From jschoenberger at demuc.de  Fri Mar  1 03:23:38 2013
From: jschoenberger at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Fri, 1 Mar 2013 09:23:38 +0100
Subject: Segfaults from CTMF
In-Reply-To: <CAEym_HpMZibSbPxVrFGJa83KrFYw5PxcQUgyKu-HJH0-6tJNCQ@mail.gmail.com>
References: <CAEym_HpMZibSbPxVrFGJa83KrFYw5PxcQUgyKu-HJH0-6tJNCQ@mail.gmail.com>
Message-ID: <73C77D74-6FD3-4AC3-9369-662DB6EB17EF@demuc.de>

Works for me on OSX 10.8, Python 2.7.3, Cython 0.18 and Cython 0.16 (Intel Core i7).

Johannes Sch?nberger

Am 01.03.2013 um 01:35 schrieb Tony Yu <tsyu80 at gmail.com>:

> I'm getting segfaults when running the median filter due to the SSE/MMX/Altivec speed ups for ctmf (PR #432). Here's a short snippet for testing:
> 
> from skimage import data
> from skimage.filter import median_filter
> 
> median_filter(data.camera())
> 
> Is any one else getting a segfault? I'm running OSX 10.8 on a Intel Core i7 machine with Cython 0.16, Python 2.7.3.
> 
> Thanks,
> -Tony
> 
> -- 
> 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.
> For more options, visit https://groups.google.com/groups/opt_out.
>  
>  



From tsyu80 at gmail.com  Fri Mar  1 10:48:24 2013
From: tsyu80 at gmail.com (Tony Yu)
Date: Fri, 1 Mar 2013 09:48:24 -0600
Subject: Segfaults from CTMF
In-Reply-To: <CAHGWWxFBSOXh2VNZ+fG7G6dDTbNQyvkF7dZ=e4-sHUr=sG=bng@mail.gmail.com>
References: <CAEym_HpMZibSbPxVrFGJa83KrFYw5PxcQUgyKu-HJH0-6tJNCQ@mail.gmail.com>
 <CAHGWWxFBSOXh2VNZ+fG7G6dDTbNQyvkF7dZ=e4-sHUr=sG=bng@mail.gmail.com>
Message-ID: <CAEym_HqgJ_fGRJM389yvFBE6x2=TNxyoERyvjfrYJxn3-VaoEw@mail.gmail.com>

On Thu, Feb 28, 2013 at 8:17 PM, Thouis (Ray) Jones <thouis at gmail.com>wrote:

> I'm on OSX 10.8, python 2.7.3, Cython 0.18.  I wonder if it's the
> cython version.  Your code works for me.
>
> Do you have a traceback?


There's no python traceback, but I've copied the crash report below. The
relevant line in the Cython code is:

https://github.com/scikit-image/scikit-image/blob/master/skimage/filter/_ctmf.pyx#L366


Also, do you know which path it's going down
> (SSE/MMX/Altivec/unaccelerated)?
>
>

It's crashing on the SSE path. The MMX (and unaccelerated) path works fine.

Crash report
~~~~~~~~~

Crashed Thread:  0  Dispatch queue: com.apple.main-thread

Exception Type:  EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: EXC_I386_GPFLT

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   _ctmf.so                       0x058c77ea
__pyx_f_7skimage_6filter_5_ctmf_accumulate + 490 (_ctmf.c:2277)
1   _ctmf.so                       0x058cb4a0
__pyx_pw_7skimage_6filter_5_ctmf_1median_filter + 8864 (_ctmf.c:3673)
2   org.python.python             0x000cb2d1 PyEval_EvalFrameEx + 21649
3   org.python.python             0x000cd02a PyEval_EvalCodeEx + 2042
4   org.python.python             0x000cb253 PyEval_EvalFrameEx + 21523
5   org.python.python             0x000cd02a PyEval_EvalCodeEx + 2042
6   org.python.python             0x000cd1b7 PyEval_EvalCode + 87
7   org.python.python             0x000f1898 PyRun_FileExFlags + 168
8   org.python.python             0x000f27c3 PyRun_SimpleFileExFlags + 867
9   org.python.python             0x0010ba58 Py_Main + 3560
10  org.python.python             0x00001fb6 0x1000 + 4022



> Ray
>
>
> On Thu, Feb 28, 2013 at 7:35 PM, Tony Yu <tsyu80 at gmail.com> wrote:
> > I'm getting segfaults when running the median filter due to the
> > SSE/MMX/Altivec speed ups for ctmf (PR #432). Here's a short snippet for
> > testing:
> >
> >
> > from skimage import data
> > from skimage.filter import median_filter
> >
> > median_filter(data.camera())
> >
> >
> > Is any one else getting a segfault? I'm running OSX 10.8 on a Intel Core
> i7
> > machine with Cython 0.16, Python 2.7.3.
> >
> > Thanks,
> > -Tony
> >
> > --
> > 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.
> > For more options, visit https://groups.google.com/groups/opt_out.
> >
> >
>
> --
> 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.
> For more options, visit https://groups.google.com/groups/opt_out.
>
>
>
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From tsyu80 at gmail.com  Fri Mar  1 19:02:42 2013
From: tsyu80 at gmail.com (Tony Yu)
Date: Fri, 1 Mar 2013 18:02:42 -0600
Subject: Segfaults from CTMF
In-Reply-To: <CAEym_HqgJ_fGRJM389yvFBE6x2=TNxyoERyvjfrYJxn3-VaoEw@mail.gmail.com>
References: <CAEym_HpMZibSbPxVrFGJa83KrFYw5PxcQUgyKu-HJH0-6tJNCQ@mail.gmail.com>
 <CAHGWWxFBSOXh2VNZ+fG7G6dDTbNQyvkF7dZ=e4-sHUr=sG=bng@mail.gmail.com> <CAEym_HqgJ_fGRJM389yvFBE6x2=TNxyoERyvjfrYJxn3-VaoEw@mail.gmail.com>
Message-ID: <CAEym_Ho8gnSGFm0u9g9U1F4Uy_mKw2Qaok8SOQwm3nh8gtff2Q@mail.gmail.com>

On Fri, Mar 1, 2013 at 9:48 AM, Tony Yu <tsyu80 at gmail.com> wrote:

>
>
> On Thu, Feb 28, 2013 at 8:17 PM, Thouis (Ray) Jones <thouis at gmail.com>wrote:
>
>> I'm on OSX 10.8, python 2.7.3, Cython 0.18.  I wonder if it's the
>> cython version.  Your code works for me.
>>
>> Do you have a traceback?
>
>
> There's no python traceback, but I've copied the crash report below. The
> relevant line in the Cython code is:
>
>
> https://github.com/scikit-image/scikit-image/blob/master/skimage/filter/_ctmf.pyx#L366
>
>
> Also, do you know which path it's going down
>> (SSE/MMX/Altivec/unaccelerated)?
>>
>>
>
> It's crashing on the SSE path. The MMX (and unaccelerated) path works fine.
>
> Crash report
> ~~~~~~~~~
>
>  Crashed Thread:  0  Dispatch queue: com.apple.main-thread
>
> Exception Type:  EXC_BAD_ACCESS (SIGSEGV)
> Exception Codes: EXC_I386_GPFLT
>
> Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
> 0   _ctmf.so                       0x058c77ea
> __pyx_f_7skimage_6filter_5_ctmf_accumulate + 490 (_ctmf.c:2277)
> 1   _ctmf.so                       0x058cb4a0
> __pyx_pw_7skimage_6filter_5_ctmf_1median_filter + 8864 (_ctmf.c:3673)
> 2   org.python.python             0x000cb2d1 PyEval_EvalFrameEx + 21649
> 3   org.python.python             0x000cd02a PyEval_EvalCodeEx + 2042
> 4   org.python.python             0x000cb253 PyEval_EvalFrameEx + 21523
> 5   org.python.python             0x000cd02a PyEval_EvalCodeEx + 2042
> 6   org.python.python             0x000cd1b7 PyEval_EvalCode + 87
> 7   org.python.python             0x000f1898 PyRun_FileExFlags + 168
> 8   org.python.python             0x000f27c3 PyRun_SimpleFileExFlags + 867
> 9   org.python.python             0x0010ba58 Py_Main + 3560
> 10  org.python.python             0x00001fb6 0x1000 + 4022
>
>
>
>> Ray
>>
>>
>> On Thu, Feb 28, 2013 at 7:35 PM, Tony Yu <tsyu80 at gmail.com> wrote:
>> > I'm getting segfaults when running the median filter due to the
>> > SSE/MMX/Altivec speed ups for ctmf (PR #432). Here's a short snippet for
>> > testing:
>> >
>> >
>> > from skimage import data
>> > from skimage.filter import median_filter
>> >
>> > median_filter(data.camera())
>> >
>> >
>> > Is any one else getting a segfault? I'm running OSX 10.8 on a Intel
>> Core i7
>> > machine with Cython 0.16, Python 2.7.3.
>> >
>> > Thanks,
>> > -Tony
>>
>>
I forgot to mention in my original email: This is running 32-bit Python. I
have a separate machine running 64-bit Python and everything is fine.

-T
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From nathan.faggian at gmail.com  Mon Mar  4 16:40:12 2013
From: nathan.faggian at gmail.com (Nathan Faggian)
Date: Mon, 4 Mar 2013 13:40:12 -0800 (PST)
Subject: Announcement: scikits-image 0.8.0
In-Reply-To: <65398392-BB03-4863-9624-A97654C6E558@demuc.de>
References: <65398392-BB03-4863-9624-A97654C6E558@demuc.de>
Message-ID: <7d668247-2edf-4e0d-9eeb-7185e37b547a@googlegroups.com>

Great work!

On Tuesday, 5 March 2013 07:41:56 UTC+11, Johannes Sch?nberger wrote:
>
>
> Announcement: scikits-image 0.8.0 
> ================================= 
>
> We're happy to announce the 8th version of scikit-image! 
>
> scikit-image is an image processing toolbox for SciPy that includes 
> algorithms 
> for segmentation, geometric transformations, color space manipulation, 
> analysis, filtering, morphology, feature detection, and more. 
