikit-image/55d7ee35-aae3-458f-8245-1d35756dd0ce%40googlegroups.com
>> <https://groups.google.com/d/msgid/scikit-image/55d7ee35-aae3-458f-8245-1d35756dd0ce%40googlegroups.com?utm_medium=email&utm_source=footer>
>> .
>>
>> For more options, visit https://groups.google.com/d/optout.
>>
>
> How about posting this message when skimage is installed? It could be
> added to the setup.py script. But that would be visible only for users
> installing skimage from source, since pip / conda / enpkg would most
> probably suppress the message.
>
> Would it make sense to add a message in the LICENSE file?
>
> --
> JD
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> To post to this group, send email to scikit-image at googlegroups.com.
> To view this discussion on the web, visit
> https://groups.google.com/d/msgid/scikit-image/CAB%3DsuEkN-VdjQ%3DZ6%3DRXKnMX2mwotjqVJ2X3HO1ihRH8k-iDQ8w%40mail.gmail.com
> <https://groups.google.com/d/msgid/scikit-image/CAB%3DsuEkN-VdjQ%3DZ6%3DRXKnMX2mwotjqVJ2X3HO1ihRH8k-iDQ8w%40mail.gmail.com?utm_medium=email&utm_source=footer>
> .
>
> For more options, visit https://groups.google.com/d/optout.
>
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From deshpande.jaidev at gmail.com  Tue Apr 26 07:40:22 2016
From: deshpande.jaidev at gmail.com (Jaidev Deshpande)
Date: Tue, 26 Apr 2016 17:10:22 +0530
Subject: Opinion poll: feedback URL upon import
In-Reply-To: <55d7ee35-aae3-458f-8245-1d35756dd0ce@googlegroups.com>
References: <CABDkGQ=WbpDLxo4pu-UQFTM=eAVzv+76yKLnbAo6awgNWAqW8A@mail.gmail.com>
 <20160426064948.GB940933@phare.normalesup.org> <D8144ED0-C052-4A55-AF46-7E772BB224B8@googlemail.com>
 <55d7ee35-aae3-458f-8245-1d35756dd0ce@googlegroups.com>
Message-ID: <CAB=suEkN-VdjQ=Z6=RXKnMX2mwotjqVJ2X3HO1ihRH8k-iDQ8w@mail.gmail.com>

On Tue, Apr 26, 2016 at 3:40 PM, 'Robin Wilson' via scikit-image <
scikit-image at googlegroups.com> wrote:

> I agree with the others: please don't do this!
>
> However, being more obvious about wanting feedback, via the website,
> mailing list, in conference presentations etc, is definitely a good idea.
>
> Robin
>
> On Tuesday, 26 April 2016 08:05:42 UTC+1, Christoph wrote:
>>
>> Hi,
>>
>> I agree with Emma, as a scikit-image user, I would find it annoying.
>> Especially if it catches on and many other Python packages start doing
>> the same.
>>
>> It?s probably very rare, but if people check the text output of their
>> library or application and use scikit-image somewhere, this could even
>> break their test build.
>>
>> In Astropy there has also been some discussion about how to get feedback
>> from users. There the discussion was more along the lines of wanting to
>> collect info which platform, versions are in use, and which sub-packages
>> and functions in the Astropy package are used. I.e. there was discussion
>> about adding some code to send such usage stats info to a server, like many
>> apps do. This didn?t happen, I think the idea has been dropped.
>>
>> It would be very nice and important to get more feedback from users!
>>
>> But it seems to me that asking for it on the website like Emma proposes
>> or in conversations and presentations might be the safer way.
>>
>> Christoph
>>
>>
>>
>> On 26 Apr 2016, at 08:49, Emmanuelle Gouillart <emmanuelle... at nsup.org>
>> wrote:
>>
>> Hi St?fan
>>
>> I'm quite against it, since it's a feature that would push scikit-image
>> to be more an application and less a self-standing library: we would like
>> any other package to be able to import skimage in their code without
>> bothering about such messages. Indeed, such a message at import is only
>> useful/relevant for people that use scikit-image deliberately and as an
>> important part of their workflow, not so much for people that import
>> skimage in another projects, or that just use a couple of functions of
>> scikit-image (but it's not the core part of their workflow). I consider
>> it important for scikit-image to be a versatile block of the ecosystem,
>> and not only an application at the end of the "food chain".
>>
>> We could advertise the feedback form in a different way, for example by
>> making it very visible on the website. With 20000 unique visitors coming
>> to the website every month, I hope that we could get some feedback...
>>
>> Best,
>> Emma
>>
>> On Mon, Apr 25, 2016 at 11:29:03PM +0000, St?fan van der Walt wrote:
>>
>> Hi all,
>>
>>
>> It has been difficult to discover use cases of scikit-image out in the
>> wild
>> (even though I know they are plentiful, and users would excitedly tell me
>> about
>> them at conferences once the topic is broached).
>>
>>
>> So, I was wondering if it would be considered bad form to print a message
>> upon
>> importing scikit-image, something along the lines of:
>>
>>
>> "Thank you for using scikit-image v0.12! Please help us by telling us
>> about
>> your use-case at http://scikit-image.org/feedback?v=0.12.3"
>>
>>
>> Thanks for your feedback,
>>
>>
>> St?fan
>>
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image... at googlegroups.com.
>> To post to this group, send an email to scikit... at googlegroups.com.
>> To view this discussion on the web, visit
>> https://groups.google.com/d/msgid/scikit-image/20160426064948.GB940933%40phare.normalesup.org
>> .
>> For more options, visit https://groups.google.com/d/optout.
>>
>>
>> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> To post to this group, send email to scikit-image at googlegroups.com.
> To view this discussion on the web, visit
> https://groups.google.com/d/msgid/scikit-image/55d7ee35-aae3-458f-8245-1d35756dd0ce%40googlegroups.com
> <https://groups.google.com/d/msgid/scikit-image/55d7ee35-aae3-458f-8245-1d35756dd0ce%40googlegroups.com?utm_medium=email&utm_source=footer>
> .
>
> For more options, visit https://groups.google.com/d/optout.
>

How about posting this message when skimage is installed? It could be added
to the setup.py script. But that would be visible only for users installing
skimage from source, since pip / conda / enpkg would most probably suppress
the message.

Would it make sense to add a message in the LICENSE file?

-- 
JD
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From jni.soma at gmail.com  Wed Apr 27 03:06:22 2016
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Wed, 27 Apr 2016 00:06:22 -0700
Subject: Opinion poll: feedback URL upon import
In-Reply-To: <CADe6jSp756gGkgXYhdjvGzzD2q3g2-y9+iK+SEWQpOetq1pWaQ@mail.gmail.com>
References: <CADe6jSp756gGkgXYhdjvGzzD2q3g2-y9+iK+SEWQpOetq1pWaQ@mail.gmail.com>
Message-ID: <CA+JHcKTn6zehuanT6ZqBhkd1W5LujxV=7CNbhUfTmPHjm+uf3w@mail.gmail.com>

-1, as others. The suggestions given so far are good: prominent message on
the website, and in the main docstring.

Juan.


From: 'Kevin Keraudren' via scikit-image <scikit-image at googlegroups.com>
<scikit-image at googlegroups.com>
Reply: scikit-image at googlegroups.com <scikit-image at googlegroups.com>
<scikit-image at googlegroups.com>
Date: 26 April 2016 at 9:49:15 PM
To: scikit-image at googlegroups.com <scikit-image at googlegroups.com>
<scikit-image at googlegroups.com>
Subject:  Re: Opinion poll: feedback URL upon import

