From hughesadam87 at gmail.com  Wed Jan  1 23:40:28 2014
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Wed, 1 Jan 2014 20:40:28 -0800 (PST)
Subject: Is there a bug in polygon?
Message-ID: <0f5eeb09-d6b2-4298-9ff0-62c6a56b2e2f@googlegroups.com>

I'm implementing draw.polygon from this example (
http://scikit-image.org/docs/dev/auto_examples/plot_shapes.html)

I connected the dots to the verticies provided in poly and plotted over the 
imshow result:

In [105]: plt.imshow(poly)                                                 
                                                                            
               
In [107]: plt.plot(*zip(*poly), ls='--')                                   
                                                                            
               
In [108]: plt.scatter(*zip(*poly))                                         
                                                                            
               

Which results in the attatched image.  This is unexpected, no?
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From jni.soma at gmail.com  Wed Jan  1 07:23:55 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Wed, 1 Jan 2014 23:23:55 +1100
Subject: Job opening in Melbourne
Message-ID: <CA+JHcKT_SQnnMKtwjXebsOAAE=vYY0SyFf-hqjHm5=XWAa5cMw@mail.gmail.com>

Hi all,

Sorry if this is a bit spammy, but I thought some readers of this list
might be interested!

The Victorian Centre for Functional Genomics (VCFG), part of the Peter
MacCallum Cancer Institute, is looking for a bioinformatician to analyse
high content imaging screens. This is image analysis on a big scale
(millions of images per screen), combined with genetic function and pathway
analysis.

I've been using scikit-image, scikit-learn, and pandas to analyse two of
their screens, so it'd be great to collaborate with another Pythonista on
upcoming ones!

Here's a link to the job posting:
http://petermac.mercury.com.au/ViewPosition.aspx?id=11414

and to the PDF "position description":
http://australianbioinformatics.net/storage/VCFG_Bioinformatics_Position_Description.pdf

You can contact Kaylene Simpson (VCFG Head) at
Kaylene.Simpson at petermac.orgwith any questions. The application
deadline is January 13th (Australia
time! ;).

Happy New Year everyone!

Juan.
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From hughesadam87 at gmail.com  Wed Jan  1 23:46:48 2014
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Wed, 1 Jan 2014 23:46:48 -0500
Subject: Is there a bug in polygon?
In-Reply-To: <0f5eeb09-d6b2-4298-9ff0-62c6a56b2e2f@googlegroups.com>
References: <0f5eeb09-d6b2-4298-9ff0-62c6a56b2e2f@googlegroups.com>
Message-ID: <CAMHV+dAGVWGCf1N-XuH_8U94k1DuxANiTZkoLpeXBG1NOz+J6A@mail.gmail.com>

Hmm, nevermind.  It looks like the x,y coordinates were implicitly reversed
in the call to polygon (which takes y coordinates first).  Sorry

rr, cc = polygon(poly*[:, 0**]*, *poly[:, 1**]*, img.shape)



On Wed, Jan 1, 2014 at 11:40 PM, Adam Hughes <hughesadam87 at gmail.com> wrote:

> I'm implementing draw.polygon from this example (
> http://scikit-image.org/docs/dev/auto_examples/plot_shapes.html)
>
> I connected the dots to the verticies provided in poly and plotted over
> the imshow result:
>
> In [105]: plt.imshow(poly)
>
>
> In [107]: plt.plot(*zip(*poly), ls='--')
>
>
> In [108]: plt.scatter(*zip(*poly))
>
>
>
> Which results in the attatched image.  This is unexpected, no?
>
> --
> 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/HWuYnK3eIUM/unsubscribe.
> To unsubscribe from this group and all of its topics, 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 jsch at demuc.de  Sun Jan  5 20:11:30 2014
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Sun, 5 Jan 2014 20:11:30 -0500
Subject: Image filters
Message-ID: <A8DBD659-57C6-4C7C-8F16-E5B790125BAB@demuc.de>

Hi everyone,

Interesting and those filters could be incorporated into scikit-image in my opinion:

	http://jason2506.github.io/imfilter/

What do others think?