>
> For more information, examples, and documentation, please visit our 
> website: 
>
>     http://scikit-image.org 
>
>
> New Features 
> ------------ 
>
> - New rank filter package with many new functions and a very fast 
> underlying 
>   local histogram algorithm, especially for large structuring elements 
>   `skimage.filter.rank.*` 
> - New function for small object removal 
>   `skimage.morphology.remove_small_objects` 
> - New circular hough transformation `skimage.transform.hough_circle` 
> - New function to draw circle perimeter `skimage.draw.circle_perimeter` 
> and 
>   ellipse perimeter `skimage.draw.ellipse_perimeter` 
> - New dense DAISY feature descriptor `skimage.feature.daisy` 
> - New bilateral filter `skimage.filter.denoise_bilateral` 
> - New faster TV denoising filter based on split-Bregman algorithm 
>   `skimage.filter.denoise_tv_bregman` 
> - New linear hough peak detection `skimage.transform.hough_peaks` 
> - New Scharr edge detection `skimage.filter.scharr` 
> - New geometric image scaling as convenience function 
>   `skimage.transform.rescale` 
> - New theme for documentation and website 
> - Faster median filter through vectorization 
> `skimage.filter.median_filter` 
> - Grayscale images supported for SLIC segmentation 
> - Unified peak detection with more options 
> `skimage.feature.peak_local_max` 
> - `imread` can read images via URL and knows more formats 
> `skimage.io.imread` 
>
> Additionally, this release adds lots of bug fixes, new examples, and 
> performance enhancements. 
>
>
> Contributors to this release 
> ---------------------------- 
>
> This release was only possible due to the efforts of many contributors, 
> both 
> new and old. 
>
> - Adam Ginsburg 
> - Anders Boesen Lindbo Larsen 
> - Andreas Mueller 
> - Christoph Gohlke 
> - Christos Psaltis 
> - Colin Lea 
> - Fran?ois Boulogne 
> - Jan Margeta 
> - Johannes Sch?nberger 
> - Josh Warner (Mac) 
> - Juan Nunez-Iglesias 
> - Luis Pedro Coelho 
> - Marianne Corvellec 
> - Matt McCormick 
> - Nicolas Pinto 
> - Olivier Debeir 
> - Paul Ivanov 
> - Sergey Karayev 
> - Stefan van der Walt 
> - Steven Silvester 
> - Thouis (Ray) Jones 
> - Tony S Yu 
>
>
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From ronnie.ghose at gmail.com  Mon Mar  4 17:12:25 2013
From: ronnie.ghose at gmail.com (Ronnie Ghose)
Date: Mon, 4 Mar 2013 17:12:25 -0500
Subject: Announcement: scikits-image 0.8.0
In-Reply-To: <51351A5B.4080200@gemini.edu>
References: <65398392-BB03-4863-9624-A97654C6E558@demuc.de>
 <7d668247-2edf-4e0d-9eeb-7185e37b547a@googlegroups.com> <51351A5B.4080200@gemini.edu>
Message-ID: <CAHazPTnKAc8EsQUJqW9S4PdaQUOf=Qg-CTc==yWidmtYV6nZUQ@mail.gmail.com>

... wow this is pretty cool :). Question though, how can we make an
interactive version too? I'm thinking sliders in matplotlib ... but can
matplotlib shows gifs like their image? imho this sort of method involves a
lot of manual tweaking.


On Mon, Mar 4, 2013 at 5:04 PM, James Turner <jturner at gemini.edu> wrote:

> Great.
>
> Since that's out of the way, I saw this in the news today and
> thought some of you might be interested :-).
>
>   http://people.csail.mit.edu/**mrub/vidmag/<http://people.csail.mit.edu/mrub/vidmag/>
>
> James.
>
> --
> 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@**googlegroups.com<scikit-image%2Bunsubscribe at googlegroups.com>
> .
> For more options, visit https://groups.google.com/**groups/opt_out<https://groups.google.com/groups/opt_out>
> .
>
>
>
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From otrov at hush.ai  Mon Mar  4 11:19:47 2013
From: otrov at hush.ai (zetah)
Date: Mon, 04 Mar 2013 17:19:47 +0100
Subject: Segmenting contours
In-Reply-To: <20130228124657.4843C14DBD4@smtp.hushmail.com>
References: <c2e8b991-a614-4ff7-9c7d-6b995a35877b@googlegroups.com> <CABDkGQ=4JK+S-kyqA5LnxuSjLVG8F=+p0thHM06MP5eXUyt92A@mail.gmail.com> <082300a7-fd43-4779-b665-af8b62f8c49c@googlegroups.com> <CABDkGQ=GZsx8mn9LyzM9aSm4kYOE13v2xX3musv0WthNvYWfow@mail.gmail.com> <a2da073e-89e3-4ec1-b0ad-2deb47969a7a@googlegroups.com> <6f6dd4b2-5083-4db8-8abf-1cb3bf537170@googlegroups.com> <CABDkGQnNrh5Fis4e+1R-=Y=BGHUzgVNmTGtVUJeQKwo1zj-kRw@mail.gmail.com> <e828dab6-efdd-42de-90b0-b545995eac01@googlegroups.com> <d2f126b1-a1be-45e9-be11-b413bf4ee100@googlegroups.com> <CABDkGQmdxV8Lix8r3wXsytWTOXMCer4aJ5_vyUoBvcG2N+4tAQ@mail.gmail.com> <20130228124657.4843C14DBD4@smtp.hushmail.com>
Message-ID: <20130304161948.318146F448@smtp.hushmail.com>

Stefan,

I found the algorithm implemented in CGAL ipelet demo package, so except the implementation it can be applied in ipe GUI. I'm impressed by those ipelets, as they make this vector drawing program magical, allowing computational geometry algorithms in vector application.

I also went the route with Python, and it doesn't look that hard as expected. Triangulation can be applied on binary image as is, but it's better if contours are sampled. "Only" thing left for me to do is applying the crust i.e filtering the triangulation, which I interrupted as I was introduced to this huge package CGAL.


Cheers



From jturner at gemini.edu  Mon Mar  4 17:04:11 2013
From: jturner at gemini.edu (James Turner)
Date: Mon, 4 Mar 2013 19:04:11 -0300
Subject: Announcement: scikits-image 0.8.0
In-Reply-To: <7d668247-2edf-4e0d-9eeb-7185e37b547a@googlegroups.com>
References: <65398392-BB03-4863-9624-A97654C6E558@demuc.de> <7d668247-2edf-4e0d-9eeb-7185e37b547a@googlegroups.com>
Message-ID: <51351A5B.4080200@gemini.edu>

Great.

Since that's out of the way, I saw this in the news today and
thought some of you might be interested :-).

   http://people.csail.mit.edu/mrub/vidmag/

James.


From jschoenberger at demuc.de  Mon Mar  4 15:41:56 2013
From: jschoenberger at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Mon, 4 Mar 2013 21:41:56 +0100
Subject: Announcement: scikits-image 0.8.0
Message-ID: <65398392-BB03-4863-9624-A97654C6E558@demuc.de>


Announcement: scikits-image 0.8.0
=================================

We're happy to announce the 8th version of scikit-image!

scikit-image is an image processing toolbox for SciPy that includes algorithms
for segmentation, geometric transformations, color space manipulation,
analysis, filtering, morphology, feature detection, and more.

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

    http://scikit-image.org


New Features
------------

- New rank filter package with many new functions and a very fast underlying
  local histogram algorithm, especially for large structuring elements
  `skimage.filter.rank.*`
- New function for small object removal
  `skimage.morphology.remove_small_objects`
- New circular hough transformation `skimage.transform.hough_circle`
- New function to draw circle perimeter `skimage.draw.circle_perimeter` and
  ellipse perimeter `skimage.draw.ellipse_perimeter`
- New dense DAISY feature descriptor `skimage.feature.daisy`
- New bilateral filter `skimage.filter.denoise_bilateral`
- New faster TV denoising filter based on split-Bregman algorithm
  `skimage.filter.denoise_tv_bregman`
- New linear hough peak detection `skimage.transform.hough_peaks`
- New Scharr edge detection `skimage.filter.scharr`
- New geometric image scaling as convenience function
  `skimage.transform.rescale`
- New theme for documentation and website
- Faster median filter through vectorization `skimage.filter.median_filter`
- Grayscale images supported for SLIC segmentation
- Unified peak detection with more options `skimage.feature.peak_local_max`
- `imread` can read images via URL and knows more formats `skimage.io.imread`

Additionally, this release adds lots of bug fixes, new examples, and
performance enhancements.


Contributors to this release
----------------------------

This release was only possible due to the efforts of many contributors, both
new and old.

- Adam Ginsburg
- Anders Boesen Lindbo Larsen
- Andreas Mueller
- Christoph Gohlke
- Christos Psaltis
- Colin Lea
- Fran?ois Boulogne
- Jan Margeta
- Johannes Sch?nberger
- Josh Warner (Mac)
- Juan Nunez-Iglesias
- Luis Pedro Coelho
- Marianne Corvellec
- Matt McCormick
- Nicolas Pinto
- Olivier Debeir
- Paul Ivanov
- Sergey Karayev
- Stefan van der Walt
- Steven Silvester
- Thouis (Ray) Jones
- Tony S Yu



From amueller at ais.uni-bonn.de  Mon Mar  4 17:23:03 2013
From: amueller at ais.uni-bonn.de (Andreas Mueller)
Date: Mon, 04 Mar 2013 23:23:03 +0100
Subject: Announcement: scikits-image 0.8.0
In-Reply-To: <65398392-BB03-4863-9624-A97654C6E558@demuc.de>
References: <65398392-BB03-4863-9624-A97654C6E558@demuc.de>
Message-ID: <51351EC7.2090501@ais.uni-bonn.de>

On 03/04/2013 09:41 PM, Johannes Sch?nberger wrote:
> Announcement: scikits-image 0.8.0
> =================================
>
> We're happy to announce the 8th version of scikit-image!
>
> scikit-image is an image processing toolbox for SciPy that includes algorithms
> for segmentation, geometric transformations, color space manipulation,
> analysis, filtering, morphology, feature detection, and more.
>
> For more information, examples, and documentation, please visit our website:
>
>      http://scikit-image.org
>
Congratulations to everyone involved and thanks for the hard work!

Did anyone do any detection with Daisy yet?


From jschoenberger at demuc.de  Mon Mar  4 17:49:38 2013
From: jschoenberger at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Mon, 4 Mar 2013 23:49:38 +0100
Subject: Announcement: scikits-image 0.8.0
In-Reply-To: <65398392-BB03-4863-9624-A97654C6E558@demuc.de>
References: <65398392-BB03-4863-9624-A97654C6E558@demuc.de>
Message-ID: <D6DC2380-8652-4501-BF84-028087CB575A@demuc.de>

Another feature I forgot to mention:

 - New corner detection functions `skimage.feature.corner_*`


Johannes Sch?nberger

Am 04.03.2013 um 21:41 schrieb Johannes Sch?nberger <jschoenberger at demuc.de>:

> 
> Announcement: scikits-image 0.8.0
> =================================
> 
> We're happy to announce the 8th version of scikit-image!