Noisy output at import is bad. In addition to the suggestions previously
> made, what about also mentioning the feedback url in the main docstring of
> skimage, something like here:
> https://github.com/scikit-image/scikit-image/blob/master/skimage/__init__.py#L9
>
> On Tue, Apr 26, 2016 at 12:40 PM, Jaidev Deshpande <
> deshpande.jaidev at gmail.com> wrote:
>
>>
>>
>> On Tue, Apr 26, 2016 at 3:40 PM, 'Robin Wilson' via scikit-image <
>> scikit-image at googlegroups.com> wrote:
>>
>>> I agree with the others: please don't do this!
>>>
>>> However, being more obvious about wanting feedback, via the website,
>>> mailing list, in conference presentations etc, is definitely a good idea.
>>>
>>> Robin
>>>
>>> On Tuesday, 26 April 2016 08:05:42 UTC+1, Christoph wrote:
>>>>
>>>> Hi,
>>>>
>>>> I agree with Emma, as a scikit-image user, I would find it annoying.
>>>> Especially if it catches on and many other Python packages start doing
>>>> the same.
>>>>
>>>> It?s probably very rare, but if people check the text output of their
>>>> library or application and use scikit-image somewhere, this could even
>>>> break their test build.
>>>>
>>>> In Astropy there has also been some discussion about how to get
>>>> feedback from users. There the discussion was more along the lines of
>>>> wanting to collect info which platform, versions are in use, and which
>>>> sub-packages and functions in the Astropy package are used. I.e. there was
>>>> discussion about adding some code to send such usage stats info to a
>>>> server, like many apps do. This didn?t happen, I think the idea has been
>>>> dropped.
>>>>
>>>> It would be very nice and important to get more feedback from users!
>>>>
>>>> But it seems to me that asking for it on the website like Emma proposes
>>>> or in conversations and presentations might be the safer way.
>>>>
>>>> Christoph
>>>>
>>>>
>>>>
>>>> On 26 Apr 2016, at 08:49, Emmanuelle Gouillart <emmanuelle... at nsup.org>
>>>> wrote:
>>>>
>>>> Hi St?fan
>>>>
>>>> I'm quite against it, since it's a feature that would push scikit-image
>>>> to be more an application and less a self-standing library: we would
>>>> like
>>>> any other package to be able to import skimage in their code without
>>>> bothering about such messages. Indeed, such a message at import is only
>>>> useful/relevant for people that use scikit-image deliberately and as an
>>>> important part of their workflow, not so much for people that import
>>>> skimage in another projects, or that just use a couple of functions of
>>>> scikit-image (but it's not the core part of their workflow). I consider
>>>> it important for scikit-image to be a versatile block of the ecosystem,
>>>> and not only an application at the end of the "food chain".
>>>>
>>>> We could advertise the feedback form in a different way, for example by
>>>> making it very visible on the website. With 20000 unique visitors coming
>>>> to the website every month, I hope that we could get some feedback...
>>>>
>>>> Best,
>>>> Emma
>>>>
>>>> On Mon, Apr 25, 2016 at 11:29:03PM +0000, St?fan van der Walt wrote:
>>>>
>>>> Hi all,
>>>>
>>>>
>>>> It has been difficult to discover use cases of scikit-image out in the
>>>> wild
>>>> (even though I know they are plentiful, and users would excitedly tell
>>>> me about
>>>> them at conferences once the topic is broached).
>>>>
>>>>
>>>> So, I was wondering if it would be considered bad form to print a
>>>> message upon
>>>> importing scikit-image, something along the lines of:
>>>>
>>>>
>>>> "Thank you for using scikit-image v0.12! Please help us by telling us
>>>> about
>>>> your use-case at http://scikit-image.org/feedback?v=0.12.3"
>>>>
>>>>
>>>> Thanks for your feedback,
>>>>
>>>>
>>>> St?fan
>>>>
>>>>
>>>> --
>>>> You received this message because you are subscribed to the Google
>>>> Groups "scikit-image" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>> an email to scikit-image... at googlegroups.com.
>>>> To post to this group, send an email to scikit... at googlegroups.com.
>>>> To view this discussion on the web, visit
>>>> https://groups.google.com/d/msgid/scikit-image/20160426064948.GB940933%40phare.normalesup.org
>>>> .
>>>> For more options, visit https://groups.google.com/d/optout.
>>>>
>>>>
>>>> --
>>> You received this message because you are subscribed to the Google
>>> Groups "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>> To post to this group, send email to scikit-image at googlegroups.com.
>>> To view this discussion on the web, visit
>>> https://groups.google.com/d/msgid/scikit-image/55d7ee35-aae3-458f-8245-1d35756dd0ce%40googlegroups.com
>>> <https://groups.google.com/d/msgid/scikit-image/55d7ee35-aae3-458f-8245-1d35756dd0ce%40googlegroups.com?utm_medium=email&utm_source=footer>.
>>>
>>>
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>
>> How about posting this message when skimage is installed? It could be
>> added to the setup.py script. But that would be visible only for users
>> installing skimage from source, since pip / conda / enpkg would most
>> probably suppress the message.
>>
>> Would it make sense to add a message in the LICENSE file?
>>
>> --
>> JD
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> To post to this group, send email to scikit-image at googlegroups.com.
>> To view this discussion on the web, visit
>> https://groups.google.com/d/msgid/scikit-image/CAB%3DsuEkN-VdjQ%3DZ6%3DRXKnMX2mwotjqVJ2X3HO1ihRH8k-iDQ8w%40mail.gmail.com
>> <https://groups.google.com/d/msgid/scikit-image/CAB%3DsuEkN-VdjQ%3DZ6%3DRXKnMX2mwotjqVJ2X3HO1ihRH8k-iDQ8w%40mail.gmail.com?utm_medium=email&utm_source=footer>.
>>
>>
>> For more options, visit https://groups.google.com/d/optout.
>>
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> To post to this group, send email to scikit-image at googlegroups.com.
> To view this discussion on the web, visit
> https://groups.google.com/d/msgid/scikit-image/CADe6jSp756gGkgXYhdjvGzzD2q3g2-y9%2BiK%2BSEWQpOetq1pWaQ%40mail.gmail.com
> <https://groups.google.com/d/msgid/scikit-image/CADe6jSp756gGkgXYhdjvGzzD2q3g2-y9%2BiK%2BSEWQpOetq1pWaQ%40mail.gmail.com?utm_medium=email&utm_source=footer>
> .
> For more options, visit https://groups.google.com/d/optout.
>
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From raphael at aims.ac.za  Wed Apr 27 19:54:49 2016
From: raphael at aims.ac.za (Raphael Okoye)
Date: Wed, 27 Apr 2016 16:54:49 -0700 (PDT)
Subject: dev version installation
In-Reply-To: <CABDkGQnVjuw6VwzmZaAyLG7U6VsrisaahJzmB-AsX_EwWhPL=w@mail.gmail.com>
References: <25621627-8a66-44c8-bac2-47df2b6895ae@googlegroups.com>
 <2b7816bd-1968-4d0c-9474-c5d0b32e284e@googlegroups.com> <bb569e80-6ee9-4b4d-b039-eeaa12da6f0c@googlegroups.com>
 <CABDkGQm28AC4Z7DhUZV5ektOe57DxisyrOTpEhiymUJAJ43fMg@mail.gmail.com> <64e392f5-f347-4d55-958c-6196b71bde37@googlegroups.com>
 <CABDkGQnVjuw6VwzmZaAyLG7U6VsrisaahJzmB-AsX_EwWhPL=w@mail.gmail.com>
Message-ID: <15d85674-3903-459f-a9a9-1ae32469dee6@googlegroups.com>

hi all,

 I need help with installation of  the latest version of scikit image(the 
version I have is 0.11.3 kindly find attached). I currently run Ubuntu 
14.04 LTS. I'm not sure if   sudo apt-get build-dep python-scikit-image     
is the way to go.  Any guidance will be highly appreciated. 

Thank you.
Raphael

On Tuesday, 2 February 2016 14:11:46 UTC-8, stefanv wrote:
>
> On 2 February 2016 at 13:21, Simone Codeluppi <sim... at codeluppi.org 
> <javascript:>> wrote: 
> > from $ git log HEAD^... I get: 
>
>
> This output is a bit strange, so perhaps try: 
>
> $ git checkout master 
> $ git fetch 
> $ git reset --hard origin/master 
>
> St?fan 
>
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From raphael at aims.ac.za  Wed Apr 27 19:59:41 2016
From: raphael at aims.ac.za (Raphael Okoye)
Date: Wed, 27 Apr 2016 16:59:41 -0700 (PDT)
Subject: release: scikit-image 0.12 is out!
In-Reply-To: <20160307215009.GA1343452@phare.normalesup.org>
References: <20160307215009.GA1343452@phare.normalesup.org>
Message-ID: <535f10b2-e9af-479c-834c-f4ea10d6eaeb@googlegroups.com>

hi Emmanuel,

 

 I need help with installation of  the latest version of scikit image(the 
version I have is 0.11.3 kindly find attached). I currently run Ubuntu 
14.04 LTS and running python 3.4.3. I'm not sure if   sudo apt-get build-dep 
python-scikit-image     is the way to go or if 

pip install --upgrade scikit-image do the necessary upgrade for me.   Any 
guidance will be highly appreciated. 

Thank you.

On Monday, 7 March 2016 13:50:11 UTC-8, Emmanuelle Gouillart wrote:
>
> Announcement: scikit-image 0.12 
> =============================== 
>
> The scikit-image team is very pleased to announce the release of version 
> 0.12 of scikit-image. 
>
> scikit-image is an image processing toolbox for Python and SciPy, that 
> includes algorithms for segmentation, geometric transformations, color 
> space manipulation, analysis, filtering, morphology, feature detection, 
> and more, for 2-D and 3-D (sometimes n-D) images. 
>
> For more information, examples, and documentation, please visit our 
> website: 
>
> http://scikit-image.org 
>
> and our example gallery 
>
> http://scikit-image.org/docs/dev/auto_examples/ 
>
> This release includes new features such as image inpainting, seam 
> carving, image comparison metrics, and a parallelization framework based 
> on dask. The release has also improved the support of 3-D images, with 
> 3-D skeletonization, 3-D phantom data. and partial support of 
> measure.regionprops for 3-D images. Also note that the handling of 
> background pixels by measure.label, a function labeling connected 
> components, has changed to be consistent with scipy.ndimage.label. 
>
> For this release, we merged over 200 pull requests from 64 contributors, 
> with bug fixes, cleanups, improved documentation and new features. 
> Release notes are available on 
>
> http://scikit-image.org/docs/0.12.x/release_notes_and_installation.html#release-notes 
> and include a more detailed list of changes, and the complete list of 
> contributors to this release. 
>
> The release can be downloaded on PyPi 
> https://pypi.python.org/pypi/scikit-image or directly installed using pip 
>
> pip install --upgrade scikit-image 
>
> Please let us know any issues you might have on the issue tracker 
> https://github.com/scikit-image/scikit-image/issues 
>
> Many thanks to all the developers who made this release possible, and a 
> warm welcome to our new contributors. 
>
> Happy image processing! 
> The scikit-image team 
>
>
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From raphael at aims.ac.za  Wed Apr 27 20:05:03 2016
From: raphael at aims.ac.za (Raphael Okoye)
Date: Wed, 27 Apr 2016 17:05:03 -0700
Subject: dev version installation
In-Reply-To: <15d85674-3903-459f-a9a9-1ae32469dee6@googlegroups.com>
References: <25621627-8a66-44c8-bac2-47df2b6895ae@googlegroups.com>
	<2b7816bd-1968-4d0c-9474-c5d0b32e284e@googlegroups.com>
	<bb569e80-6ee9-4b4d-b039-eeaa12da6f0c@googlegroups.com>
	<CABDkGQm28AC4Z7DhUZV5ektOe57DxisyrOTpEhiymUJAJ43fMg@mail.gmail.com>
	<64e392f5-f347-4d55-958c-6196b71bde37@googlegroups.com>
	<CABDkGQnVjuw6VwzmZaAyLG7U6VsrisaahJzmB-AsX_EwWhPL=w@mail.gmail.com>
	<15d85674-3903-459f-a9a9-1ae32469dee6@googlegroups.com>
Message-ID: <CAFCvXeMquU1ztDA38MNmkr9G=KnHRjjK08d_iY9mbOkc9GW1Wg@mail.gmail.com>

I forgot to mention that I run Python 3.4.3. Thanks

On 27 April 2016 at 16:54, Raphael Okoye <raphael at aims.ac.za> wrote:

> hi all,
>
>  I need help with installation of  the latest version of scikit image(the
> version I have is 0.11.3 kindly find attached). I currently run Ubuntu
> 14.04 LTS. I'm not sure if   sudo apt-get build-dep python-scikit-image
> is the way to go.  Any guidance will be highly appreciated.
>
> Thank you.
> Raphael
>
> On Tuesday, 2 February 2016 14:11:46 UTC-8, stefanv wrote:
>>
>> On 2 February 2016 at 13:21, Simone Codeluppi <sim... at codeluppi.org>
>> wrote:
>> > from $ git log HEAD^... I get:
>>
>>
>> This output is a bit strange, so perhaps try:
>>
>> $ git checkout master
>> $ git fetch
>> $ git reset --hard origin/master
>>
>> St?fan
>>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "scikit-image" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/scikit-image/oo0ukOiuexk/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> scikit-image+unsubscribe at googlegroups.com.
> To post to this group, send email to scikit-image at googlegroups.com.
> To view this discussion on the web, visit
> https://groups.google.com/d/msgid/scikit-image/15d85674-3903-459f-a9a9-1ae32469dee6%40googlegroups.com
> <https://groups.google.com/d/msgid/scikit-image/15d85674-3903-459f-a9a9-1ae32469dee6%40googlegroups.com?utm_medium=email&utm_source=footer>
> .
> For more options, visit https://groups.google.com/d/optout.
>
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From raphael at aims.ac.za  Thu Apr 28 02:51:16 2016
From: raphael at aims.ac.za (Raphael Okoye)
Date: Wed, 27 Apr 2016 23:51:16 -0700
Subject: release: scikit-image 0.12 is out!
In-Reply-To: <20160428064551.GB879717@phare.normalesup.org>
References: <20160307215009.GA1343452@phare.normalesup.org>
	<535f10b2-e9af-479c-834c-f4ea10d6eaeb@googlegroups.com>
	<20160428064344.GA879717@phare.normalesup.org>
	<20160428064551.GB879717@phare.normalesup.org>
Message-ID: <CAFCvXeOCCjEa01VikTHR45s8fHArNkWFR-Zh53JX+PcWwogCjg@mail.gmail.com>

hi Emmanuelle,


  hehehe...hope u have your coffee now..Thanks for the reply. So pip
install --upgrade scikit-image will land me in which version? 0.12.0? On
the announcements on the website http://scikit-image.org/ it seems that's
the latest stable version (although the right top corner of the page says
0.12.3 is the latest) .

On 27 April 2016 at 23:45, Emmanuelle Gouillart <
emmanuelle.gouillart at nsup.org> wrote:

> Sorry, I meant for 0.12. Morning answers before coffee are not reliable
> :-)
>
> On Thu, Apr 28, 2016 at 08:43:44AM +0200, Emmanuelle Gouillart wrote:
> > Hi Raphael,
>
> > I don't think we have an Ubuntu package yet for 0.11. The way to go would
> > be to use pip, with "pip install --upgrade scikit-image".
>
> > Cheers,
> > Emma
>
> > On Wed, Apr 27, 2016 at 04:59:41PM -0700, Raphael Okoye wrote:
> > > hi Emmanuel,
>
> > >
>
> > >  I need help with installation of  the latest version of scikit
> image(the
> > > version I have is 0.11.3 kindly find attached). I currently run Ubuntu
> 14.04
> > > LTS and running python 3.4.3. I'm not sure if   sudo apt-get build-dep
> python-
> > > scikit-image     is the way to go or if
>
> > > pip install --upgrade scikit-image do the necessary upgrade for me.
> Any
> > > guidance will be highly appreciated.
>
> > > Thank you.
>
> > > On Monday, 7 March 2016 13:50:11 UTC-8, Emmanuelle Gouillart wrote:
>
> > >     Announcement: scikit-image 0.12
> > >     ===============================
>
> > >     The scikit-image team is very pleased to announce the release of
> version
> > >     0.12 of scikit-image.
>
> > >     scikit-image is an image processing toolbox for Python and SciPy,
> that
> > >     includes algorithms for segmentation, geometric transformations,
> color
> > >     space manipulation, analysis, filtering, morphology, feature
> detection,
> > >     and more, for 2-D and 3-D (sometimes n-D) images.
>
> > >     For more information, examples, and documentation, please visit our
> > >     website:
>
> > >     http://scikit-image.org
>
> > >     and our example gallery
>
> > >     http://scikit-image.org/docs/dev/auto_examples/
>
> > >     This release includes new features such as image inpainting, seam
> > >     carving, image comparison metrics, and a parallelization framework
> based
> > >     on dask. The release has also improved the support of 3-D images,
> with
> > >     3-D skeletonization, 3-D phantom data. and partial support of
> > >     measure.regionprops for 3-D images. Also note that the handling of
> > >     background pixels by measure.label, a function labeling connected
> > >     components, has changed to be consistent with scipy.ndimage.label.
>
> > >     For this release, we merged over 200 pull requests from 64
> contributors,
> > >     with bug fixes, cleanups, improved documentation and new features.
> > >     Release notes are available on
> > >
> http://scikit-image.org/docs/0.12.x/release_notes_and_installation.html#
> > >     release-notes
> > >     and include a more detailed list of changes, and the complete list
> of
> > >     contributors to this release.
>
> > >     The release can be downloaded on PyPi
> > >     https://pypi.python.org/pypi/scikit-image or directly installed
> using pip
>
> > >     pip install --upgrade scikit-image
>
> > >     Please let us know any issues you might have on the issue tracker
> > >     https://github.com/scikit-image/scikit-image/issues
>
> > >     Many thanks to all the developers who made this release possible,
> and a
> > >     warm welcome to our new contributors.
>
> > >     Happy image processing!
> > >     The scikit-image team
>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "scikit-image" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/scikit-image/WmLXbbWdAew/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> scikit-image+unsubscribe at googlegroups.com.
> To post to this group, send an email to scikit-image at googlegroups.com.
> To view this discussion on the web, visit
> https://groups.google.com/d/msgid/scikit-image/20160428064551.GB879717%40phare.normalesup.org
> .
> For more options, visit https://groups.google.com/d/optout.
>
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From raphael at aims.ac.za  Thu Apr 28 03:51:19 2016
From: raphael at aims.ac.za (Raphael Okoye)
Date: Thu, 28 Apr 2016 00:51:19 -0700
Subject: release: scikit-image 0.12 is out!
In-Reply-To: <20160428065927.GA905027@phare.normalesup.org>
References: <20160307215009.GA1343452@phare.normalesup.org>
	<535f10b2-e9af-479c-834c-f4ea10d6eaeb@googlegroups.com>
	<20160428064344.GA879717@phare.normalesup.org>
	<20160428064551.GB879717@phare.normalesup.org>
	<CAFCvXeOCCjEa01VikTHR45s8fHArNkWFR-Zh53JX+PcWwogCjg@mail.gmail.com>
	<20160428065927.GA905027@phare.normalesup.org>
Message-ID: <CAFCvXePoc+LGo2RjKB9_4zHMeK1TmeQBWznTmViYU=H0++=cCA@mail.gmail.com>

do I need  upgrade cython before proceeding to upgrade scikit image?
something along the lines of pip install cython --upgrade --user or pip3
install cython --upgrade --user (pip3 since I'm using python 3.4.3?)

On 27 April 2016 at 23:59, Emmanuelle Gouillart <
emmanuelle.gouillart at nsup.org> wrote:

> not yet I'm afraid :-)
> pip install will get you the latest version, so it should be 0.12.3
>
> On Wed, Apr 27, 2016 at 11:51:16PM -0700, Raphael Okoye wrote:
> > hi Emmanuelle,
>
>
> >   hehehe...hope u have your coffee now..Thanks for the reply. So pip
> install
> > --upgrade scikit-image will land me in which version? 0.12.0? On the
> > announcements on the website http://scikit-image.org/ it seems that's
> the
> > latest stable version (although the right top corner of the page says
> 0.12.3 is
> > the latest) .
>
> > On 27 April 2016 at 23:45, Emmanuelle Gouillart <
> emmanuelle.gouillart at nsup.org>
> > wrote:
>
> >     Sorry, I meant for 0.12. Morning answers before coffee are not
> reliable
> >     :-)
>
> >     On Thu, Apr 28, 2016 at 08:43:44AM +0200, Emmanuelle Gouillart wrote:
> >     > Hi Raphael,
>
> >     > I don't think we have an Ubuntu package yet for 0.11. The way to
> go would
> >     > be to use pip, with "pip install --upgrade scikit-image".
>
> >     > Cheers,
> >     > Emma
>
> >     > On Wed, Apr 27, 2016 at 04:59:41PM -0700, Raphael Okoye wrote:
> >     > > hi Emmanuel,
>
> >     > >
>
> >     > >  I need help with installation of  the latest version of scikit
> image
> >     (the
> >     > > version I have is 0.11.3 kindly find attached). I currently run
> Ubuntu
> >     14.04
> >     > > LTS and running python 3.4.3. I'm not sure if   sudo apt-get
> build-dep
> >     python-
> >     > > scikit-image     is the way to go or if
>
> >     > > pip install --upgrade scikit-image do the necessary upgrade for
> me.
> >     Any
> >     > > guidance will be highly appreciated.
>
> >     > > Thank you.
>
> >     > > On Monday, 7 March 2016 13:50:11 UTC-8, Emmanuelle Gouillart
> wrote:
>
> >     > >     Announcement: scikit-image 0.12
> >     > >     ===============================
>
> >     > >     The scikit-image team is very pleased to announce the
> release of
> >     version
> >     > >     0.12 of scikit-image.
>
> >     > >     scikit-image is an image processing toolbox for Python and
> SciPy,
> >     that
> >     > >     includes algorithms for segmentation, geometric
> transformations,
> >     color
> >     > >     space manipulation, analysis, filtering, morphology, feature
> >     detection,
> >     > >     and more, for 2-D and 3-D (sometimes n-D) images.
>
> >     > >     For more information, examples, and documentation, please
> visit our
> >     > >     website:
>
> >     > >     http://scikit-image.org
>
> >     > >     and our example gallery
>
> >     > >     http://scikit-image.org/docs/dev/auto_examples/
>
> >     > >     This release includes new features such as image inpainting,
> seam
> >     > >     carving, image comparison metrics, and a parallelization
> framework
> >     based
> >     > >     on dask. The release has also improved the support of 3-D
> images,
> >     with
> >     > >     3-D skeletonization, 3-D phantom data. and partial support of
> >     > >     measure.regionprops for 3-D images. Also note that the
> handling of
> >     > >     background pixels by measure.label, a function labeling
> connected
> >     > >     components, has changed to be consistent with
> scipy.ndimage.label.
>
> >     > >     For this release, we merged over 200 pull requests from 64
> >     contributors,
> >     > >     with bug fixes, cleanups, improved documentation and new
> features.
> >     > >     Release notes are available on
> >     > >     http://scikit-image.org/docs/0.12.x/
> >     release_notes_and_installation.html#
> >     > >     release-notes
> >     > >     and include a more detailed list of changes, and the
> complete list
> >     of
> >     > >     contributors to this release.
>
> >     > >     The release can be downloaded on PyPi
> >     > >     https://pypi.python.org/pypi/scikit-image or directly
> installed
> >     using pip
>
> >     > >     pip install --upgrade scikit-image
>
> >     > >     Please let us know any issues you might have on the issue
> tracker
> >     > >     https://github.com/scikit-image/scikit-image/issues
>
> >     > >     Many thanks to all the developers who made this release
> possible,
> >     and a
> >     > >     warm welcome to our new contributors.
>
> >     > >     Happy image processing!
> >     > >     The scikit-image team
>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "scikit-image" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/scikit-image/WmLXbbWdAew/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> scikit-image+unsubscribe at googlegroups.com.
> To post to this group, send an email to scikit-image at googlegroups.com.
> To view this discussion on the web, visit
> https://groups.google.com/d/msgid/scikit-image/20160428065927.GA905027%40phare.normalesup.org
> .
> For more options, visit https://groups.google.com/d/optout.
>
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From emmanuelle.gouillart at nsup.org  Thu Apr 28 02:43:44 2016
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Thu, 28 Apr 2016 08:43:44 +0200
Subject: release: scikit-image 0.12 is out!
In-Reply-To: <535f10b2-e9af-479c-834c-f4ea10d6eaeb@googlegroups.com>
References: <20160307215009.GA1343452@phare.normalesup.org>
 <535f10b2-e9af-479c-834c-f4ea10d6eaeb@googlegroups.com>
Message-ID: <20160428064344.GA879717@phare.normalesup.org>