From ronnie.ghose at gmail.com  Sun Jan  5 21:47:34 2014
From: ronnie.ghose at gmail.com (Ronnie Ghose)
Date: Sun, 5 Jan 2014 21:47:34 -0500
Subject: Image filters
In-Reply-To: <CA+JHcKRdws=_J24iOEaDQW3kOVnRdYBOH-M_VtO4B2xx8Eh+Jg@mail.gmail.com>
References: <A8DBD659-57C6-4C7C-8F16-E5B790125BAB@demuc.de> <CA+JHcKRdws=_J24iOEaDQW3kOVnRdYBOH-M_VtO4B2xx8Eh+Jg@mail.gmail.com>
Message-ID: <CAHazPT=teew1u3tyHHJ4JmRR7QXGQAX71w4yxK6Jfd1S+-Tmtw@mail.gmail.com>

+ To Juan's Idea.. they look nice ... but I can't see intellectual
applications? Maybe have a reference to them or the like, I don't know if
we want to spend time maintaining them necessarily


On Sun, Jan 5, 2014 at 9:45 PM, Juan Nunez-Iglesias <jni.soma at gmail.com>wrote:

> I'm ambivalent. They are cool and would be nice for publicity, but let's
> not forget that it's *scikit-*image, and these filters have questionable
> scientific use (at least that I can think of ? I've been shown more than
> once to lack imagination! =). In addition, the object-based implementation
> wouldn't fit very well with skimage's more functional interface.
>
> I wouldn't be opposed to including them but I also would not want to spend
> my time on them.
>
> Juan.
>
>
>
> On Mon, Jan 6, 2014 at 12:11 PM, Johannes Sch?nberger <jsch at demuc.de>wrote:
>
>> Hi everyone,
>>
>> Interesting and those filters could be incorporated into scikit-image in
>> my opinion:
>>
>>         http://jason2506.github.io/imfilter/
>>
>> What do others think?
>>
>> --
>> 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 jantod at gmail.com  Mon Jan  6 06:34:22 2014
From: jantod at gmail.com (Janto Dreijer)
Date: Mon, 6 Jan 2014 03:34:22 -0800 (PST)
Subject: incoherent face orientation in marching cubes
Message-ID: <008f5bbb-a5d7-4243-9f79-770e0503ce96@googlegroups.com>

I am trying to create an STL file from the results of running marching 
cubes.
Attached is the modified version of the marching cubes usage example from 
the documentation.
It seems that skimage does not yield coherent face orientations. See 
attached image (the gaps are faces in the other direction).

Using meshlab's "re-orient all faces coherently" command seems to help a 
bit...

Is it just me or is this a bug in skimage?

Regards
Janto
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From jsch at demuc.de  Mon Jan  6 09:14:42 2014
From: jsch at demuc.de (=?windows-1252?Q?Johannes_Sch=F6nberger?=)
Date: Mon, 6 Jan 2014 09:14:42 -0500
Subject: Image filters
In-Reply-To: <CAHazPT=teew1u3tyHHJ4JmRR7QXGQAX71w4yxK6Jfd1S+-Tmtw@mail.gmail.com>
References: <A8DBD659-57C6-4C7C-8F16-E5B790125BAB@demuc.de> <CA+JHcKRdws=_J24iOEaDQW3kOVnRdYBOH-M_VtO4B2xx8Eh+Jg@mail.gmail.com> <CAHazPT=teew1u3tyHHJ4JmRR7QXGQAX71w4yxK6Jfd1S+-Tmtw@mail.gmail.com>
Message-ID: <F6F22FBD-3F64-4280-981E-E3BDAAC7A6CF@demuc.de>

Yes, I definitely agree on all your points, but we could ask the author of the package if she/he is willing to do it?