> 
> scikit-image is an image processing toolbox for SciPy that includes algorithms
> for segmentation, geometric transformations, color space manipulation,
> analysis, filtering, morphology, feature detection, and more.
> 
> For more information, examples, and documentation, please visit our website:
> 
>    http://scikit-image.org
> 
> 
> New Features
> ------------
> 
> - New rank filter package with many new functions and a very fast underlying
>  local histogram algorithm, especially for large structuring elements
>  `skimage.filter.rank.*`
> - New function for small object removal
>  `skimage.morphology.remove_small_objects`
> - New circular hough transformation `skimage.transform.hough_circle`
> - New function to draw circle perimeter `skimage.draw.circle_perimeter` and
>  ellipse perimeter `skimage.draw.ellipse_perimeter`
> - New dense DAISY feature descriptor `skimage.feature.daisy`
> - New bilateral filter `skimage.filter.denoise_bilateral`
> - New faster TV denoising filter based on split-Bregman algorithm
>  `skimage.filter.denoise_tv_bregman`
> - New linear hough peak detection `skimage.transform.hough_peaks`
> - New Scharr edge detection `skimage.filter.scharr`
> - New geometric image scaling as convenience function
>  `skimage.transform.rescale`
> - New theme for documentation and website
> - Faster median filter through vectorization `skimage.filter.median_filter`
> - Grayscale images supported for SLIC segmentation
> - Unified peak detection with more options `skimage.feature.peak_local_max`
> - `imread` can read images via URL and knows more formats `skimage.io.imread`
> 
> Additionally, this release adds lots of bug fixes, new examples, and
> performance enhancements.
> 
> 
> Contributors to this release
> ----------------------------
> 
> This release was only possible due to the efforts of many contributors, both
> new and old.
> 
> - Adam Ginsburg
> - Anders Boesen Lindbo Larsen
> - Andreas Mueller
> - Christoph Gohlke
> - Christos Psaltis
> - Colin Lea
> - Fran?ois Boulogne
> - Jan Margeta
> - Johannes Sch?nberger
> - Josh Warner (Mac)
> - Juan Nunez-Iglesias
> - Luis Pedro Coelho
> - Marianne Corvellec
> - Matt McCormick
> - Nicolas Pinto
> - Olivier Debeir
> - Paul Ivanov
> - Sergey Karayev
> - Stefan van der Walt
> - Steven Silvester
> - Thouis (Ray) Jones
> - Tony S Yu
> 
> -- 
> 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.
> For more options, visit https://groups.google.com/groups/opt_out.
> 
> 



From jturner at gemini.edu  Tue Mar  5 11:32:18 2013
From: jturner at gemini.edu (James Turner)
Date: Tue, 5 Mar 2013 13:32:18 -0300
Subject: Announcement: scikits-image 0.8.0
In-Reply-To: <CABDkGQmXXQ-wwsH8ce10PVUQVyE9uGJi5synO=xpLHKFA07TqQ@mail.gmail.com>
References: <65398392-BB03-4863-9624-A97654C6E558@demuc.de> <7d668247-2edf-4e0d-9eeb-7185e37b547a@googlegroups.com> <51351A5B.4080200@gemini.edu> <CABDkGQmXXQ-wwsH8ce10PVUQVyE9uGJi5synO=xpLHKFA07TqQ@mail.gmail.com>
Message-ID: <51361E12.3040401@gemini.edu>

Actually, I now notice that their page says "This work is patent
pending". That's pretty antisocial, though with applications in
commercial devices I can see why they'd be tempted...


>> Since that's out of the way, I saw this in the news today and
>> thought some of you might be interested :-).
>>
>>    http://people.csail.mit.edu/mrub/vidmag/
>
> That'd be fun!  Step one would be to fix the current GStreamerVideo, though.
>
> St??????fan


From stefan at sun.ac.za  Tue Mar  5 07:00:23 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 5 Mar 2013 14:00:23 +0200
Subject: Announcement: scikits-image 0.8.0
In-Reply-To: <51351A5B.4080200@gemini.edu>
References: <65398392-BB03-4863-9624-A97654C6E558@demuc.de>
 <7d668247-2edf-4e0d-9eeb-7185e37b547a@googlegroups.com> <51351A5B.4080200@gemini.edu>
Message-ID: <CABDkGQmXXQ-wwsH8ce10PVUQVyE9uGJi5synO=xpLHKFA07TqQ@mail.gmail.com>

On Tue, Mar 5, 2013 at 12:04 AM, James Turner <jturner at gemini.edu> wrote:
> Since that's out of the way, I saw this in the news today and
> thought some of you might be interested :-).
>
>   http://people.csail.mit.edu/mrub/vidmag/

That'd be fun!  Step one would be to fix the current GStreamerVideo, though.

St?fan


From francois.boulogne at gmail.com  Wed Mar  6 15:57:44 2013
From: francois.boulogne at gmail.com (=?UTF-8?Q?Fran=C3=A7ois?=)
Date: Wed, 6 Mar 2013 12:57:44 -0800 (PST)
Subject: Contribution: circles and hough transform
In-Reply-To: <CABDkGQkm-pL3UdH0BhRFpu2d81HUiBmNVBu4yE6du1DeHsGb2g@mail.gmail.com>
References: <32b3855a-c23e-4b88-a5d0-e0aea8b6f926@googlegroups.com>
 <CABDkGQnQE--Q44o4P-Pxcnhkfm_TpHmUqaExnU-2pRt2Eothog@mail.gmail.com>
 <e74ede00-1153-4fd5-ab5f-1b7e4a5a5016@googlegroups.com> <2cfab5a8-27ff-4621-9b68-942581fbcf81@googlegroups.com>
 <CABDkGQn25uvv=qys8CQg5S=UcJdLfx4yPH=N37DagfjOD=qXig@mail.gmail.com> <C1BC5C50-4928-4716-AF11-C87C5E489338@gmail.com>
 <CABDkGQkm-pL3UdH0BhRFpu2d81HUiBmNVBu4yE6du1DeHsGb2g@mail.gmail.com>
Message-ID: <64a82cf8-cb8c-4231-ae81-3a9c7a630be3@googlegroups.com>

Hi,

FYI, I plan to work on the detection of ellipses quite soon. Stefan 
indicated to me a reference which seems fairly simple to implement.

Cheers,
Fran?ois.
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From jschoenberger at demuc.de  Wed Mar  6 10:58:26 2013
From: jschoenberger at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Wed, 6 Mar 2013 16:58:26 +0100
Subject: Announcement: scikits-image 0.8.0
In-Reply-To: <51361E12.3040401@gemini.edu>
References: <65398392-BB03-4863-9624-A97654C6E558@demuc.de> <7d668247-2edf-4e0d-9eeb-7185e37b547a@googlegroups.com> <51351A5B.4080200@gemini.edu> <CABDkGQmXXQ-wwsH8ce10PVUQVyE9uGJi5synO=xpLHKFA07TqQ@mail.gmail.com> <51361E12.3040401@gemini.edu>
Message-ID: <41CB4C5F-EB14-46F9-A0D3-5C7D0D723872@demuc.de>

0.8.1 has been released with a few minor important bug fixes.

Johannes Sch?nberger


From jschoenberger at demuc.de  Wed Mar  6 17:37:49 2013
From: jschoenberger at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Wed, 6 Mar 2013 23:37:49 +0100
Subject: Announcement: scikits-image 0.8.0
In-Reply-To: <41CB4C5F-EB14-46F9-A0D3-5C7D0D723872@demuc.de>
References: <65398392-BB03-4863-9624-A97654C6E558@demuc.de> <7d668247-2edf-4e0d-9eeb-7185e37b547a@googlegroups.com> <51351A5B.4080200@gemini.edu> <CABDkGQmXXQ-wwsH8ce10PVUQVyE9uGJi5synO=xpLHKFA07TqQ@mail.gmail.com> <51361E12.3040401@gemini.edu> <41CB4C5F-EB14-46F9-A0D3-5C7D0D723872@demuc.de>
Message-ID: <DD21BC26-0952-4F5E-8F8D-334CA8B92BA4@demuc.de>

Again, 0.8.2 has been pushed as a fix for a bug which has been introduced by 0.8.1. Let me know if you experience any other remaining bugs.

Johannes Sch?nberger

Am 06.03.2013 um 16:58 schrieb Johannes Sch?nberger <jschoenberger at demuc.de>:

> 0.8.1 has been released with a few minor important bug fixes.
> 
> Johannes Sch?nberger
> 
> -- 
> 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.
> For more options, visit https://groups.google.com/groups/opt_out.
> 
> 



From stefan at sun.ac.za  Thu Mar  7 06:30:26 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 7 Mar 2013 13:30:26 +0200
Subject: Announcement: scikits-image 0.8.0
In-Reply-To: <CAHazPTnKAc8EsQUJqW9S4PdaQUOf=Qg-CTc==yWidmtYV6nZUQ@mail.gmail.com>
References: <65398392-BB03-4863-9624-A97654C6E558@demuc.de>
 <7d668247-2edf-4e0d-9eeb-7185e37b547a@googlegroups.com> <51351A5B.4080200@gemini.edu>
 <CAHazPTnKAc8EsQUJqW9S4PdaQUOf=Qg-CTc==yWidmtYV6nZUQ@mail.gmail.com>
Message-ID: <CABDkGQmDKwnkyK9mqfdZLbcJCwx-Jr5CEiEASUWKWY9RKAOa+Q@mail.gmail.com>

Hi Ronnie

On Tue, Mar 5, 2013 at 12:12 AM, Ronnie Ghose <ronnie.ghose at gmail.com> wrote:
> ... wow this is pretty cool :). Question though, how can we make an
> interactive version too? I'm thinking sliders in matplotlib ... but can
> matplotlib shows gifs like their image? imho this sort of method involves a
> lot of manual tweaking.

We already have one :)  `skimage.viewer`

Have a look at the examples under the "viewer_examples" directory in
the Git repo.