Hi Raphael,

I don't think we have an Ubuntu package yet for 0.11. The way to go would
be to use pip, with "pip install --upgrade scikit-image".

Cheers,
Emma

On Wed, Apr 27, 2016 at 04:59:41PM -0700, Raphael Okoye wrote:
> hi Emmanuel,

> ??

> ??I need help with installation of ??the latest version of scikit image(the
> version I have is 0.11.3 kindly find attached). I currently run Ubuntu 14.04
> LTS and running python 3.4.3. I'm not sure if??????sudo apt-get build-dep python-
> scikit-image ?????? is the way to go or if??

> pip install --upgrade scikit-image do the necessary upgrade for me.???? Any
> guidance will be highly appreciated.??

> Thank you.

> On Monday, 7 March 2016 13:50:11 UTC-8, Emmanuelle Gouillart wrote:

>     Announcement: scikit-image 0.12
>     ===============================

>     The scikit-image team is very pleased to announce the release of version
>     0.12 of scikit-image.

>     scikit-image is an image processing toolbox for Python and SciPy, that
>     includes algorithms for segmentation, geometric transformations, color
>     space manipulation, analysis, filtering, morphology, feature detection,
>     and more, for 2-D and 3-D (sometimes n-D) images.

>     For more information, examples, and documentation, please visit our
>     website:

>     http://scikit-image.org

>     and our example gallery

>     http://scikit-image.org/docs/dev/auto_examples/

>     This release includes new features such as image inpainting, seam
>     carving, image comparison metrics, and a parallelization framework based
>     on dask. The release has also improved the support of 3-D images, with
>     3-D skeletonization, 3-D phantom data. and partial support of
>     measure.regionprops for 3-D images. Also note that the handling of
>     background pixels by measure.label, a function labeling connected
>     components, has changed to be consistent with scipy.ndimage.label.

>     For this release, we merged over 200 pull requests from 64 contributors,
>     with bug fixes, cleanups, improved documentation and new features.
>     Release notes are available on
>     http://scikit-image.org/docs/0.12.x/release_notes_and_installation.html#
>     release-notes
>     and include a more detailed list of changes, and the complete list of
>     contributors to this release.

>     The release can be downloaded on PyPi
>     https://pypi.python.org/pypi/scikit-image or directly installed using pip

>     pip install --upgrade scikit-image

>     Please let us know any issues you might have on the issue tracker
>     https://github.com/scikit-image/scikit-image/issues

>     Many thanks to all the developers who made this release possible, and a
>     warm welcome to our new contributors.

>     Happy image processing!
>     The scikit-image team


From emmanuelle.gouillart at nsup.org  Thu Apr 28 02:45:51 2016
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Thu, 28 Apr 2016 08:45:51 +0200
Subject: release: scikit-image 0.12 is out!
In-Reply-To: <20160428064344.GA879717@phare.normalesup.org>
References: <20160307215009.GA1343452@phare.normalesup.org>
 <535f10b2-e9af-479c-834c-f4ea10d6eaeb@googlegroups.com>
 <20160428064344.GA879717@phare.normalesup.org>
Message-ID: <20160428064551.GB879717@phare.normalesup.org>

Sorry, I meant for 0.12. Morning answers before coffee are not reliable
:-)

On Thu, Apr 28, 2016 at 08:43:44AM +0200, Emmanuelle Gouillart wrote:
> Hi Raphael,

> I don't think we have an Ubuntu package yet for 0.11. The way to go would
> be to use pip, with "pip install --upgrade scikit-image".

> Cheers,
> Emma

> On Wed, Apr 27, 2016 at 04:59:41PM -0700, Raphael Okoye wrote:
> > hi Emmanuel,

> > ??

> > ??I need help with installation of ??the latest version of scikit image(the
> > version I have is 0.11.3 kindly find attached). I currently run Ubuntu 14.04
> > LTS and running python 3.4.3. I'm not sure if??????sudo apt-get build-dep python-
> > scikit-image ?????? is the way to go or if??

> > pip install --upgrade scikit-image do the necessary upgrade for me.???? Any
> > guidance will be highly appreciated.??

> > Thank you.

> > On Monday, 7 March 2016 13:50:11 UTC-8, Emmanuelle Gouillart wrote:

> >     Announcement: scikit-image 0.12
> >     ===============================

> >     The scikit-image team is very pleased to announce the release of version
> >     0.12 of scikit-image.

> >     scikit-image is an image processing toolbox for Python and SciPy, that
> >     includes algorithms for segmentation, geometric transformations, color
> >     space manipulation, analysis, filtering, morphology, feature detection,
> >     and more, for 2-D and 3-D (sometimes n-D) images.

> >     For more information, examples, and documentation, please visit our
> >     website:

> >     http://scikit-image.org

> >     and our example gallery

> >     http://scikit-image.org/docs/dev/auto_examples/

> >     This release includes new features such as image inpainting, seam
> >     carving, image comparison metrics, and a parallelization framework based
> >     on dask. The release has also improved the support of 3-D images, with
> >     3-D skeletonization, 3-D phantom data. and partial support of
> >     measure.regionprops for 3-D images. Also note that the handling of
> >     background pixels by measure.label, a function labeling connected
> >     components, has changed to be consistent with scipy.ndimage.label.

> >     For this release, we merged over 200 pull requests from 64 contributors,
> >     with bug fixes, cleanups, improved documentation and new features.
> >     Release notes are available on
> >     http://scikit-image.org/docs/0.12.x/release_notes_and_installation.html#
> >     release-notes
> >     and include a more detailed list of changes, and the complete list of
> >     contributors to this release.

> >     The release can be downloaded on PyPi
> >     https://pypi.python.org/pypi/scikit-image or directly installed using pip

> >     pip install --upgrade scikit-image

> >     Please let us know any issues you might have on the issue tracker
> >     https://github.com/scikit-image/scikit-image/issues

> >     Many thanks to all the developers who made this release possible, and a
> >     warm welcome to our new contributors.

> >     Happy image processing!
> >     The scikit-image team


From emmanuelle.gouillart at nsup.org  Thu Apr 28 02:59:27 2016
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Thu, 28 Apr 2016 08:59:27 +0200
Subject: release: scikit-image 0.12 is out!
In-Reply-To: <CAFCvXeOCCjEa01VikTHR45s8fHArNkWFR-Zh53JX+PcWwogCjg@mail.gmail.com>
References: <20160307215009.GA1343452@phare.normalesup.org>
 <535f10b2-e9af-479c-834c-f4ea10d6eaeb@googlegroups.com>
 <20160428064344.GA879717@phare.normalesup.org>
 <20160428064551.GB879717@phare.normalesup.org>
 <CAFCvXeOCCjEa01VikTHR45s8fHArNkWFR-Zh53JX+PcWwogCjg@mail.gmail.com>
Message-ID: <20160428065927.GA905027@phare.normalesup.org>

not yet I'm afraid :-)
pip install will get you the latest version, so it should be 0.12.3

On Wed, Apr 27, 2016 at 11:51:16PM -0700, Raphael Okoye wrote:
> hi Emmanuelle,


> ?? hehehe...hope u have your coffee now..Thanks for the reply. So pip install
> --upgrade scikit-image will land me in which version? 0.12.0? On the
> announcements on the website http://scikit-image.org/ it seems that's the
> latest stable version (although the right top corner of the page says 0.12.3 is
> the latest) .

> On 27 April 2016 at 23:45, Emmanuelle Gouillart <emmanuelle.gouillart at nsup.org>
> wrote:

>     Sorry, I meant for 0.12. Morning answers before coffee are not reliable
>     :-)

>     On Thu, Apr 28, 2016 at 08:43:44AM +0200, Emmanuelle Gouillart wrote:
>     > Hi Raphael,

>     > I don't think we have an Ubuntu package yet for 0.11. The way to go would
>     > be to use pip, with "pip install --upgrade scikit-image".

>     > Cheers,
>     > Emma

>     > On Wed, Apr 27, 2016 at 04:59:41PM -0700, Raphael Okoye wrote:
>     > > hi Emmanuel,

>     > > ??

>     > > ??I need help with installation of ??the latest version of scikit image
>     (the
>     > > version I have is 0.11.3 kindly find attached). I currently run Ubuntu
>     14.04
>     > > LTS and running python 3.4.3. I'm not sure if??????sudo apt-get build-dep
>     python-
>     > > scikit-image ?????? is the way to go or if??

>     > > pip install --upgrade scikit-image do the necessary upgrade for me.????
>     Any
>     > > guidance will be highly appreciated.??

>     > > Thank you.