Johannes

Am 05.01.2014 um 21:47 schrieb Ronnie Ghose <ronnie.ghose at gmail.com>:

> + To Juan's Idea.. they look nice ... but I can't see intellectual applications? Maybe have a reference to them or the like, I don't know if we want to spend time maintaining them necessarily
> 
> 
> On Sun, Jan 5, 2014 at 9:45 PM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> I'm ambivalent. They are cool and would be nice for publicity, but let's not forget that it's scikit-image, and these filters have questionable scientific use (at least that I can think of ? I've been shown more than once to lack imagination! =). In addition, the object-based implementation wouldn't fit very well with skimage's more functional interface.
> 
> I wouldn't be opposed to including them but I also would not want to spend my time on them.
> 
> Juan.
> 
> 
> 
> On Mon, Jan 6, 2014 at 12:11 PM, Johannes Sch?nberger <jsch at demuc.de> wrote:
> Hi everyone,
> 
> Interesting and those filters could be incorporated into scikit-image in my opinion:
> 
>         http://jason2506.github.io/imfilter/
> 
> What do others think?
> 
> --
> 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.



From jni.soma at gmail.com  Sun Jan  5 21:45:32 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Mon, 6 Jan 2014 13:45:32 +1100
Subject: Image filters
In-Reply-To: <A8DBD659-57C6-4C7C-8F16-E5B790125BAB@demuc.de>
References: <A8DBD659-57C6-4C7C-8F16-E5B790125BAB@demuc.de>
Message-ID: <CA+JHcKRdws=_J24iOEaDQW3kOVnRdYBOH-M_VtO4B2xx8Eh+Jg@mail.gmail.com>

I'm ambivalent. They are cool and would be nice for publicity, but let's
not forget that it's *scikit-*image, and these filters have questionable
scientific use (at least that I can think of ? I've been shown more than
once to lack imagination! =). In addition, the object-based implementation
wouldn't fit very well with skimage's more functional interface.

I wouldn't be opposed to including them but I also would not want to spend
my time on them.

Juan.



On Mon, Jan 6, 2014 at 12:11 PM, Johannes Sch?nberger <jsch at demuc.de> wrote:

> Hi everyone,
>
> Interesting and those filters could be incorporated into scikit-image in
> my opinion:
>
>         http://jason2506.github.io/imfilter/
>
> What do others think?
>
> --
> 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 jsch at demuc.de  Mon Jan  6 13:48:46 2014
From: jsch at demuc.de (=?windows-1252?Q?Johannes_Sch=F6nberger?=)
Date: Mon, 6 Jan 2014 13:48:46 -0500
Subject: Raw & Central Moments
In-Reply-To: <CAB=suEnvQCZ_pQ9amj_MfJ=VbN+ZJ5gJeFkVcqahjid4efqa6A@mail.gmail.com>
References: <CAB=suEnvQCZ_pQ9amj_MfJ=VbN+ZJ5gJeFkVcqahjid4efqa6A@mail.gmail.com>
Message-ID: <337523AF-1446-454E-9BF6-6007F0C1287E@demuc.de>

Hi,

instead of:

> x_bar, y_bar = props.centroid

it must be:

> y_bar, x_bar = props.centroid

Hope that helps?

Johannes

Am 06.01.2014 um 13:11 schrieb Jaidev Deshpande <deshpande.jaidev at gmail.com>:

> Hi all,
> 
> According to the wikipedia page on image moments, central moments and raw moments are related as in this link: http://en.wikipedia.org/wiki/Image_moment#Central_moments
> 
> I?ve been trying to examine these relationships using the skimage.measure module.
> 
> I created an ellipse image as per the measure region properties example (http://scikit-image.org/docs/dev/auto_examples/plot_regionprops.html#example-plot-regionprops-py) and rotated it.
> 
> Then I ran the following script:
> 
> from skimage.measure import regionprops, moments, moments_central
> from skimage.morphology import label
> 
> props = regionprops(image) # where `image` is the rotated ellipse
> x_bar, y_bar = props.centroid
> 
> raw_moments = moments(image)
> central_moments = moments_central(image, x_bar, y_bar)
> 
> Now according to the wikipedia page, central_moments[2,0] should be equal to:
> raw_moments[2,0] - x_bar * raw_moments[1,0]
> 
> But that?s not working out. In fact, the value yielded by the above formula is much larger than what skimage says it should be.
> 
> What am I missing?
> 
> Thanks!
> 
> -- 
> 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.
> For more options, visit https://groups.google.com/groups/opt_out.