St?fan


From stefan at sun.ac.za  Thu Mar  7 06:33:58 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 7 Mar 2013 13:33:58 +0200
Subject: Announcement: scikits-image 0.8.0
In-Reply-To: <619caf5f-7c51-4fef-96fa-2f11887ff944@googlegroups.com>
References: <65398392-BB03-4863-9624-A97654C6E558@demuc.de>
 <51351EC7.2090501@ais.uni-bonn.de> <619caf5f-7c51-4fef-96fa-2f11887ff944@googlegroups.com>
Message-ID: <CABDkGQkccck3RzrxPOMQngSxqrpkwMcVHN2iawaG-hNf9s9TKw@mail.gmail.com>

Hi Anders

On Thu, Mar 7, 2013 at 11:50 AM, Anders Boesen Lindbo Larsen
<anders.bll at gmail.com> wrote:
> Congratulations indeed! Thanks to scikit-image Python has become my language
> of choice for vision/image processing applications! :)

That is a wonderful compliment to the project!  Thank you also for
your contribution to this (and future :) releases.

St?fan


From ronnie.ghose at gmail.com  Mon Mar 11 02:52:15 2013
From: ronnie.ghose at gmail.com (Ronnie Ghose)
Date: Mon, 11 Mar 2013 02:52:15 -0400
Subject: 3D SLIC code
In-Reply-To: <CA+JHcKTqTK6pt8Eqb=Ht+LDLDi=f0qS7a7MDGQjAYkC+QgS2Jg@mail.gmail.com>
References: <CA+JHcKTqTK6pt8Eqb=Ht+LDLDi=f0qS7a7MDGQjAYkC+QgS2Jg@mail.gmail.com>
Message-ID: <CAHazPTngYZXMRArh8dQS+E_VbtrbJO=WBYLOvHU3tRE0dE3ncA@mail.gmail.com>

+1 sounds interesting. I'm for has_channels = True, assuming you're
modifying the 2d code, since I assume the main use for it will be 2d images.


On Mon, Mar 11, 2013 at 2:43 AM, Juan Nunez-Iglesias <jni.soma at gmail.com>wrote:

> Hi all,
>
> I want to modify SLIC to handle 3D images. However, it now become rather
> tricky to automatically detect whether the final dimension is channels or
> just z, in the case of image.ndim == 3 (ie, is this a 3D grayscale image,
> or a 2D RGB image?). I was trying to do something automatically (image.ndim
> == 3 and image.shape[-1] == 3) but I think maybe the easiest thing is to
> add a "has_channels" argument, defaulting to...? I want to say False, but
> that's just my own biases. =)
>
> What do you think?
>
> Juan.
>
> --
> 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.
> For more options, visit https://groups.google.com/groups/opt_out.
>
>
>
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From ronnie.ghose at gmail.com  Mon Mar 11 03:19:09 2013
From: ronnie.ghose at gmail.com (Ronnie Ghose)
Date: Mon, 11 Mar 2013 03:19:09 -0400
Subject: 3D SLIC code
In-Reply-To: <CA+JHcKSzm=BCSW_M4V343ZWYeACxujZop9j8u7z5teCgve8iyA@mail.gmail.com>
References: <CA+JHcKTqTK6pt8Eqb=Ht+LDLDi=f0qS7a7MDGQjAYkC+QgS2Jg@mail.gmail.com>
 <CAHazPTngYZXMRArh8dQS+E_VbtrbJO=WBYLOvHU3tRE0dE3ncA@mail.gmail.com> <CA+JHcKSzm=BCSW_M4V343ZWYeACxujZop9j8u7z5teCgve8iyA@mail.gmail.com>
Message-ID: <CAHazPT=4YEVWb4_Fzom+cq=veQcBbcXBYmg5MX5Lnm_EhjVpAA@mail.gmail.com>

+1


On Mon, Mar 11, 2013 at 3:07 AM, Juan Nunez-Iglesias <jni.soma at gmail.com>wrote:

> On Mon, Mar 11, 2013 at 5:52 PM, Ronnie Ghose <ronnie.ghose at gmail.com>wrote:
>
>> assuming you're modifying the 2d code,
>>
>
> My intention is to reduce the 2D case to 3D with Z = 1. This would be ~20%
> slower for 2D, but
> 1) SLIC is lightning fast in the first place, so a 20% bump is not a huge
> deal, and
> 2) the benefit is a vastly simplified code base relative to duplicating a
> whole lot of code specifically for 3D.
>
> I definitely have no problems with defaulting has_channels to True. Plus a
> user could do:
>
> slic_bw = functools.partial(slic, has_channels=False)
>
> and be done with it. ;)
>
> --
> 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.
> For more options, visit https://groups.google.com/groups/opt_out.
>
>
>
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From ronnie.ghose at gmail.com  Mon Mar 11 03:39:52 2013
From: ronnie.ghose at gmail.com (Ronnie Ghose)
Date: Mon, 11 Mar 2013 03:39:52 -0400
Subject: 3D SLIC code
In-Reply-To: <CABDkGQmZ_=wXbVgvDu_zgccrxB_GgiGVi6u6QEfKZm2oc9F+Ww@mail.gmail.com>
References: <CA+JHcKTqTK6pt8Eqb=Ht+LDLDi=f0qS7a7MDGQjAYkC+QgS2Jg@mail.gmail.com>
 <CABDkGQmZ_=wXbVgvDu_zgccrxB_GgiGVi6u6QEfKZm2oc9F+Ww@mail.gmail.com>
Message-ID: <CAHazPTmJ0eRyTuEaLd_1XJ-29d+sjzOf4bpw9ifUMC6y4ZfP7A@mail.gmail.com>

... ehhh... I would prefer 2d rgb to be the default in general as I think
that is the generl use case? . This calls for a discussion imho.


On Mon, Mar 11, 2013 at 3:36 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> On Mon, Mar 11, 2013 at 8:43 AM, Juan Nunez-Iglesias <jni.soma at gmail.com>
> wrote:
> > I want to modify SLIC to handle 3D images. However, it now become rather
> > tricky to automatically detect whether the final dimension is channels or
> > just z, in the case of image.ndim == 3 (ie, is this a 3D grayscale
> image, or
> > a 2D RGB image?). I was trying to do something automatically (image.ndim
> ==
> > 3 and image.shape[-1] == 3) but I think maybe the easiest thing is to
> add a
> > "has_channels" argument, defaulting to...? I want to say False, but
> that's
> > just my own biases. =)
>
> In `random_walker`, we've opted for "multichannel=False":
>
>     data : array_like
>         Image to be segmented in phases. Gray-level `data` can be two- or
>         three-dimensional; multichannel data can be three- or four-
>         dimensional (multichannel=True) with the highest dimension denoting
>         channels. Data spacing is assumed isotropic unless depth keyword
>         argument is used.
>
>     multichannel : bool, default False
>         If True, input data is parsed as multichannel data (see 'data'
> above
>         for proper input format in this case)
>
> 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.
> For more options, visit https://groups.google.com/groups/opt_out.
>
>
>
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From ronnie.ghose at gmail.com  Mon Mar 11 04:13:52 2013
From: ronnie.ghose at gmail.com (Ronnie Ghose)
Date: Mon, 11 Mar 2013 04:13:52 -0400
Subject: 3D SLIC code
In-Reply-To: <CABDkGQ=Ro4=SaL28ACnoBcSHJKGyDqm7dYLV14SnVzwEgYhFSw@mail.gmail.com>
References: <CA+JHcKTqTK6pt8Eqb=Ht+LDLDi=f0qS7a7MDGQjAYkC+QgS2Jg@mail.gmail.com>
 <CABDkGQmZ_=wXbVgvDu_zgccrxB_GgiGVi6u6QEfKZm2oc9F+Ww@mail.gmail.com>
 <CAHazPTmJ0eRyTuEaLd_1XJ-29d+sjzOf4bpw9ifUMC6y4ZfP7A@mail.gmail.com>
 <CABDkGQnsab9E__k2V_3i_ORmuTFGoQp55rvPpkVPrmzw=XVcEQ@mail.gmail.com>
 <CA+JHcKQjmV46XNuvF+e77XhcmyeXbb1KC6B+rwfY3oKPC1nugQ@mail.gmail.com> <CABDkGQ=Ro4=SaL28ACnoBcSHJKGyDqm7dYLV14SnVzwEgYhFSw@mail.gmail.com>
Message-ID: <CAHazPTmayg6w0K51nEig-hqRR=Ks_76FJcyzkJc=MffsyT454A@mail.gmail.com>

Thanks.


On Mon, Mar 11, 2013 at 4:03 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> On Mon, Mar 11, 2013 at 10:00 AM, Juan Nunez-Iglesias
> <jni.soma at gmail.com> wrote:
> > Also, I intend to assume isotropic 3D to begin with, and add support for
> > non-isotropic data in a subsequent PR... Does that make sense? Or do you
> > prefer I do it all at once?
>
> Let's do them one step at a time.  Thanks, Juan!
>
> 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.
> For more options, visit https://groups.google.com/groups/opt_out.
>
>
>
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From stefan at sun.ac.za  Mon Mar 11 03:36:30 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 11 Mar 2013 09:36:30 +0200
Subject: 3D SLIC code
In-Reply-To: <CA+JHcKTqTK6pt8Eqb=Ht+LDLDi=f0qS7a7MDGQjAYkC+QgS2Jg@mail.gmail.com>
References: <CA+JHcKTqTK6pt8Eqb=Ht+LDLDi=f0qS7a7MDGQjAYkC+QgS2Jg@mail.gmail.com>
Message-ID: <CABDkGQmZ_=wXbVgvDu_zgccrxB_GgiGVi6u6QEfKZm2oc9F+Ww@mail.gmail.com>

On Mon, Mar 11, 2013 at 8:43 AM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> I want to modify SLIC to handle 3D images. However, it now become rather
> tricky to automatically detect whether the final dimension is channels or
> just z, in the case of image.ndim == 3 (ie, is this a 3D grayscale image, or
> a 2D RGB image?). I was trying to do something automatically (image.ndim ==
> 3 and image.shape[-1] == 3) but I think maybe the easiest thing is to add a
> "has_channels" argument, defaulting to...? I want to say False, but that's
> just my own biases. =)

In `random_walker`, we've opted for "multichannel=False":

    data : array_like
        Image to be segmented in phases. Gray-level `data` can be two- or
        three-dimensional; multichannel data can be three- or four-
        dimensional (multichannel=True) with the highest dimension denoting
        channels. Data spacing is assumed isotropic unless depth keyword
        argument is used.