>     > > On Monday, 7 March 2016 13:50:11 UTC-8, Emmanuelle Gouillart wrote:

>     > >?? ?? ??Announcement: scikit-image 0.12
>     > >?? ?? ??===============================

>     > >?? ?? ??The scikit-image team is very pleased to announce the release of
>     version
>     > >?? ?? ??0.12 of scikit-image.

>     > >?? ?? ??scikit-image is an image processing toolbox for Python and SciPy,
>     that
>     > >?? ?? ??includes algorithms for segmentation, geometric transformations,
>     color
>     > >?? ?? ??space manipulation, analysis, filtering, morphology, feature
>     detection,
>     > >?? ?? ??and more, for 2-D and 3-D (sometimes n-D) images.

>     > >?? ?? ??For more information, examples, and documentation, please visit our
>     > >?? ?? ??website:

>     > >?? ?? ??http://scikit-image.org

>     > >?? ?? ??and our example gallery

>     > >?? ?? ??http://scikit-image.org/docs/dev/auto_examples/

>     > >?? ?? ??This release includes new features such as image inpainting, seam
>     > >?? ?? ??carving, image comparison metrics, and a parallelization framework
>     based
>     > >?? ?? ??on dask. The release has also improved the support of 3-D images,
>     with
>     > >?? ?? ??3-D skeletonization, 3-D phantom data. and partial support of
>     > >?? ?? ??measure.regionprops for 3-D images. Also note that the handling of
>     > >?? ?? ??background pixels by measure.label, a function labeling connected
>     > >?? ?? ??components, has changed to be consistent with scipy.ndimage.label.

>     > >?? ?? ??For this release, we merged over 200 pull requests from 64
>     contributors,
>     > >?? ?? ??with bug fixes, cleanups, improved documentation and new features.
>     > >?? ?? ??Release notes are available on
>     > >?? ?? ??http://scikit-image.org/docs/0.12.x/
>     release_notes_and_installation.html#
>     > >?? ?? ??release-notes
>     > >?? ?? ??and include a more detailed list of changes, and the complete list
>     of
>     > >?? ?? ??contributors to this release.

>     > >?? ?? ??The release can be downloaded on PyPi
>     > >?? ?? ??https://pypi.python.org/pypi/scikit-image or directly installed
>     using pip

>     > >?? ?? ??pip install --upgrade scikit-image

>     > >?? ?? ??Please let us know any issues you might have on the issue tracker
>     > >?? ?? ??https://github.com/scikit-image/scikit-image/issues

>     > >?? ?? ??Many thanks to all the developers who made this release possible,
>     and a
>     > >?? ?? ??warm welcome to our new contributors.

>     > >?? ?? ??Happy image processing!
>     > >?? ?? ??The scikit-image team


From georgeshattab at gmail.com  Thu Apr 28 12:46:42 2016
From: georgeshattab at gmail.com (GeorgesVis)
Date: Thu, 28 Apr 2016 09:46:42 -0700 (PDT)
Subject: maximum square inside a contour
In-Reply-To: <e02b1a11-2b3f-47a8-8e22-387f8cc4e298@googlegroups.com>
References: <e02b1a11-2b3f-47a8-8e22-387f8cc4e298@googlegroups.com>
Message-ID: <1bcfc32e-1445-4d7d-ab4c-960ed4ce6ae3@googlegroups.com>

How about turning problem into an optimisation problem ?
You have the green square, could be considered as initial maximum square 
dimensions.

I believe it can be done by varying the position of the square along a path 
that maximises the square dimensions while all px values remain at 0 (ubyte 
image).
The path can be chosen depending on the polygon properties, if it is a 
platonic solid you use mass centre or the positions along the symmetry axis 
(example above).

Else, a more expensive approach: pick random positions (pos) and keep same 
size. Check if all px==0: increase size; else: continue to next pos.
I think you should also look at the flood fill algorithm, could also be 
helpful.


Hope this helps. 
Cheers, Georges

On Monday, 25 April 2016 13:30:21 UTC-7, Jaime Lopez Carvajal wrote:
>
> Hi friends,
>
> Someone knows how can I find a maximum square inside a contour, giving as 
> parameter the centroid point? 
> I need whole square area fall inside the contour. Any advice?
>
> Thanks in advance, Jaime?
>
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From jalopcar at gmail.com  Thu Apr 28 13:31:59 2016
From: jalopcar at gmail.com (Jaime Lopez Carvajal)
Date: Thu, 28 Apr 2016 10:31:59 -0700 (PDT)
Subject: maximum square inside a contour
In-Reply-To: <1bcfc32e-1445-4d7d-ab4c-960ed4ce6ae3@googlegroups.com>
References: <e02b1a11-2b3f-47a8-8e22-387f8cc4e298@googlegroups.com>
 <1bcfc32e-1445-4d7d-ab4c-960ed4ce6ae3@googlegroups.com>
Message-ID: <d3c1a480-b39d-4e1c-9910-07c16264beab@googlegroups.com>

Hi Georges,

I really don't have the green square, it is what I want to get. I just put 
it there for illustration purpouses.

But you give an interesting point of view. I will start from centroid, 
checking in every step if every square's corner is inside the region (as 
you said, 0 value)
it they are inside, increase their coordinates respectively, if not, take 
coordinates from the previous step to build the square.

I will give it a try, and will say how it works,

Thanks, Jaime

On Thursday, April 28, 2016 at 12:46:42 PM UTC-4, GeorgesVis wrote:
>
> How about turning problem into an optimisation problem ?
> You have the green square, could be considered as initial maximum square 
> dimensions.
>
> I believe it can be done by varying the position of the square along a 
> path that maximises the square dimensions while all px values remain at 0 
> (ubyte image).
> The path can be chosen depending on the polygon properties, if it is a 
> platonic solid you use mass centre or the positions along the symmetry axis 
> (example above).
>
> Else, a more expensive approach: pick random positions (pos) and keep same 
> size. Check if all px==0: increase size; else: continue to next pos.
> I think you should also look at the flood fill algorithm, could also be 
> helpful.
>
>
> Hope this helps. 
> Cheers, Georges
>
> On Monday, 25 April 2016 13:30:21 UTC-7, Jaime Lopez Carvajal wrote:
>>
>> Hi friends,
>>
>> Someone knows how can I find a maximum square inside a contour, giving as 
>> parameter the centroid point? 
>> I need whole square area fall inside the contour. Any advice?
>>
>> Thanks in advance, Jaime?
>>
>
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From pratapgr8 at gmail.com  Thu Apr 28 13:41:58 2016
From: pratapgr8 at gmail.com (Pratap Vardhan)
Date: Thu, 28 Apr 2016 10:41:58 -0700 (PDT)
Subject: maximum square inside a contour
In-Reply-To: <d3c1a480-b39d-4e1c-9910-07c16264beab@googlegroups.com>
References: <e02b1a11-2b3f-47a8-8e22-387f8cc4e298@googlegroups.com>
 <1bcfc32e-1445-4d7d-ab4c-960ed4ce6ae3@googlegroups.com>
 <d3c1a480-b39d-4e1c-9910-07c16264beab@googlegroups.com>
Message-ID: <0d971104-95b6-4109-a417-43a8b329ad5c@googlegroups.com>

If I understand it correctly -- here's one approach using morphological 
operators. 

1. Take centroid as seed point (new image).
2. Dilate it with 3x3 structuring element.
3. Check if union of seed image and contour image has created new pixels 
(i,e to check if square touched the contour)
4. If not, repeat step 1-2-3 till 3 is met.

That should give you largest possible square? I used similar approach for 
flooding problem and maze 
solving. https://www.youtube.com/watch?v=jhL8uELbVIM

Regards,
Pratap


On Thursday, April 28, 2016 at 11:01:59 PM UTC+5:30, Jaime Lopez Carvajal 
wrote:
>
> Hi Georges,
>
> I really don't have the green square, it is what I want to get. I just put 
> it there for illustration purpouses.
>
> But you give an interesting point of view. I will start from centroid, 
> checking in every step if every square's corner is inside the region (as 
> you said, 0 value)
> it they are inside, increase their coordinates respectively, if not, take 
> coordinates from the previous step to build the square.
>
> I will give it a try, and will say how it works,
>
> Thanks, Jaime
>
> On Thursday, April 28, 2016 at 12:46:42 PM UTC-4, GeorgesVis wrote:
>>
>> How about turning problem into an optimisation problem ?
>> You have the green square, could be considered as initial maximum square 
>> dimensions.
>>
>> I believe it can be done by varying the position of the square along a 
>> path that maximises the square dimensions while all px values remain at 0 
>> (ubyte image).
>> The path can be chosen depending on the polygon properties, if it is a 
>> platonic solid you use mass centre or the positions along the symmetry axis 
>> (example above).
>>
>> Else, a more expensive approach: pick random positions (pos) and keep 
>> same size. Check if all px==0: increase size; else: continue to next pos.
>> I think you should also look at the flood fill algorithm, could also be 
>> helpful.
>>
>>
>> Hope this helps. 
>> Cheers, Georges
>>
>> On Monday, 25 April 2016 13:30:21 UTC-7, Jaime Lopez Carvajal wrote:
>>>
>>> Hi friends,
>>>
>>> Someone knows how can I find a maximum square inside a contour, giving 
>>> as parameter the centroid point? 
>>> I need whole square area fall inside the contour. Any advice?
>>>
>>> Thanks in advance, Jaime?
>>>
>>
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From stefanv at berkeley.edu  Fri Apr 29 03:41:50 2016
From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Fri, 29 Apr 2016 07:41:50 +0000
Subject: Opinion poll: feedback URL upon import
In-Reply-To: <CA+JHcKTn6zehuanT6ZqBhkd1W5LujxV=7CNbhUfTmPHjm+uf3w@mail.gmail.com>
References: <CADe6jSp756gGkgXYhdjvGzzD2q3g2-y9+iK+SEWQpOetq1pWaQ@mail.gmail.com>
 <CA+JHcKTn6zehuanT6ZqBhkd1W5LujxV=7CNbhUfTmPHjm+uf3w@mail.gmail.com>
Message-ID: <CABDkGQnwf+iuidPM+Cf9fjQRQOw03UGR8ih1hG=KyoObP-4koQ@mail.gmail.com>

I guess this thread makes it clear what I should do:  threaten to include
such a message unless people send me usage reports :)

St?fan

On Wed, 27 Apr 2016 at 00:06 Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:

> -1, as others. The suggestions given so far are good: prominent message on
> the website, and in the main docstring.
>
> Juan.
>
>
> From: 'Kevin Keraudren' via scikit-image <scikit-image at googlegroups.com>
> <scikit-image at googlegroups.com>
> Reply: scikit-image at googlegroups.com <scikit-image at googlegroups.com>
> <scikit-image at googlegroups.com>
> Date: 26 April 2016 at 9:49:15 PM
> To: scikit-image at googlegroups.com <scikit-image at googlegroups.com>
> <scikit-image at googlegroups.com>
> Subject:  Re: Opinion poll: feedback URL upon import
>
> Noisy output at import is bad. In addition to the suggestions previously
>> made, what about also mentioning the feedback url in the main docstring of
>> skimage, something like here:
>> https://github.com/scikit-image/scikit-image/blob/master/skimage/__init__.py#L9
>>
>> On Tue, Apr 26, 2016 at 12:40 PM, Jaidev Deshpande <
>> deshpande.jaidev at gmail.com> wrote:
>>
>>>
>>>
>>> On Tue, Apr 26, 2016 at 3:40 PM, 'Robin Wilson' via scikit-image <
>>> scikit-image at googlegroups.com> wrote:
>>>
>>>> I agree with the others: please don't do this!
>>>>
>>>> However, being more obvious about wanting feedback, via the website,
>>>> mailing list, in conference presentations etc, is definitely a good idea.
>>>>
>>>> Robin
>>>>
>>>> On Tuesday, 26 April 2016 08:05:42 UTC+1, Christoph wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> I agree with Emma, as a scikit-image user, I would find it annoying.
>>>>> Especially if it catches on and many other Python packages start doing
>>>>> the same.
>>>>>
>>>>> It?s probably very rare, but if people check the text output of their
>>>>> library or application and use scikit-image somewhere, this could even
>>>>> break their test build.
>>>>>
>>>>> In Astropy there has also been some discussion about how to get
>>>>> feedback from users. There the discussion was more along the lines of
>>>>> wanting to collect info which platform, versions are in use, and which
>>>>> sub-packages and functions in the Astropy package are used. I.e. there was
>>>>> discussion about adding some code to send such usage stats info to a
>>>>> server, like many apps do. This didn?t happen, I think the idea has been
>>>>> dropped.
>>>>>
>>>>> It would be very nice and important to get more feedback from users!
>>>>>
>>>>> But it seems to me that asking for it on the website like Emma
>>>>> proposes or in conversations and presentations might be the safer way.
>>>>>
>>>>> Christoph
>>>>>
>>>>>
>>>>>
>>>>> On 26 Apr 2016, at 08:49, Emmanuelle Gouillart <emmanuelle... at nsup.org>
>>>>> wrote:
>>>>>
>>>>> Hi St?fan
>>>>>
>>>>> I'm quite against it, since it's a feature that would push scikit-image
>>>>> to be more an application and less a self-standing library: we would
>>>>> like
>>>>> any other package to be able to import skimage in their code without
>>>>> bothering about such messages. Indeed, such a message at import is only
>>>>> useful/relevant for people that use scikit-image deliberately and as an
>>>>> important part of their workflow, not so much for people that import
>>>>> skimage in another projects, or that just use a couple of functions of
>>>>> scikit-image (but it's not the core part of their workflow). I consider
>>>>> it important for scikit-image to be a versatile block of the ecosystem,
>>>>> and not only an application at the end of the "food chain".
>>>>>
>>>>> We could advertise the feedback form in a different way, for example by
>>>>> making it very visible on the website. With 20000 unique visitors
>>>>> coming
>>>>> to the website every month, I hope that we could get some feedback...
>>>>>
>>>>> Best,
>>>>> Emma
>>>>>
>>>>> On Mon, Apr 25, 2016 at 11:29:03PM +0000, St?fan van der Walt wrote:
>>>>>
>>>>> Hi all,
>>>>>
>>>>>
>>>>> It has been difficult to discover use cases of scikit-image out in the
>>>>> wild
>>>>> (even though I know they are plentiful, and users would excitedly tell
>>>>> me about
>>>>> them at conferences once the topic is broached).
>>>>>
>>>>>
>>>>> So, I was wondering if it would be considered bad form to print a
>>>>> message upon
>>>>> importing scikit-image, something along the lines of:
>>>>>
>>>>>
>>>>> "Thank you for using scikit-image v0.12! Please help us by telling us
>>>>> about
>>>>> your use-case at http://scikit-image.org/feedback?v=0.12.3"
>>>>>
>>>>>
>>>>> Thanks for your feedback,
>>>>>
>>>>>
>>>>> St?fan
>>>>>
>>>>>
>>>>> --
>>>>> You received this message because you are subscribed to the Google
>>>>> Groups "scikit-image" group.
>>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>>> an email to scikit-image... at googlegroups.com.
>>>>> To post to this group, send an email to scikit... at googlegroups.com.
>>>>> To view this discussion on the web, visit
>>>>> https://groups.google.com/d/msgid/scikit-image/20160426064948.GB940933%40phare.normalesup.org
>>>>> .
>>>>> For more options, visit https://groups.google.com/d/optout.
>>>>>
>>>>>
>>>>> --
>>>> You received this message because you are subscribed to the Google
>>>> Groups "scikit-image" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>>> To post to this group, send email to scikit-image at googlegroups.com.
>>>> To view this discussion on the web, visit
>>>> https://groups.google.com/d/msgid/scikit-image/55d7ee35-aae3-458f-8245-1d35756dd0ce%40googlegroups.com
>>>> <https://groups.google.com/d/msgid/scikit-image/55d7ee35-aae3-458f-8245-1d35756dd0ce%40googlegroups.com?utm_medium=email&utm_source=footer>.
>>>>
>>>>
>>>> For more options, visit https://groups.google.com/d/optout.
>>>>
>>>
>>> How about posting this message when skimage is installed? It could be
>>> added to the setup.py script. But that would be visible only for users
>>> installing skimage from source, since pip / conda / enpkg would most
>>> probably suppress the message.
>>>
>>> Would it make sense to add a message in the LICENSE file?
>>>
>>> --
>>> JD
>>>
>>> --
>>> You received this message because you are subscribed to the Google
>>> Groups "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>> To post to this group, send email to scikit-image at googlegroups.com.
>>> To view this discussion on the web, visit
>>> https://groups.google.com/d/msgid/scikit-image/CAB%3DsuEkN-VdjQ%3DZ6%3DRXKnMX2mwotjqVJ2X3HO1ihRH8k-iDQ8w%40mail.gmail.com
>>> <https://groups.google.com/d/msgid/scikit-image/CAB%3DsuEkN-VdjQ%3DZ6%3DRXKnMX2mwotjqVJ2X3HO1ihRH8k-iDQ8w%40mail.gmail.com?utm_medium=email&utm_source=footer>.
>>>
>>>
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> To post to this group, send email to scikit-image at googlegroups.com.
>> To view this discussion on the web, visit
>> https://groups.google.com/d/msgid/scikit-image/CADe6jSp756gGkgXYhdjvGzzD2q3g2-y9%2BiK%2BSEWQpOetq1pWaQ%40mail.gmail.com
>> <https://groups.google.com/d/msgid/scikit-image/CADe6jSp756gGkgXYhdjvGzzD2q3g2-y9%2BiK%2BSEWQpOetq1pWaQ%40mail.gmail.com?utm_medium=email&utm_source=footer>
>> .
>> For more options, visit https://groups.google.com/d/optout.
>>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> To post to this group, send email to scikit-image at googlegroups.com.
> To view this discussion on the web, visit
> https://groups.google.com/d/msgid/scikit-image/CA%2BJHcKTn6zehuanT6ZqBhkd1W5LujxV%3D7CNbhUfTmPHjm%2Buf3w%40mail.gmail.com
> <https://groups.google.com/d/msgid/scikit-image/CA%2BJHcKTn6zehuanT6ZqBhkd1W5LujxV%3D7CNbhUfTmPHjm%2Buf3w%40mail.gmail.com?utm_medium=email&utm_source=footer>
> .
> For more options, visit https://groups.google.com/d/optout.
>
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From stefanv at berkeley.edu  Fri Apr 29 03:47:25 2016
From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Fri, 29 Apr 2016 07:47:25 +0000
Subject: Feature extraction for 3D model
In-Reply-To: <45772dd8-3a9e-40ae-934e-eb6a2021cf8d@googlegroups.com>
References: <30db04dd-0c2e-45df-a69f-16eb49bdee50@googlegroups.com> <45772dd8-3a9e-40ae-934e-eb6a2021cf8d@googlegroups.com>
Message-ID: <CABDkGQmyq6RkW9DDHRZxRMHtgORRBbqxb1h3WRwMsBZv7=N79g@mail.gmail.com>

Hi Zichao

I took a look at your file and it seems to be... from Minecraft?

I guess a good place to start would be:

https://en.wikipedia.org/wiki/Wavefront_.obj_file

and

https://pypi.python.org/pypi/PyWavefront/0.1

Regards
St?fan

On Mon, 29 Feb 2016 at 00:31 Zichao Li <rylanlzc at gmail.com> wrote:

> Dear Stefanv,
>
> Here is one of my .obj files. Please take a look.
>
> Best,
> Zichao
>
> ? 2016?2?29???? UTC+8??12:34:52?Zichao Li???
>
>> I have about 1Gb 3d models contained in .obj file and now I'd like to do
>> some feature extraction: color, texture, shape etc. I wonder how can i do
>> it with scikit-image? I can't find relative explanation in documents.
>> Thanks a lot!
>>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> To post to this group, send email to scikit-image at googlegroups.com.
> To view this discussion on the web, visit
> https://groups.google.com/d/msgid/scikit-image/45772dd8-3a9e-40ae-934e-eb6a2021cf8d%40googlegroups.com
> <https://groups.google.com/d/msgid/scikit-image/45772dd8-3a9e-40ae-934e-eb6a2021cf8d%40googlegroups.com?utm_medium=email&utm_source=footer>
> .
> For more options, visit https://groups.google.com/d/optout.
>
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From stefanv at berkeley.edu  Fri Apr 29 03:57:49 2016
From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Fri, 29 Apr 2016 07:57:49 +0000
Subject: Maximum Area Convex Subset (MACS)
In-Reply-To: <72770f60-a235-49c3-b635-be80d75b21fd@googlegroups.com>
References: <72770f60-a235-49c3-b635-be80d75b21fd@googlegroups.com>
Message-ID: <CABDkGQ=59enz4nmi81UnfUwnmqsySfcriN3vKHmL1+4vLHE5QQ@mail.gmail.com>

On Wed, 20 Apr 2016 at 01:40 <amiksvi at gmail.com> wrote:

> Let's assume I have an image with 0's as background B and a connected set
> S made of 1. Is there an easy way with scikit-image to find the maximum (in
> terms of area) subset of S that is convex.
>

I may be wrong, but my gut feeling is that this would require a search over
quite a large space of options.  There may be some ways to simplify the
search, e.g. you could fit the largest circle that inscribes your object,
and then only consider all  combinations of the remaining pixels; still a
lot of work.