From silvertrumpet999 at gmail.com  Mon Jan  6 18:46:29 2014
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Mon, 6 Jan 2014 15:46:29 -0800 (PST)
Subject: incoherent face orientation in marching cubes
In-Reply-To: <008f5bbb-a5d7-4243-9f79-770e0503ce96@googlegroups.com>
References: <008f5bbb-a5d7-4243-9f79-770e0503ce96@googlegroups.com>
Message-ID: <0e23eadd-9bdc-41bf-8e90-f0c0bfed2422@googlegroups.com>

It's not just you. The algorithm is a naive implementation of marching 
cubes. It does not provide surface normals or specific face orientations, 
because these were not described in the original paper. All it gives you is 
faces with associated vertices. These correctly describe each face in 3D 
space, but due to the way the algorithm takes advantage of symmetry roughly 
half of the orientations will differ from the counterclockwise convention.

For some purposes, e.g. finding total surface area, this is sufficient. For 
visualization, some packages can handle this without issue (if you have 
Mayavi and run the example in the docs, the ellipsoids are lit correctly). 
However, it seems STL files really do require normals.

>From a cursory look at your example, it seems you're effectively writing a 
normal of [0, 0, 0] to each face (a 'facet' in STL). This is likely part of 
the problem. A true normal vector would have length 1, and should be 
derived from the data. It's possibly why some of the faces appear to be 
rendering transparent.

Once you do a little linear algebra to get surface normals from face 
vertices, then you'll run into what I described above. I would like to 
support this feature, though, and have a few ideas on how to tweak the 
current implementation to fix the orientation issue.


On Monday, January 6, 2014 5:34:22 AM UTC-6, Janto Dreijer wrote:
>
> I am trying to create an STL file from the results of running marching 
> cubes.
> Attached is the modified version of the marching cubes usage example from 
> the documentation.
> It seems that skimage does not yield coherent face orientations. See 
> attached image (the gaps are faces in the other direction).
>
> Using meshlab's "re-orient all faces coherently" command seems to help a 
> bit...
>
> Is it just me or is this a bug in skimage?
>
> Regards
> Janto
>
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From silvertrumpet999 at gmail.com  Mon Jan  6 19:08:44 2014
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Mon, 6 Jan 2014 16:08:44 -0800 (PST)
Subject: incoherent face orientation in marching cubes
In-Reply-To: <0e23eadd-9bdc-41bf-8e90-f0c0bfed2422@googlegroups.com>
References: <008f5bbb-a5d7-4243-9f79-770e0503ce96@googlegroups.com>
 <0e23eadd-9bdc-41bf-8e90-f0c0bfed2422@googlegroups.com>
Message-ID: <f7ae6672-f37e-4e0d-8ce5-32dfcc5a5a22@googlegroups.com>

Also - assuming that screenshot is from Meshlab - try Ctrl+D and/or Ctrl+F 
to toggle double-sided lighting or different colors for front/back, to 
ensure all the faces are in fact making the transition.