    multichannel : bool, default False
        If True, input data is parsed as multichannel data (see 'data' above
        for proper input format in this case)

St?fan


From stefan at sun.ac.za  Mon Mar 11 03:52:28 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 11 Mar 2013 09:52:28 +0200
Subject: 3D SLIC code
In-Reply-To: <CAHazPTmJ0eRyTuEaLd_1XJ-29d+sjzOf4bpw9ifUMC6y4ZfP7A@mail.gmail.com>
References: <CA+JHcKTqTK6pt8Eqb=Ht+LDLDi=f0qS7a7MDGQjAYkC+QgS2Jg@mail.gmail.com>
 <CABDkGQmZ_=wXbVgvDu_zgccrxB_GgiGVi6u6QEfKZm2oc9F+Ww@mail.gmail.com> <CAHazPTmJ0eRyTuEaLd_1XJ-29d+sjzOf4bpw9ifUMC6y4ZfP7A@mail.gmail.com>
Message-ID: <CABDkGQnsab9E__k2V_3i_ORmuTFGoQp55rvPpkVPrmzw=XVcEQ@mail.gmail.com>

On Mon, Mar 11, 2013 at 9:39 AM, Ronnie Ghose <ronnie.ghose at gmail.com> wrote:
> ... ehhh... I would prefer 2d rgb to be the default in general as I think
> that is the generl use case? . This calls for a discussion imho.

Yes, I think for this algorithm you're right.

St?fan


From stefan at sun.ac.za  Mon Mar 11 04:03:13 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 11 Mar 2013 10:03:13 +0200
Subject: 3D SLIC code
In-Reply-To: <CA+JHcKQjmV46XNuvF+e77XhcmyeXbb1KC6B+rwfY3oKPC1nugQ@mail.gmail.com>
References: <CA+JHcKTqTK6pt8Eqb=Ht+LDLDi=f0qS7a7MDGQjAYkC+QgS2Jg@mail.gmail.com>
 <CABDkGQmZ_=wXbVgvDu_zgccrxB_GgiGVi6u6QEfKZm2oc9F+Ww@mail.gmail.com>
 <CAHazPTmJ0eRyTuEaLd_1XJ-29d+sjzOf4bpw9ifUMC6y4ZfP7A@mail.gmail.com>
 <CABDkGQnsab9E__k2V_3i_ORmuTFGoQp55rvPpkVPrmzw=XVcEQ@mail.gmail.com> <CA+JHcKQjmV46XNuvF+e77XhcmyeXbb1KC6B+rwfY3oKPC1nugQ@mail.gmail.com>
Message-ID: <CABDkGQ=Ro4=SaL28ACnoBcSHJKGyDqm7dYLV14SnVzwEgYhFSw@mail.gmail.com>

On Mon, Mar 11, 2013 at 10:00 AM, Juan Nunez-Iglesias
<jni.soma at gmail.com> wrote:
> Also, I intend to assume isotropic 3D to begin with, and add support for
> non-isotropic data in a subsequent PR... Does that make sense? Or do you
> prefer I do it all at once?

Let's do them one step at a time.  Thanks, Juan!

St?fan


From colincsl at gmail.com  Mon Mar 11 20:32:32 2013
From: colincsl at gmail.com (Colin Lea)
Date: Mon, 11 Mar 2013 17:32:32 -0700 (PDT)
Subject: 3D SLIC code
In-Reply-To: <CAHazPTmayg6w0K51nEig-hqRR=Ks_76FJcyzkJc=MffsyT454A@mail.gmail.com>
References: <CA+JHcKTqTK6pt8Eqb=Ht+LDLDi=f0qS7a7MDGQjAYkC+QgS2Jg@mail.gmail.com>
 <CABDkGQmZ_=wXbVgvDu_zgccrxB_GgiGVi6u6QEfKZm2oc9F+Ww@mail.gmail.com>
 <CAHazPTmJ0eRyTuEaLd_1XJ-29d+sjzOf4bpw9ifUMC6y4ZfP7A@mail.gmail.com>
 <CABDkGQnsab9E__k2V_3i_ORmuTFGoQp55rvPpkVPrmzw=XVcEQ@mail.gmail.com>
 <CA+JHcKQjmV46XNuvF+e77XhcmyeXbb1KC6B+rwfY3oKPC1nugQ@mail.gmail.com> <CABDkGQ=Ro4=SaL28ACnoBcSHJKGyDqm7dYLV14SnVzwEgYhFSw@mail.gmail.com>
 <CAHazPTmayg6w0K51nEig-hqRR=Ks_76FJcyzkJc=MffsyT454A@mail.gmail.com>
Message-ID: <3243e3d1-6c8d-4002-9342-fed84bffcba8@googlegroups.com>

Seems like a silly question, but when you say 3D you mean an RGB image 
right? I work with kinect data everyday so I originally thought you were 
talking about incorporating depth data.



On Monday, March 11, 2013 4:13:52 AM UTC-4, Ronnie Ghose wrote:
>
> Thanks. 
>
>
> On Mon, Mar 11, 2013 at 4:03 AM, St?fan van der Walt <ste... at sun.ac.za<javascript:>
> > wrote:
>
>> On Mon, Mar 11, 2013 at 10:00 AM, Juan Nunez-Iglesias
>> <jni.... at gmail.com <javascript:>> wrote:
>> > Also, I intend to assume isotropic 3D to begin with, and add support for
>> > non-isotropic data in a subsequent PR... Does that make sense? Or do you
>> > prefer I do it all at once?
>>
>> Let's do them one step at a time.  Thanks, Juan!
>>
>> 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:>.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>>
>>
>
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From jni.soma at gmail.com  Mon Mar 11 02:43:26 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Mon, 11 Mar 2013 17:43:26 +1100
Subject: 3D SLIC code
Message-ID: <CA+JHcKTqTK6pt8Eqb=Ht+LDLDi=f0qS7a7MDGQjAYkC+QgS2Jg@mail.gmail.com>

Hi all,

I want to modify SLIC to handle 3D images. However, it now become rather
tricky to automatically detect whether the final dimension is channels or
just z, in the case of image.ndim == 3 (ie, is this a 3D grayscale image,
or a 2D RGB image?). I was trying to do something automatically (image.ndim
== 3 and image.shape[-1] == 3) but I think maybe the easiest thing is to
add a "has_channels" argument, defaulting to...? I want to say False, but
that's just my own biases. =)

What do you think?

Juan.
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From jni.soma at gmail.com  Mon Mar 11 03:07:39 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Mon, 11 Mar 2013 18:07:39 +1100
Subject: 3D SLIC code
In-Reply-To: <CAHazPTngYZXMRArh8dQS+E_VbtrbJO=WBYLOvHU3tRE0dE3ncA@mail.gmail.com>
References: <CA+JHcKTqTK6pt8Eqb=Ht+LDLDi=f0qS7a7MDGQjAYkC+QgS2Jg@mail.gmail.com>
 <CAHazPTngYZXMRArh8dQS+E_VbtrbJO=WBYLOvHU3tRE0dE3ncA@mail.gmail.com>
Message-ID: <CA+JHcKSzm=BCSW_M4V343ZWYeACxujZop9j8u7z5teCgve8iyA@mail.gmail.com>

On Mon, Mar 11, 2013 at 5:52 PM, Ronnie Ghose <ronnie.ghose at gmail.com>wrote:

> assuming you're modifying the 2d code,
>

My intention is to reduce the 2D case to 3D with Z = 1. This would be ~20%
slower for 2D, but
1) SLIC is lightning fast in the first place, so a 20% bump is not a huge
deal, and
2) the benefit is a vastly simplified code base relative to duplicating a
whole lot of code specifically for 3D.

I definitely have no problems with defaulting has_channels to True. Plus a
user could do:

slic_bw = functools.partial(slic, has_channels=False)

and be done with it. ;)
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From jni.soma at gmail.com  Mon Mar 11 04:00:28 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Mon, 11 Mar 2013 19:00:28 +1100
Subject: 3D SLIC code
In-Reply-To: <CABDkGQnsab9E__k2V_3i_ORmuTFGoQp55rvPpkVPrmzw=XVcEQ@mail.gmail.com>
References: <CA+JHcKTqTK6pt8Eqb=Ht+LDLDi=f0qS7a7MDGQjAYkC+QgS2Jg@mail.gmail.com>
 <CABDkGQmZ_=wXbVgvDu_zgccrxB_GgiGVi6u6QEfKZm2oc9F+Ww@mail.gmail.com>
 <CAHazPTmJ0eRyTuEaLd_1XJ-29d+sjzOf4bpw9ifUMC6y4ZfP7A@mail.gmail.com> <CABDkGQnsab9E__k2V_3i_ORmuTFGoQp55rvPpkVPrmzw=XVcEQ@mail.gmail.com>
Message-ID: <CA+JHcKQjmV46XNuvF+e77XhcmyeXbb1KC6B+rwfY3oKPC1nugQ@mail.gmail.com>

Ok so I interpret that we have a consensus of the following:
1) Use a "multichannel" named argument that defaults to True, rather than
try some fancy guesswork based on the input data dimension.
2) Make 2D a special case of 3D to keep codebase simple, at a performance
cost relative to a pure 2D implementation.

I'll go ahead with this implementation unless someone objects...

Also, I intend to assume isotropic 3D to begin with, and add support for
non-isotropic data in a subsequent PR... Does that make sense? Or do you
prefer I do it all at once?

On Mon, Mar 11, 2013 at 6:52 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> On Mon, Mar 11, 2013 at 9:39 AM, Ronnie Ghose <ronnie.ghose at gmail.com>
> wrote:
> > ... ehhh... I would prefer 2d rgb to be the default in general as I think
> > that is the generl use case? . This calls for a discussion imho.
>
> Yes, I think for this algorithm you're right.
>
> 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.
> For more options, visit https://groups.google.com/groups/opt_out.