[... time passes ...]

Well, I guess I should have asked Bruce Merry first:

http://stackoverflow.com/a/23639901/214686

Care to implement this for us as a PR?  The algorithm is O(N^3).

St?fan
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From stefanv at berkeley.edu  Fri Apr 29 04:05:30 2016
From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Fri, 29 Apr 2016 08:05:30 +0000
Subject: img_as_float
In-Reply-To: <455ac4c1-d145-4b30-93da-217adb817538@googlegroups.com>
References: <12E733D0-B357-4C02-8980-05218ADEBD19@demuc.de>
 <d3792a24-c8f1-4af1-ae68-2495d81c2b26@googlegroups.com> <75C45B40-769F-4CEA-920E-811476E2E77C@demuc.de>
 <30071aab-6083-4943-98b8-26edff888071@googlegroups.com> <CABDkGQmJMkvWU1axigoYm+mPe7NOyGvXLd8DYW_W07-yuRHPtA@mail.gmail.com>
 <2533ca46-2701-4178-9560-28a9a6ed84b7@googlegroups.com> <455ac4c1-d145-4b30-93da-217adb817538@googlegroups.com>
Message-ID: <CABDkGQmyY3dH7D4S073hi4B2Uu-BYK7FNpaS=m2g6avjspi6xw@mail.gmail.com>

One more comment on this issue:

a) *Most* of the time we want to use floating point numbers so that we can
do operations like image / 2 without worrying about rounding.
b) Some users have very large images and *must* use ubytes to fit their
data into memory.

I therefore see a fairly fundamental clash in requirements that cannot
easily be removed.

As things stand, however, we probably already cause headaches for users
with (2), because many of our intermediate stages convert images to
floating point format.  So if we had to settle on a single format, floating
point is what I'd go for.

But then, of course, you open the lovely can of worms of reading in your
uint64 stored images (which sometimes happen to store values between 0 and
255 only), and having no idea why you are dealing with some crazy floating
point number.

So, let's keep thinking about this one!

St?fan

On Thu, 18 Feb 2016 at 16:10 Josh Warner <silvertrumpet999 at gmail.com> wrote:

> Sometimes the input dtype needs to change, at least along the way. As just
> one example:
>
>    - uint8 or uint16 inputs with a chain of calculations, including
>    transformations or exposure tweaks. In this instance, all intermediate
>    calculations should be carried out with full floating-point precision. If
>    forced back into their originating dtype at each step, the result would
>    have terrible compounded error.
>
> Returning to the original dtype at the end would be reasonable, but you
> only want to do this once. Because of our functional approach (vs. VTK's
> pipelining or similar), there is no way for us to know which step is the
> final one. So - if desired - the user needs to handle this, because from
> such functions we'll always return the higher precision.
>
> We always return a new object, unless the function explicitly operates on
> the input. When this is possible it is enabled by a standard `out=None`
> kwarg like in numpy/scipy.
>
> One of the biggest things the "float images are on range [0, 1]" saves us
> from is worrying about aliasing. At all. We just do calculations, it
> doesn't matter if the input image gets squared a few times along the way.
> Try to do a few simple numpy operations on a uint8 array and see how fast
> the results aren't what you expect. Now, we can relax this and still be
> mostly OK because float64 is big. But concerns like this are a huge
> potential maintenance headache. I think what Stefan means by "full
> potential range" is that you have to plan calculations in advance,
> examining every intermediate step for its maximum potential range, against
> your dtype.
>
> Certain exposure calculations are explicitly defined with normalized
> images on the range [0, 1], because they heavily use exponential functions.
> An input with a greater range must be handled carefully by any such
> function. This is the greatest danger in simply removing the normalization
> step from the package, IMO. A lot of things will break, and depending on
> the algorithm the fix may vary.
>
> Perhaps that helps pull back the curtain a little...
>
> Josh
>
> On Thursday, February 18, 2016 at 4:00:04 PM UTC-7, Michael Aye wrote:
>>
>> I am not opposed to supporting range preservation, but we do have to
>>
>>> think a bit about the implications:
>>>
>>> - what do you do when the data-type of values change?
>>>
>>
>> What are the situations where they *have* to change?
>>
>>
>>> - what do you do when your operation due to, e.g., rounding issues
>>> push values outside the input range?
>>>
>>
>> Return a new object instead of changing the original, maybe?
>>
>>
>>> - what do you do when you need to know the full potential range of the
>>> data?
>>>
>>>  don't understand, do you mean the full potential range per data-type?
>> isn't that defined by the data-type the input image has?
>>
>> The ``preserve_range`` flag has allowed us to do whatever we do
>>> normally, unless the user gave explicit permission to change data
>>> types, ranges, etc.  It also serves as a nice tag for "I, the
>>> developer, thought about this issue".
>>>
>>> And that's quite cool that that's offered, but the question is, I guess,
>> which default is best and why?
>> Which default setting would confuse the least new (and old) users?
>>
>> Michael
>>
> --
> You received this message because you are subscribed to the Google Groups
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> <https://groups.google.com/d/msgid/scikit-image/455ac4c1-d145-4b30-93da-217adb817538%40googlegroups.com?utm_medium=email&utm_source=footer>
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From siqueiraaf at gmail.com  Sat Apr 30 00:51:51 2016
From: siqueiraaf at gmail.com (Alexandre Fioravante de Siqueira)
Date: Fri, 29 Apr 2016 21:51:51 -0700 (PDT)
Subject: Please share your use cases
In-Reply-To: <CABDkGQkQgf7sGpd0agAReX5MHiNUx6zohsRuoXEuzS1Gq_rQiw@mail.gmail.com>
References: <CABDkGQn3MncBAF3w-oDxE23p_GkX90AtK1Y_O3+O1muLLOtq3A@mail.gmail.com>
 <CABDkGQmFfrbRQrQgqLSWm-Y2gXVoWPaEAkYpoWutDRKhPO6YkQ@mail.gmail.com>
 <CABDkGQnDMxk87RmvA3e32XBUGLBKOHgS7OD1v5DkFO6hpbZn=A@mail.gmail.com>
 <CABDkGQkQgf7sGpd0agAReX5MHiNUx6zohsRuoXEuzS1Gq_rQiw@mail.gmail.com>
Message-ID: <47b8c672-afcd-4adb-b8e5-f00b1d9e5211@googlegroups.com>

Hi St?fan,
is this valid yet? I could send you the preliminary results of my research.
Thanks!

Alex

Em quarta-feira, 13 de abril de 2016 19:49:03 UTC+2, stefanv escreveu:
>
> Hi, everyone
>
> I am giving a talk on scikit-image soon, and would like to highlight how 
> it is being used in practice. 
>
> Please share your own applications with links to images or plots, or let 
> me know if you spot someone else doing something cool! 
>
> Thanks, 
> St?fan 
>
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From amueller at ais.uni-bonn.de  Fri Apr 29 21:53:57 2016
From: amueller at ais.uni-bonn.de (Andreas Mueller)
Date: Fri, 29 Apr 2016 21:53:57 -0400
Subject: Opinion poll: feedback URL upon import
In-Reply-To: <CABDkGQnwf+iuidPM+Cf9fjQRQOw03UGR8ih1hG=KyoObP-4koQ@mail.gmail.com>
References: <CADe6jSp756gGkgXYhdjvGzzD2q3g2-y9+iK+SEWQpOetq1pWaQ@mail.gmail.com>
 <CA+JHcKTn6zehuanT6ZqBhkd1W5LujxV=7CNbhUfTmPHjm+uf3w@mail.gmail.com>
 <CABDkGQnwf+iuidPM+Cf9fjQRQOw03UGR8ih1hG=KyoObP-4koQ@mail.gmail.com>
Message-ID: <57241035.4000904@ais.uni-bonn.de>

There was some discussion about whether we could use jupyter to get some 
feedback from users, i.e. a single opt-in for the jupyter
platform, instead one for each library (which would be pretty bad).

One method that I recently used was greping notebooks on github. 
Unfortunately their API doesn't allow
global code searches. Their website does, though, if someone wants to 
write a scraper ;)

I wonder if / how other open source libraries handle this. I guess boost 
doesn't care ;)
But maybe web frameworks do? We could try tapping other scientific 
computing communities like
julia or octave, or go out to web folks?
The scipy stack is probably not the only one that has this issue.