Regards,
Josh

On Monday, January 6, 2014 5:46:29 PM UTC-6, Josh Warner wrote:
>
> It's not just you. The algorithm is a naive implementation of marching 
> cubes. It does not provide surface normals or specific face orientations, 
> because these were not described in the original paper. All it gives you is 
> faces with associated vertices. These correctly describe each face in 3D 
> space, but due to the way the algorithm takes advantage of symmetry roughly 
> half of the orientations will differ from the counterclockwise convention.
>
> For some purposes, e.g. finding total surface area, this is sufficient. 
> For visualization, some packages can handle this without issue (if you have 
> Mayavi and run the example in the docs, the ellipsoids are lit correctly). 
> However, it seems STL files really do require normals.
>
> From a cursory look at your example, it seems you're effectively writing a 
> normal of [0, 0, 0] to each face (a 'facet' in STL). This is likely part of 
> the problem. A true normal vector would have length 1, and should be 
> derived from the data. It's possibly why some of the faces appear to be 
> rendering transparent.
>
> Once you do a little linear algebra to get surface normals from face 
> vertices, then you'll run into what I described above. I would like to 
> support this feature, though, and have a few ideas on how to tweak the 
> current implementation to fix the orientation issue.
>
>
> On Monday, January 6, 2014 5:34:22 AM UTC-6, Janto Dreijer wrote:
>>
>> I am trying to create an STL file from the results of running marching 
>> cubes.
>> Attached is the modified version of the marching cubes usage example from 
>> the documentation.
>> It seems that skimage does not yield coherent face orientations. See 
>> attached image (the gaps are faces in the other direction).
>>
>> Using meshlab's "re-orient all faces coherently" command seems to help a 
>> bit...
>>
>> Is it just me or is this a bug in skimage?
>>
>> Regards
>> Janto
>>
>
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From ronnie.ghose at gmail.com  Mon Jan  6 18:48:57 2014
From: ronnie.ghose at gmail.com (Ronnie Ghose)
Date: Mon, 6 Jan 2014 18:48:57 -0500
Subject: Image filters
In-Reply-To: <CA+JHcKT5_jWAojhkpb+XsEkN5vYTDy+2OX7rTOvMwOCk51K=+A@mail.gmail.com>
References: <A8DBD659-57C6-4C7C-8F16-E5B790125BAB@demuc.de>
 <CA+JHcKRdws=_J24iOEaDQW3kOVnRdYBOH-M_VtO4B2xx8Eh+Jg@mail.gmail.com>
 <CAHazPT=teew1u3tyHHJ4JmRR7QXGQAX71w4yxK6Jfd1S+-Tmtw@mail.gmail.com>
 <F6F22FBD-3F64-4280-981E-E3BDAAC7A6CF@demuc.de> <CA+JHcKT5_jWAojhkpb+XsEkN5vYTDy+2OX7rTOvMwOCk51K=+A@mail.gmail.com>
Message-ID: <CAHazPTkmM21Vco3ifjJ5GG8GwH=FRxK9ZcrYHujLcGbkuLWy=g@mail.gmail.com>

the code is actually very simple - it shouldn't be too much work. quite a
lot of random boilerplate though


On Mon, Jan 6, 2014 at 6:47 PM, Juan Nunez-Iglesias <jni.soma at gmail.com>wrote:

> You should know as well as anybody that reviewing the PR will be a lot of
> work! =) Again, if someone else volunteers, I'm happy for it to go ahead.
> But certainly if we invite the PR, it should be reviewed quickly. We don't
> want to invite someone and then have the PR languish in review.
>
>
> On Tue, Jan 7, 2014 at 1:14 AM, Johannes Sch?nberger <jsch at demuc.de>wrote:
>
>> Yes, I definitely agree on all your points, but we could ask the author
>> of the package if she/he is willing to do it?
>>
>> Johannes
>>
>> Am 05.01.2014 um 21:47 schrieb Ronnie Ghose <ronnie.ghose at gmail.com>:
>>
>> > + To Juan's Idea.. they look nice ... but I can't see intellectual
>> applications? Maybe have a reference to them or the like, I don't know if
>> we want to spend time maintaining them necessarily
>> >
>> >
>> > On Sun, Jan 5, 2014 at 9:45 PM, Juan Nunez-Iglesias <jni.soma at gmail.com>
>> wrote:
>> > I'm ambivalent. They are cool and would be nice for publicity, but
>> let's not forget that it's scikit-image, and these filters have
>> questionable scientific use (at least that I can think of ? I've been shown
>> more than once to lack imagination! =). In addition, the object-based
>> implementation wouldn't fit very well with skimage's more functional
>> interface.
>> >
>> > I wouldn't be opposed to including them but I also would not want to
>> spend my time on them.
>> >
>> > Juan.
>> >
>> >
>> >
>> > On Mon, Jan 6, 2014 at 12:11 PM, Johannes Sch?nberger <jsch at demuc.de>
>> wrote:
>> > Hi everyone,
>> >
>> > Interesting and those filters could be incorporated into scikit-image
>> in my opinion:
>> >
>> >         http://jason2506.github.io/imfilter/
>> >
>> > What do others think?
>> >
>> > --
>> > 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
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>> > For more options, visit https://groups.google.com/groups/opt_out.
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From jsch at demuc.de  Mon Jan  6 19:13:48 2014
From: jsch at demuc.de (=?windows-1252?Q?Johannes_Sch=F6nberger?=)
Date: Mon, 6 Jan 2014 19:13:48 -0500
Subject: Image filters
In-Reply-To: <CAHazPTkmM21Vco3ifjJ5GG8GwH=FRxK9ZcrYHujLcGbkuLWy=g@mail.gmail.com>
References: <A8DBD659-57C6-4C7C-8F16-E5B790125BAB@demuc.de> <CA+JHcKRdws=_J24iOEaDQW3kOVnRdYBOH-M_VtO4B2xx8Eh+Jg@mail.gmail.com> <CAHazPT=teew1u3tyHHJ4JmRR7QXGQAX71w4yxK6Jfd1S+-Tmtw@mail.gmail.com> <F6F22FBD-3F64-4280-981E-E3BDAAC7A6CF@demuc.de> <CA+JHcKT5_jWAojhkpb+XsEkN5vYTDy+2OX7rTOvMwOCk51K=+A@mail.gmail.com> <CAHazPTkmM21Vco3ifjJ5GG8GwH=FRxK9ZcrYHujLcGbkuLWy=g@mail.gmail.com>
Message-ID: <84A6EF14-7B95-44EC-B342-4F4ED6324E7C@demuc.de>