>
>
>
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From ronnie.ghose at gmail.com  Mon Mar 11 21:53:11 2013
From: ronnie.ghose at gmail.com (Ronnie Ghose)
Date: Mon, 11 Mar 2013 21:53:11 -0400
Subject: 3D SLIC code
In-Reply-To: <3243e3d1-6c8d-4002-9342-fed84bffcba8@googlegroups.com>
References: <CA+JHcKTqTK6pt8Eqb=Ht+LDLDi=f0qS7a7MDGQjAYkC+QgS2Jg@mail.gmail.com>
 <CABDkGQmZ_=wXbVgvDu_zgccrxB_GgiGVi6u6QEfKZm2oc9F+Ww@mail.gmail.com>
 <CAHazPTmJ0eRyTuEaLd_1XJ-29d+sjzOf4bpw9ifUMC6y4ZfP7A@mail.gmail.com>
 <CABDkGQnsab9E__k2V_3i_ORmuTFGoQp55rvPpkVPrmzw=XVcEQ@mail.gmail.com>
 <CA+JHcKQjmV46XNuvF+e77XhcmyeXbb1KC6B+rwfY3oKPC1nugQ@mail.gmail.com>
 <CABDkGQ=Ro4=SaL28ACnoBcSHJKGyDqm7dYLV14SnVzwEgYhFSw@mail.gmail.com>
 <CAHazPTmayg6w0K51nEig-hqRR=Ks_76FJcyzkJc=MffsyT454A@mail.gmail.com> <3243e3d1-6c8d-4002-9342-fed84bffcba8@googlegroups.com>
Message-ID: <CAHazPTksvuRuk7jjGrCyg=A8k_=bRh-csigQV1K6mfXmAr0mYg@mail.gmail.com>

it would make more sense if you scroll up, but yes a RGB / Grayscale image.
the conflict was that # dims 3d grayscale = # dims 2d RGB.


On Mon, Mar 11, 2013 at 8:32 PM, Colin Lea <colincsl at gmail.com> wrote:

> Seems like a silly question, but when you say 3D you mean an RGB image
> right? I work with kinect data everyday so I originally thought you were
> talking about incorporating depth data.
>
>
>
> On Monday, March 11, 2013 4:13:52 AM UTC-4, Ronnie Ghose wrote:
>
>> Thanks.
>>
>>
>> On Mon, Mar 11, 2013 at 4:03 AM, St?fan van der Walt <ste... at sun.ac.za>wrote:
>>
>>> On Mon, Mar 11, 2013 at 10:00 AM, Juan Nunez-Iglesias
>>> <jni.... at gmail.com> wrote:
>>> > Also, I intend to assume isotropic 3D to begin with, and add support
>>> for
>>> > non-isotropic data in a subsequent PR... Does that make sense? Or do
>>> you
>>> > prefer I do it all at once?
>>>
>>> Let's do them one step at a time.  Thanks, Juan!
>>>
>>> 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...@**googlegroups.com.
>>>
>>> For more options, visit https://groups.google.com/**groups/opt_out<https://groups.google.com/groups/opt_out>
>>> .
>>>
>>>
>>>
>>  --
> 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.
> For more options, visit https://groups.google.com/groups/opt_out.
>
>
>
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From jni.soma at gmail.com  Mon Mar 11 22:35:23 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Tue, 12 Mar 2013 13:35:23 +1100
Subject: 3D SLIC code
In-Reply-To: <CAHazPTksvuRuk7jjGrCyg=A8k_=bRh-csigQV1K6mfXmAr0mYg@mail.gmail.com>
References: <CA+JHcKTqTK6pt8Eqb=Ht+LDLDi=f0qS7a7MDGQjAYkC+QgS2Jg@mail.gmail.com>
 <CABDkGQmZ_=wXbVgvDu_zgccrxB_GgiGVi6u6QEfKZm2oc9F+Ww@mail.gmail.com>
 <CAHazPTmJ0eRyTuEaLd_1XJ-29d+sjzOf4bpw9ifUMC6y4ZfP7A@mail.gmail.com>
 <CABDkGQnsab9E__k2V_3i_ORmuTFGoQp55rvPpkVPrmzw=XVcEQ@mail.gmail.com>
 <CA+JHcKQjmV46XNuvF+e77XhcmyeXbb1KC6B+rwfY3oKPC1nugQ@mail.gmail.com>
 <CABDkGQ=Ro4=SaL28ACnoBcSHJKGyDqm7dYLV14SnVzwEgYhFSw@mail.gmail.com>
 <CAHazPTmayg6w0K51nEig-hqRR=Ks_76FJcyzkJc=MffsyT454A@mail.gmail.com>
 <3243e3d1-6c8d-4002-9342-fed84bffcba8@googlegroups.com> <CAHazPTksvuRuk7jjGrCyg=A8k_=bRh-csigQV1K6mfXmAr0mYg@mail.gmail.com>
Message-ID: <CA+JHcKQEPZRaNZ40uQeb_DwuzXj=r765QfTzBtrbbLcVCddM2w@mail.gmail.com>

> On Mon, Mar 11, 2013 at 8:32 PM, Colin Lea <colincsl at gmail.com> wrote:
>
>> Seems like a silly question, but when you say 3D you mean an RGB image
>> right? I work with kinect data everyday so I originally thought you were
>> talking about incorporating depth data.
>
>
Currently SLIC supports 2D grayscale and 2D RGB. I want to add support for
3D grayscale and 3D RGB, indeed incorporating depth information. (Though
for 3D microscopy, which is pretty different from Kinect!)
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From jschoenberger at demuc.de  Thu Mar 14 10:54:51 2013
From: jschoenberger at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Thu, 14 Mar 2013 15:54:51 +0100
Subject: 3D SLIC code
In-Reply-To: <CA+JHcKQXJVz2MwgqJ-maXQZYSs2W+_6iQoc0EW0rsioZqT8tSw@mail.gmail.com>
References: <CA+JHcKTqTK6pt8Eqb=Ht+LDLDi=f0qS7a7MDGQjAYkC+QgS2Jg@mail.gmail.com> <CABDkGQmZ_=wXbVgvDu_zgccrxB_GgiGVi6u6QEfKZm2oc9F+Ww@mail.gmail.com> <CAHazPTmJ0eRyTuEaLd_1XJ-29d+sjzOf4bpw9ifUMC6y4ZfP7A@mail.gmail.com> <CABDkGQnsab9E__k2V_3i_ORmuTFGoQp55rvPpkVPrmzw=XVcEQ@mail.gmail.com> <CA+JHcKQjmV46XNuvF+e77XhcmyeXbb1KC6B+rwfY3oKPC1nugQ@mail.gmail.com> <CABDkGQ=Ro4=SaL28ACnoBcSHJKGyDqm7dYLV14SnVzwEgYhFSw@mail.gmail.com> <CAHazPTmayg6w0K51nEig-hqRR=Ks_76FJcyzkJc=MffsyT454A@mail.gmail.com> <3243e3d1-6c8d-4002-9342-fed84bffcba8@googlegroups.com> <CAHazPTksvuRuk7jjGrCyg=A8k_=bRh-csigQV1K6mfXmAr0mYg@mail.gmail.com> <CA+JHcKQEPZRaNZ40uQeb_DwuzXj=r765QfTzBtrbbLcVCddM2w@mail.gmail.com> <CA+JHcKQXJVz2MwgqJ-maXQZYSs2W+_6iQoc0EW0rsioZqT8tSw@mail.gmail.com>
Message-ID: <68F35D44-C601-4480-B6B9-E707FA2D6639@demuc.de>

There is a short introduction to debugging Cython:

http://docs.cython.org/src/userguide/debugging.html

Johannes Sch?nberger

Am 14.03.2013 um 15:41 schrieb Juan Nunez-Iglesias <jni.soma at gmail.com>:

> Anyone got tips for debugging Cython code? My usual approach of calling a function using pdb.run() inside iPython isn't working very well. =)
> 
> -- 
> 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.
> For more options, visit https://groups.google.com/groups/opt_out.
>  
>  



From google at terre-adelie.org  Thu Mar 14 10:57:01 2013
From: google at terre-adelie.org (Jerome Kieffer)
Date: Thu, 14 Mar 2013 15:57:01 +0100
Subject: [JOB] 18 months contract on Python/Qt for microscopy
Message-ID: <20130314155701.055e94eb.google@terre-adelie.org>

Dear Pythonistas 

I would like to advertise about a job proposition at the European synchrotron (Grenoble, France).
It is a position for building the software part of the most powerful "X-ray nanoscope" (NiNa ID16/ESRF) for 18 months.

Skills: Python/Qt/C++ Developer
More info on:
http://esrf.profilsearch.com/recrute/intranet/fo_annonce_voir.php?id=198

Cheers
-- 
Jerome Kieffer <google at terre-adelie.org>


From stefan at sun.ac.za  Thu Mar 14 11:11:32 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 14 Mar 2013 17:11:32 +0200
Subject: 3D SLIC code
In-Reply-To: <68F35D44-C601-4480-B6B9-E707FA2D6639@demuc.de>
References: <CA+JHcKTqTK6pt8Eqb=Ht+LDLDi=f0qS7a7MDGQjAYkC+QgS2Jg@mail.gmail.com>
 <CABDkGQmZ_=wXbVgvDu_zgccrxB_GgiGVi6u6QEfKZm2oc9F+Ww@mail.gmail.com>
 <CAHazPTmJ0eRyTuEaLd_1XJ-29d+sjzOf4bpw9ifUMC6y4ZfP7A@mail.gmail.com>
 <CABDkGQnsab9E__k2V_3i_ORmuTFGoQp55rvPpkVPrmzw=XVcEQ@mail.gmail.com>
 <CA+JHcKQjmV46XNuvF+e77XhcmyeXbb1KC6B+rwfY3oKPC1nugQ@mail.gmail.com>
 <CABDkGQ=Ro4=SaL28ACnoBcSHJKGyDqm7dYLV14SnVzwEgYhFSw@mail.gmail.com>
 <CAHazPTmayg6w0K51nEig-hqRR=Ks_76FJcyzkJc=MffsyT454A@mail.gmail.com>
 <3243e3d1-6c8d-4002-9342-fed84bffcba8@googlegroups.com> <CAHazPTksvuRuk7jjGrCyg=A8k_=bRh-csigQV1K6mfXmAr0mYg@mail.gmail.com>
 <CA+JHcKQEPZRaNZ40uQeb_DwuzXj=r765QfTzBtrbbLcVCddM2w@mail.gmail.com>
 <CA+JHcKQXJVz2MwgqJ-maXQZYSs2W+_6iQoc0EW0rsioZqT8tSw@mail.gmail.com> <68F35D44-C601-4480-B6B9-E707FA2D6639@demuc.de>
Message-ID: <CABDkGQkcwMsjwZcGamStniPcUU7y0S9BM9kBi_qku4aN4UZtrg@mail.gmail.com>

On Thu, Mar 14, 2013 at 4:54 PM, Johannes Sch?nberger
<jschoenberger at demuc.de> wrote:
> There is a short introduction to debugging Cython:
>
> http://docs.cython.org/src/userguide/debugging.html

Thanks for this--I wasn't even aware of cygdb!