On 04/29/2016 03:41 AM, St?fan van der Walt wrote:
> I guess this thread makes it clear what I should do:  threaten to 
> include such a message unless people send me usage reports :)
>
> St?fan
>
> On Wed, 27 Apr 2016 at 00:06 Juan Nunez-Iglesias <jni.soma at gmail.com 
> <mailto:jni.soma at gmail.com>> wrote:
>
>     -1, as others. The suggestions given so far are good: prominent
>     message on the website, and in the main docstring.
>
>     Juan.
>
>
>     From: 'Kevin Keraudren' via scikit-image
>     <scikit-image at googlegroups.com> <mailto:scikit-image at googlegroups.com>
>     Reply: scikit-image at googlegroups.com
>     <mailto:scikit-image at googlegroups.com>
>     <scikit-image at googlegroups.com> <mailto:scikit-image at googlegroups.com>
>     Date: 26 April 2016 at 9:49:15 PM
>     To: scikit-image at googlegroups.com
>     <mailto:scikit-image at googlegroups.com>
>     <scikit-image at googlegroups.com> <mailto:scikit-image at googlegroups.com>
>     Subject: Re: Opinion poll: feedback URL upon import
>
>>     Noisy output at import is bad. In addition to the suggestions
>>     previously made, what about also mentioning the feedback url in
>>     the main docstring of skimage, something like here:
>>     https://github.com/scikit-image/scikit-image/blob/master/skimage/__init__.py#L9
>>
>>     On Tue, Apr 26, 2016 at 12:40 PM, Jaidev Deshpande
>>     <deshpande.jaidev at gmail.com <mailto:deshpande.jaidev at gmail.com>>
>>     wrote:
>>
>>
>>
>>         On Tue, Apr 26, 2016 at 3:40 PM, 'Robin Wilson' via
>>         scikit-image <scikit-image at googlegroups.com
>>         <mailto:scikit-image at googlegroups.com>> wrote:
>>
>>             I agree with the others: please don't do this!
>>
>>             However, being more obvious about wanting feedback, via
>>             the website, mailing list, in conference presentations
>>             etc, is definitely a good idea.
>>
>>             Robin
>>
>>             On Tuesday, 26 April 2016 08:05:42 UTC+1, Christoph wrote:
>>
>>                 Hi,
>>
>>                 I agree with Emma, as a scikit-image user, I would
>>                 find it annoying.
>>                 Especially if it catches on and many other Python
>>                 packages start doing the same.
>>
>>                 It?s probably very rare, but if people check the text
>>                 output of their library or application and use
>>                 scikit-image somewhere, this could even break their
>>                 test build.
>>
>>                 In Astropy there has also been some discussion about
>>                 how to get feedback from users. There the discussion
>>                 was more along the lines of wanting to collect info
>>                 which platform, versions are in use, and which
>>                 sub-packages and functions in the Astropy package are
>>                 used. I.e. there was discussion about adding some
>>                 code to send such usage stats info to a server, like
>>                 many apps do. This didn?t happen, I think the idea
>>                 has been dropped.
>>
>>                 It would be very nice and important to get more
>>                 feedback from users!
>>
>>                 But it seems to me that asking for it on the website
>>                 like Emma proposes or in conversations and
>>                 presentations might be the safer way.
>>
>>                 Christoph
>>
>>
>>
>>>                 On 26 Apr 2016, at 08:49, Emmanuelle Gouillart
>>>                 <emmanuelle... at nsup.org> wrote:
>>>
>>>                 Hi St?fan
>>>
>>>                 I'm quite against it, since it's a feature that
>>>                 would push scikit-image
>>>                 to be more an application and less a self-standing
>>>                 library: we would like
>>>                 any other package to be able to import skimage in
>>>                 their code without
>>>                 bothering about such messages. Indeed, such a
>>>                 message at import is only
>>>                 useful/relevant for people that use scikit-image
>>>                 deliberately and as an
>>>                 important part of their workflow, not so much for
>>>                 people that import
>>>                 skimage in another projects, or that just use a
>>>                 couple of functions of
>>>                 scikit-image (but it's not the core part of their
>>>                 workflow). I consider
>>>                 it important for scikit-image to be a versatile
>>>                 block of the ecosystem,
>>>                 and not only an application at the end of the "food
>>>                 chain".
>>>
>>>                 We could advertise the feedback form in a different
>>>                 way, for example by
>>>                 making it very visible on the website. With 20000
>>>                 unique visitors coming
>>>                 to the website every month, I hope that we could get
>>>                 some feedback...
>>>
>>>                 Best,
>>>                 Emma
>>>
>>>                 On Mon, Apr 25, 2016 at 11:29:03PM +0000, St?fan van
>>>                 der Walt wrote:
>>>>                 Hi all,
>>>
>>>>                 It has been difficult to discover use cases of
>>>>                 scikit-image out in the wild
>>>>                 (even though I know they are plentiful, and users
>>>>                 would excitedly tell me about
>>>>                 them at conferences once the topic is broached).
>>>
>>>>                 So, I was wondering if it would be considered bad
>>>>                 form to print a message upon
>>>>                 importing scikit-image, something along the lines of:
>>>
>>>>                 "Thank you for using scikit-image v0.12! Please
>>>>                 help us by telling us about
>>>>                 your use-case at
>>>>                 http://scikit-image.org/feedback?v=0.12.3"
>>>
>>>>                 Thanks for your feedback,
>>>
>>>>                 St?fan
>>>
>>>                 --
>>>                 You received this message because you are subscribed
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>>>                 For more options,
>>>                 visithttps://groups.google.com/d/optout.
>>
>>             --
>>             You received this message because you are subscribed to
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>>             To view this discussion on the web, visit
>>             https://groups.google.com/d/msgid/scikit-image/55d7ee35-aae3-458f-8245-1d35756dd0ce%40googlegroups.com
>>             <https://groups.google.com/d/msgid/scikit-image/55d7ee35-aae3-458f-8245-1d35756dd0ce%40googlegroups.com?utm_medium=email&utm_source=footer>.
>>
>>
>>             For more options, visit https://groups.google.com/d/optout.
>>
>>
>>         How about posting this message when skimage is installed? It
>>         could be added to the setup.py script. But that would be
>>         visible only for users installing skimage from source, since
>>         pip / conda / enpkg would most probably suppress the message.
>>
>>         Would it make sense to add a message in the LICENSE file?
>>
>>         --
>>         JD
>>
>>         --
>>         You received this message because you are subscribed to the
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>>         <https://groups.google.com/d/msgid/scikit-image/CAB%3DsuEkN-VdjQ%3DZ6%3DRXKnMX2mwotjqVJ2X3HO1ihRH8k-iDQ8w%40mail.gmail.com?utm_medium=email&utm_source=footer>.
>>
>>
>>         For more options, visit https://groups.google.com/d/optout.
>>
>>
>>     --
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>>     <https://groups.google.com/d/msgid/scikit-image/CADe6jSp756gGkgXYhdjvGzzD2q3g2-y9%2BiK%2BSEWQpOetq1pWaQ%40mail.gmail.com?utm_medium=email&utm_source=footer>.
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From raphael at aims.ac.za  Sat Apr 30 02:02:50 2016
From: raphael at aims.ac.za (Raphael)
Date: Fri, 29 Apr 2016 23:02:50 -0700 (PDT)
Subject: blob detection and dust removal
Message-ID: <687d9e93-0b25-44a8-a19d-8ed00aefdea2@googlegroups.com>

hi folks,  

  Got a problem removing dust and identifying blobs/crytals. Kindly see my 
code below


from __future__ import division, print_function
import matplotlib.pyplot as plt
import numpy as np
from skimage import io, feature, color, measure, draw, img_as_float, 
exposure
from skimage.filters.rank import median
from skimage.feature import blob_dog, blob_log, blob_doh
from skimage.morphology import disk

#raw image
image_raw = 
img_as_float((io.imread('/home/raphael/Documents/ScikitImage/Run 
4-2_00061cropped.tif'))) (RawImage.tif attached) 
plt.imshow(image_raw)

#converted to grayscale

img_gray = 
color.rgb2gray(io.imread('/home/raphael/Documents/ScikitImage/Run 
4-2_00061cropped.tif'))
plt.imshow(image_gray)


#applied median filter to take out small dust particles. But the big dust 
particle on the top right corner still persists (see median1.png attached)
img_filtered=median(img_gray,disk(10))
plt.imshow(img_filtered)


#applied  adapthist to make image more clearer (see adaptive.png)

img_equalized=exposure.equalize_adapthist(img_filtered)
plt.imshow(img_equalized)

#trying to detect the crystals/blobs. I followed the example here 
http://scikit-image.org/docs/dev/auto_examples/features_detection/plot_blob.html 
But this gave an error. matplotlib was not happy with the data type
blobs_doh = blob_doh(img_equalized,  max_sigma=30, threshold=.1)
plt.imshow(blobs_doh) 

My problems are:

1. I could not get the dust particle out especially the really big one on 
the top right. How can I get it out? 

2. I could not detect the crystals/blobs in the image using blob_doh

Any ideas/suggestions is highly appreciated.  Thank you!
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From stefanv at berkeley.edu  Sat Apr 30 16:49:30 2016
From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Sat, 30 Apr 2016 20:49:30 +0000
Subject: Please share your use cases
In-Reply-To: <47b8c672-afcd-4adb-b8e5-f00b1d9e5211@googlegroups.com>
References: <CABDkGQn3MncBAF3w-oDxE23p_GkX90AtK1Y_O3+O1muLLOtq3A@mail.gmail.com>
 <CABDkGQmFfrbRQrQgqLSWm-Y2gXVoWPaEAkYpoWutDRKhPO6YkQ@mail.gmail.com>
 <CABDkGQnDMxk87RmvA3e32XBUGLBKOHgS7OD1v5DkFO6hpbZn=A@mail.gmail.com>
 <CABDkGQkQgf7sGpd0agAReX5MHiNUx6zohsRuoXEuzS1Gq_rQiw@mail.gmail.com> <47b8c672-afcd-4adb-b8e5-f00b1d9e5211@googlegroups.com>
Message-ID: <CABDkGQ=QRxbGRaHSooNGbFwUNtdrdRnWknLUbAXxnhFsEQJ+dA@mail.gmail.com>

Hi Alex

On Fri, 29 Apr 2016 at 21:51 Alexandre Fioravante de Siqueira <
siqueiraaf at gmail.com> wrote:

> is this valid yet? I could send you the preliminary results of my research.
> Thanks!
>

It is, and please do!  My talk is on Tuesday.

So far I have examples from astronomy (thanks Christoph!) and  pathology
(thanks Quentin and Romain!).

Regards
St?fan
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From stefanv at berkeley.edu  Sat Apr 30 16:55:32 2016
From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Sat, 30 Apr 2016 20:55:32 +0000
Subject: Opinion poll: feedback URL upon import
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On Fri, 29 Apr 2016 at 18:54 Andreas Mueller <amueller at ais.uni-bonn.de>
wrote:

> There was some discussion about whether we could use jupyter to get some
> feedback from users, i.e. a single opt-in for the jupyter
> platform, instead one for each library (which would be pretty bad).
>

I think this is still on Nathaniel's radar; he's been quite busy with the
manylinux work, but now that that's almost done I guess he'll round back on
this project.


> I wonder if / how other open source libraries handle this. I guess boost
> doesn't care ;)
> But maybe web frameworks do? We could try tapping other scientific
> computing communities like
> julia or octave, or go out to web folks?
>

I had another good suggestion from a colleague yesterday that we can have a
showcase section on the website, where authors & companies can get free
publication for work using scikit-image.

I also want to add a survey bubble to the website, to gauge where we can
best improve.

St?fan
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