Yes, the code in the package is a bit over-complicated :-)

It's probably easier to re-implement the rather simple functionality... maybe I'll have some spare time on a flight :-)

The question is where this code should go. I don't think it's a good idea to place those "artistic" filters directly into skimage.filter, maybe better skimage.filter.effects...

Am 06.01.2014 um 18:48 schrieb Ronnie Ghose <ronnie.ghose at gmail.com>:

> the code is actually very simple - it shouldn't be too much work. quite a lot of random boilerplate though 
> 
> 
> On Mon, Jan 6, 2014 at 6:47 PM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> You should know as well as anybody that reviewing the PR will be a lot of work! =) Again, if someone else volunteers, I'm happy for it to go ahead. But certainly if we invite the PR, it should be reviewed quickly. We don't want to invite someone and then have the PR languish in review.
> 
> 
> On Tue, Jan 7, 2014 at 1:14 AM, Johannes Sch?nberger <jsch at demuc.de> wrote:
> Yes, I definitely agree on all your points, but we could ask the author of the package if she/he is willing to do it?
> 
> Johannes
> 
> Am 05.01.2014 um 21:47 schrieb Ronnie Ghose <ronnie.ghose at gmail.com>:
> 
> > + To Juan's Idea.. they look nice ... but I can't see intellectual applications? Maybe have a reference to them or the like, I don't know if we want to spend time maintaining them necessarily
> >
> >
> > On Sun, Jan 5, 2014 at 9:45 PM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> > I'm ambivalent. They are cool and would be nice for publicity, but let's not forget that it's scikit-image, and these filters have questionable scientific use (at least that I can think of ? I've been shown more than once to lack imagination! =). In addition, the object-based implementation wouldn't fit very well with skimage's more functional interface.
> >
> > I wouldn't be opposed to including them but I also would not want to spend my time on them.
> >
> > Juan.
> >
> >
> >
> > On Mon, Jan 6, 2014 at 12:11 PM, Johannes Sch?nberger <jsch at demuc.de> wrote:
> > Hi everyone,
> >
> > Interesting and those filters could be incorporated into scikit-image in my opinion:
> >
> >         http://jason2506.github.io/imfilter/
> >
> > What do others think?
> >
> > --
> > 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.
> 
> --
> 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.
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> 
> 
> -- 
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> 
> -- 
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From deshpande.jaidev at gmail.com  Mon Jan  6 13:11:31 2014
From: deshpande.jaidev at gmail.com (Jaidev Deshpande)
Date: Mon, 6 Jan 2014 23:41:31 +0530
Subject: Raw & Central Moments
Message-ID: <CAB=suEnvQCZ_pQ9amj_MfJ=VbN+ZJ5gJeFkVcqahjid4efqa6A@mail.gmail.com>

Hi all,

According to the wikipedia page on image moments, central moments and raw
moments are related as in this link:
<http://en.wikipedia.org/wiki/Image_moment#Central_moments>
http://en.wikipedia.org/wiki/Image_moment#Central_moments

I?ve been trying to examine these relationships using the skimage.measure
module.