St?fan


From jni.soma at gmail.com  Thu Mar 14 10:41:15 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Fri, 15 Mar 2013 01:41:15 +1100
Subject: 3D SLIC code
In-Reply-To: <CA+JHcKQEPZRaNZ40uQeb_DwuzXj=r765QfTzBtrbbLcVCddM2w@mail.gmail.com>
References: <CA+JHcKTqTK6pt8Eqb=Ht+LDLDi=f0qS7a7MDGQjAYkC+QgS2Jg@mail.gmail.com>
 <CABDkGQmZ_=wXbVgvDu_zgccrxB_GgiGVi6u6QEfKZm2oc9F+Ww@mail.gmail.com>
 <CAHazPTmJ0eRyTuEaLd_1XJ-29d+sjzOf4bpw9ifUMC6y4ZfP7A@mail.gmail.com>
 <CABDkGQnsab9E__k2V_3i_ORmuTFGoQp55rvPpkVPrmzw=XVcEQ@mail.gmail.com>
 <CA+JHcKQjmV46XNuvF+e77XhcmyeXbb1KC6B+rwfY3oKPC1nugQ@mail.gmail.com>
 <CABDkGQ=Ro4=SaL28ACnoBcSHJKGyDqm7dYLV14SnVzwEgYhFSw@mail.gmail.com>
 <CAHazPTmayg6w0K51nEig-hqRR=Ks_76FJcyzkJc=MffsyT454A@mail.gmail.com>
 <3243e3d1-6c8d-4002-9342-fed84bffcba8@googlegroups.com> <CAHazPTksvuRuk7jjGrCyg=A8k_=bRh-csigQV1K6mfXmAr0mYg@mail.gmail.com>
 <CA+JHcKQEPZRaNZ40uQeb_DwuzXj=r765QfTzBtrbbLcVCddM2w@mail.gmail.com>
Message-ID: <CA+JHcKQXJVz2MwgqJ-maXQZYSs2W+_6iQoc0EW0rsioZqT8tSw@mail.gmail.com>

Anyone got tips for debugging Cython code? My usual approach of calling a
function using pdb.run() inside iPython isn't working very well. =)
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From jni.soma at gmail.com  Thu Mar 14 11:35:40 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Fri, 15 Mar 2013 02:35:40 +1100
Subject: 3D SLIC code
In-Reply-To: <CABDkGQkcwMsjwZcGamStniPcUU7y0S9BM9kBi_qku4aN4UZtrg@mail.gmail.com>
References: <CA+JHcKTqTK6pt8Eqb=Ht+LDLDi=f0qS7a7MDGQjAYkC+QgS2Jg@mail.gmail.com>
 <CABDkGQmZ_=wXbVgvDu_zgccrxB_GgiGVi6u6QEfKZm2oc9F+Ww@mail.gmail.com>
 <CAHazPTmJ0eRyTuEaLd_1XJ-29d+sjzOf4bpw9ifUMC6y4ZfP7A@mail.gmail.com>
 <CABDkGQnsab9E__k2V_3i_ORmuTFGoQp55rvPpkVPrmzw=XVcEQ@mail.gmail.com>
 <CA+JHcKQjmV46XNuvF+e77XhcmyeXbb1KC6B+rwfY3oKPC1nugQ@mail.gmail.com>
 <CABDkGQ=Ro4=SaL28ACnoBcSHJKGyDqm7dYLV14SnVzwEgYhFSw@mail.gmail.com>
 <CAHazPTmayg6w0K51nEig-hqRR=Ks_76FJcyzkJc=MffsyT454A@mail.gmail.com>
 <3243e3d1-6c8d-4002-9342-fed84bffcba8@googlegroups.com> <CAHazPTksvuRuk7jjGrCyg=A8k_=bRh-csigQV1K6mfXmAr0mYg@mail.gmail.com>
 <CA+JHcKQEPZRaNZ40uQeb_DwuzXj=r765QfTzBtrbbLcVCddM2w@mail.gmail.com>
 <CA+JHcKQXJVz2MwgqJ-maXQZYSs2W+_6iQoc0EW0rsioZqT8tSw@mail.gmail.com>
 <68F35D44-C601-4480-B6B9-E707FA2D6639@demuc.de> <CABDkGQkcwMsjwZcGamStniPcUU7y0S9BM9kBi_qku4aN4UZtrg@mail.gmail.com>
Message-ID: <CA+JHcKT8bGJcziQQLU7PXxYZMmtW_qDKLFekLi0YM8UKzTfcXg@mail.gmail.com>

Thanks for not using lmgtfy, Johannes. =) I found that page earlier but my
eyes glazed over a bit. Will try it out.

On Fri, Mar 15, 2013 at 2:11 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> On Thu, Mar 14, 2013 at 4:54 PM, Johannes Sch?nberger
> <jschoenberger at demuc.de> wrote:
> > There is a short introduction to debugging Cython:
> >
> > http://docs.cython.org/src/userguide/debugging.html
>
> Thanks for this--I wasn't even aware of cygdb!
>
> 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.
> For more options, visit https://groups.google.com/groups/opt_out.
>
>
>
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From almar.klein at gmail.com  Wed Mar 27 10:33:23 2013
From: almar.klein at gmail.com (Almar Klein)
Date: Wed, 27 Mar 2013 15:33:23 +0100
Subject: imageio progress
Message-ID: <CAB_T6=kzjsT8BBcCqaXbKt6OPZcxFfXERL3TSP9PcfmoiWThJA@mail.gmail.com>

Dear all,

Several months ago, I decided to take the code for skimage's freeimage
plugin (which was originally written by Zach Pincus) and turn it into a
stand-alone library. I discussed with Zach and a few others how to proceed
with that, and it seemed that time was a limiting factor for many, so I
ended up doing most coding on my own.

The project is called imageio <http://imageio.readthedocs.org/> and it is
now a plugin-based library with a relatively small core. The freeimage
plugin that started it all currently provides most file formats. Its now at
a stage where I think the core is pretty much finished, and focus can shift
towards different plugins for various scientific formats. But I am not
going to do that alone :)

I could use some help with:
  * People just trying it out.
  * People checking the design of the
classes<http://imageio.readthedocs.org/en/latest/classes.html>and
plugin
system <http://imageio.readthedocs.org/en/latest/plugins.html>.
  * If possible, people checking out the code a bit.
  * And of course, people writing plugins!

The way I see it, imageio can become a common backend for reading and
writing images for several libraries (including skimage), or can function
stand-alone.

Further, I plan on moving it to github to easier attract developers.

Any help and comments is much appreciated,
  Almar
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From stefan at sun.ac.za  Wed Mar 27 12:00:51 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 27 Mar 2013 18:00:51 +0200
Subject: How to extract edge from a watersheded image?
In-Reply-To: <f689e91c-94ba-4d4a-b2a2-7759f4242fa8@googlegroups.com>
References: <f689e91c-94ba-4d4a-b2a2-7759f4242fa8@googlegroups.com>
Message-ID: <CABDkGQm7nWyhFrjW4g4KW8DS7AtsYpCXA9W=BW9NZzeLtgcHig@mail.gmail.com>

Hi Zetian

On Wed, Mar 27, 2013 at 5:07 AM, Zetian Yang <zetian.yang at gmail.com> wrote:
> I have been trying the watershed algorithm in the skimage package and it is
> really fantastic. Recently I have a problem where the edge of one segmented
> image is need. Is there a convenient way to extract edges of the watersheded
> result?

I'm glad you find the package useful!  Do you need the edges as
coordinates, or do you need a bitmap of the edges?  We have marching
squares for contour finding, edge detection, etc.

St?fan


From zetian.yang at gmail.com  Wed Mar 27 19:37:54 2013
From: zetian.yang at gmail.com (Zetian Yang)
Date: Thu, 28 Mar 2013 07:37:54 +0800
Subject: How to extract edge from a watersheded image?
In-Reply-To: <CABDkGQm7nWyhFrjW4g4KW8DS7AtsYpCXA9W=BW9NZzeLtgcHig@mail.gmail.com>
References: <f689e91c-94ba-4d4a-b2a2-7759f4242fa8@googlegroups.com>
	<CABDkGQm7nWyhFrjW4g4KW8DS7AtsYpCXA9W=BW9NZzeLtgcHig@mail.gmail.com>
Message-ID: <CACvkfP4gVr04BOj0QE3WjZ6bNQBMwpFGDQm+ZnHJ1ofZsVwUAQ@mail.gmail.com>

Thanks Walt,

I need a binary image in which the edges of every labeled region are set to
1.
I've found the `find_boundaries` function in the skimage.segmentation
module, but its outcome didn't fit my requirement.

Currently, I'm using the following algorithm to solve my question.

```
bound = np.zeros(data.shape)
labels = data.max()
for label in labels:
     label_data = data==label
     bound += label_data - scipy.ndimage.binary_erosion(label_data)
```

It seemed work, but I'm not sure its correctness and is there a more
efficient method?


On Thu, Mar 28, 2013 at 12:00 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> Hi Zetian
>
> On Wed, Mar 27, 2013 at 5:07 AM, Zetian Yang <zetian.yang at gmail.com>
> wrote:
> > I have been trying the watershed algorithm in the skimage package and it
> is
> > really fantastic. Recently I have a problem where the edge of one
> segmented
> > image is need. Is there a convenient way to extract edges of the
> watersheded
> > result?
>
> I'm glad you find the package useful!  Do you need the edges as
> coordinates, or do you need a bitmap of the edges?  We have marching
> squares for contour finding, edge detection, etc.
>
> 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.
> For more options, visit https://groups.google.com/groups/opt_out.
>
>
>
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From stefan at sun.ac.za  Thu Mar 28 05:35:31 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 28 Mar 2013 11:35:31 +0200
Subject: Face detection
Message-ID: <CABDkGQkZ+34ixHUkg_uSxK4UF6L-1qeY3RJqpM7JrXQKd2DZpA@mail.gmail.com>

Hi everyone

I've been interested in getting face detection into skimage for a
while.  This morning, Nathan Faggian reminded me that the highly
popular Viola-Jones detector is patent encumbered (yes, if you're not
careful you can use patented code in packages like OpenCV).  However,
the following link seems to suggest that we can work around that by
training our own classifier with different features:

http://rafaelmizrahi.blogspot.com/2007/02/intel-opencv-face-detection-license.html

If there's any interest in working on this, or if you already have an
algorithm available, please get in touch.

St?fan


From tsyu80 at gmail.com  Thu Mar 28 22:06:04 2013
From: tsyu80 at gmail.com (Tony Yu)
Date: Thu, 28 Mar 2013 21:06:04 -0500
Subject: SciPy 2013 Tutorial
Message-ID: <CAEym_HrOZOrP-NS19qLUsBG5Owwh7Xryz8Jyrw=eOv4gMLXVRw@mail.gmail.com>

I was wondering if anyone has plans to submit a tutorial proposal for SciPy
2013 <http://conference.scipy.org/scipy2013/tutorial_overview.php>. The
proposal is due on Monday (Apr. 1st). It'd be great to have scikit-image
represented there; especially since medical imaging is one of the
mini-symposia topics.

If no one else is able, I'll probably submit something, but I have a
feeling that many of you have more (i.e. any) experience teaching image
processing than I do.

Cheers,
-Tony
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From jni.soma at gmail.com  Thu Mar 28 09:14:45 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Fri, 29 Mar 2013 00:14:45 +1100
Subject: How to extract edge from a watersheded image?
In-Reply-To: <CACvkfP4gVr04BOj0QE3WjZ6bNQBMwpFGDQm+ZnHJ1ofZsVwUAQ@mail.gmail.com>
References: <f689e91c-94ba-4d4a-b2a2-7759f4242fa8@googlegroups.com>
 <CABDkGQm7nWyhFrjW4g4KW8DS7AtsYpCXA9W=BW9NZzeLtgcHig@mail.gmail.com> <CACvkfP4gVr04BOj0QE3WjZ6bNQBMwpFGDQm+ZnHJ1ofZsVwUAQ@mail.gmail.com>
Message-ID: <CA+JHcKS2+tk_pA=f4LYYRXN_Nw24m5LYKMi5yz4JDs3Y8AQ25A@mail.gmail.com>

I think the following should work:

# ws is your watershed label mapfrom scipy import ndimage as nd
bound = nd.grey_erosion(ws) != nd.grey_dilation(ws)


The only bad thing about this is that you'll get slightly thick boundaries.
I'm not sure if that's a problem for you.

On Thu, Mar 28, 2013 at 10:37 AM, Zetian Yang <zetian.yang at gmail.com> wrote:

> Thanks Walt,
>
> I need a binary image in which the edges of every labeled region are set
> to 1.
> I've found the `find_boundaries` function in the skimage.segmentation
> module, but its outcome didn't fit my requirement.
>
> Currently, I'm using the following algorithm to solve my question.
>
> ```
> bound = np.zeros(data.shape)
> labels = data.max()
> for label in labels:
>      label_data = data==label
>      bound += label_data - scipy.ndimage.binary_erosion(label_data)
> ```
>
> It seemed work, but I'm not sure its correctness and is there a more
> efficient method?
>
>
> On Thu, Mar 28, 2013 at 12:00 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:
>
>> Hi Zetian
>>
>> On Wed, Mar 27, 2013 at 5:07 AM, Zetian Yang <zetian.yang at gmail.com>
>> wrote:
>> > I have been trying the watershed algorithm in the skimage package and
>> it is
>> > really fantastic. Recently I have a problem where the edge of one
>> segmented
>> > image is need. Is there a convenient way to extract edges of the
>> watersheded
>> > result?
>>
>> I'm glad you find the package useful!  Do you need the edges as
>> coordinates, or do you need a bitmap of the edges?  We have marching
>> squares for contour finding, edge detection, etc.
>>
>> 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.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>>
>>
>  --
> 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.
> For more options, visit https://groups.google.com/groups/opt_out.
>
>
>
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From emmanuelle.gouillart at nsup.org  Fri Mar 29 03:51:38 2013
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Fri, 29 Mar 2013 08:51:38 +0100
Subject: SciPy 2013 Tutorial
In-Reply-To: <CAEym_HrOZOrP-NS19qLUsBG5Owwh7Xryz8Jyrw=eOv4gMLXVRw@mail.gmail.com>
References: <CAEym_HrOZOrP-NS19qLUsBG5Owwh7Xryz8Jyrw=eOv4gMLXVRw@mail.gmail.com>
Message-ID: <20130329075138.GA29112@phare.normalesup.org>

Hi Tony,

I'm not going to SciPy 2013, but I've agreed to give a 1h30-long tutorial
on image processing with scikit-image at Euroscipy 2013 (August 21-24).
I'd happy to share course materials if you're interested.

I copy below the abstract I've given to the organizers.

Cheers,
Emmanuelle

Image processing with scikit-image and the SciPy stack
======================================================

Numerical image processing involves the manipulation and transformation
of images, often in order to extract information of interest from the
images. NumPy nd-arrays provide an efficient container for image data,
that can therefore be processed using the SciPy toolstack.

In this tutorial, we will first briefly see how simple operations on
images (e.g. cropping, framing) can be performed using NumPy. More
complex image processing operations will be handled principally by the
scikit-image module (occasionally by the ndimage submodule of
SciPy). Compared to other image processing modules for Python,
scikit-image is designed to work transparently with numpy nd-arrays, and
is written in pure Python and some Cython in order to promote readability
and maintainability.

The different subtopics of this tutorial include:

* input and output of images (file formats...)
* image enhancing / denoising
* image segmentation (separating an image in labeled regions)
* extraction of geometrical features (edges, lines, spheres, skeleton...)
* extraction of features for image classification

This tutorial will consist mostly of hands-on examples; no mathematical
justification of the algorithms will be given during the tutorial.
Besides the main image processing tasks, the tutorial will demonstrate
how NumPy advanced features (masks, broadcasting, manipulation of
subsets of indices) and scikit-image utilities functions make image
processing easier. The tutorial will also address the visualization of
image processing results (contours, etc.).


On Thu, Mar 28, 2013 at 09:06:04PM -0500, Tony Yu wrote:
>    I was wondering if anyone has plans to submit a [1]tutorial proposal for
>    SciPy 2013. The proposal is due on Monday (Apr. 1st). It'd be great to
>    have scikit-image represented there; especially since medical imaging is
>    one of the mini-symposia topics.
>    If no one else is able, I'll probably submit something, but I have a
>    feeling that many of you have more (i.e. any) experience teaching image
>    processing than I do.
>    Cheers,
>    -Tony


From stefan at sun.ac.za  Fri Mar 29 04:56:55 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Fri, 29 Mar 2013 10:56:55 +0200
Subject: SciPy 2013 Tutorial
In-Reply-To: <20130329075138.GA29112@phare.normalesup.org>
References: <CAEym_HrOZOrP-NS19qLUsBG5Owwh7Xryz8Jyrw=eOv4gMLXVRw@mail.gmail.com>
	<20130329075138.GA29112@phare.normalesup.org>
Message-ID: <CABDkGQkP4mTG0DxaF-8LyUru80Y+Za4GtbpJQeBPCJMvnM9UWg@mail.gmail.com>

I wish I could have made it to either SciPy this year. This tutorial
abstract looks fantastic.

On Mar 29, 2013 9:51 AM, "Emmanuelle Gouillart" <
emmanuelle.gouillart at nsup.org> wrote:
>
> Image processing with scikit-image and the SciPy stack
>
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From zetian.yang at gmail.com  Fri Mar 29 07:45:25 2013
From: zetian.yang at gmail.com (Zetian Yang)
Date: Fri, 29 Mar 2013 19:45:25 +0800
Subject: How to extract edge from a watersheded image?
In-Reply-To: <CA+JHcKS2+tk_pA=f4LYYRXN_Nw24m5LYKMi5yz4JDs3Y8AQ25A@mail.gmail.com>
References: <f689e91c-94ba-4d4a-b2a2-7759f4242fa8@googlegroups.com>
	<CABDkGQm7nWyhFrjW4g4KW8DS7AtsYpCXA9W=BW9NZzeLtgcHig@mail.gmail.com>
	<CACvkfP4gVr04BOj0QE3WjZ6bNQBMwpFGDQm+ZnHJ1ofZsVwUAQ@mail.gmail.com>
	<CA+JHcKS2+tk_pA=f4LYYRXN_Nw24m5LYKMi5yz4JDs3Y8AQ25A@mail.gmail.com>
Message-ID: <CACvkfP579knp3TMgcmZTS1GWd19iVk-HyhhpKew9LysJgo4h9Q@mail.gmail.com>

Yeah, this works well!

BTW, the unwanted thicker bounds could be removed by a simple binary
dialation.

Thanks!


On Thu, Mar 28, 2013 at 9:14 PM, Juan Nunez-Iglesias <jni.soma at gmail.com>wrote:

> I think the following should work:
>
> # ws is your watershed label mapfrom scipy import ndimage as nd
> bound = nd.grey_erosion(ws) != nd.grey_dilation(ws)
>
>
> The only bad thing about this is that you'll get slightly thick
> boundaries. I'm not sure if that's a problem for you.
>
>
> On Thu, Mar 28, 2013 at 10:37 AM, Zetian Yang <zetian.yang at gmail.com>wrote:
>
>> Thanks Walt,
>>
>> I need a binary image in which the edges of every labeled region are set
>> to 1.
>> I've found the `find_boundaries` function in the skimage.segmentation
>> module, but its outcome didn't fit my requirement.
>>
>> Currently, I'm using the following algorithm to solve my question.
>>
>> ```
>> bound = np.zeros(data.shape)
>> labels = data.max()
>> for label in labels:
>>      label_data = data==label
>>      bound += label_data - scipy.ndimage.binary_erosion(label_data)
>> ```
>>
>> It seemed work, but I'm not sure its correctness and is there a more
>> efficient method?
>>
>>
>> On Thu, Mar 28, 2013 at 12:00 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:
>>
>>> Hi Zetian
>>>
>>> On Wed, Mar 27, 2013 at 5:07 AM, Zetian Yang <zetian.yang at gmail.com>
>>> wrote:
>>> > I have been trying the watershed algorithm in the skimage package and
>>> it is
>>> > really fantastic. Recently I have a problem where the edge of one
>>> segmented
>>> > image is need. Is there a convenient way to extract edges of the
>>> watersheded
>>> > result?
>>>
>>> I'm glad you find the package useful!  Do you need the edges as
>>> coordinates, or do you need a bitmap of the edges?  We have marching
>>> squares for contour finding, edge detection, etc.
>>>
>>> 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.
>>> For more options, visit https://groups.google.com/groups/opt_out.
>>>
>>>
>>>
>>  --
>> 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.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>>
>>
>
>  --
> 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.
> For more options, visit https://groups.google.com/groups/opt_out.
>
>
>
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