I created an ellipse image as per the measure region properties
example (<http://scikit-image.org/docs/dev/auto_examples/plot_regionprops.html#example-plot-regionprops-py>
http://scikit-image.org/docs/dev/auto_examples/plot_regionprops.html#example-plot-regionprops-py)
and rotated it.

Then I ran the following script:

from skimage.measure import regionprops, moments, moments_central
from skimage.morphology import label

props = regionprops(image) # where `image` is the rotated ellipse
x_bar, y_bar = props.centroid

raw_moments = moments(image)
central_moments = moments_central(image, x_bar, y_bar)

Now according to the wikipedia page, central_moments[2,0] should be equal
to:
raw_moments[2,0] - x_bar * raw_moments[1,0]

But that?s not working out. In fact, the value yielded by the above formula
is much larger than what skimage says it should be.

What am I missing?

Thanks!
-- 
JD
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From jni.soma at gmail.com  Mon Jan  6 18:47:30 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Tue, 7 Jan 2014 10:47:30 +1100
Subject: Image filters
In-Reply-To: <F6F22FBD-3F64-4280-981E-E3BDAAC7A6CF@demuc.de>
References: <A8DBD659-57C6-4C7C-8F16-E5B790125BAB@demuc.de>
 <CA+JHcKRdws=_J24iOEaDQW3kOVnRdYBOH-M_VtO4B2xx8Eh+Jg@mail.gmail.com>
 <CAHazPT=teew1u3tyHHJ4JmRR7QXGQAX71w4yxK6Jfd1S+-Tmtw@mail.gmail.com> <F6F22FBD-3F64-4280-981E-E3BDAAC7A6CF@demuc.de>
Message-ID: <CA+JHcKT5_jWAojhkpb+XsEkN5vYTDy+2OX7rTOvMwOCk51K=+A@mail.gmail.com>

You should know as well as anybody that reviewing the PR will be a lot of
work! =) Again, if someone else volunteers, I'm happy for it to go ahead.
But certainly if we invite the PR, it should be reviewed quickly. We don't
want to invite someone and then have the PR languish in review.


On Tue, Jan 7, 2014 at 1:14 AM, Johannes Sch?nberger <jsch at demuc.de> wrote:

> Yes, I definitely agree on all your points, but we could ask the author of
> the package if she/he is willing to do it?
>
> Johannes
>
> Am 05.01.2014 um 21:47 schrieb Ronnie Ghose <ronnie.ghose at gmail.com>:
>
> > + To Juan's Idea.. they look nice ... but I can't see intellectual
> applications? Maybe have a reference to them or the like, I don't know if
> we want to spend time maintaining them necessarily
> >
> >
> > On Sun, Jan 5, 2014 at 9:45 PM, Juan Nunez-Iglesias <jni.soma at gmail.com>
> wrote:
> > I'm ambivalent. They are cool and would be nice for publicity, but let's
> not forget that it's scikit-image, and these filters have questionable
> scientific use (at least that I can think of ? I've been shown more than
> once to lack imagination! =). In addition, the object-based implementation
> wouldn't fit very well with skimage's more functional interface.
> >
> > I wouldn't be opposed to including them but I also would not want to
> spend my time on them.
> >
> > Juan.
> >
> >
> >
> > On Mon, Jan 6, 2014 at 12:11 PM, Johannes Sch?nberger <jsch at demuc.de>
> wrote:
> > Hi everyone,
> >
> > Interesting and those filters could be incorporated into scikit-image in
> my opinion:
> >
> >         http://jason2506.github.io/imfilter/
> >
> > What do others think?
> >
> > --
> > 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.
>
> --
> You received this message because you are subscribed to the Google Groups
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From jni.soma at gmail.com  Mon Jan  6 19:10:16 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Tue, 7 Jan 2014 11:10:16 +1100
Subject: Image filters
In-Reply-To: <CAHazPTkmM21Vco3ifjJ5GG8GwH=FRxK9ZcrYHujLcGbkuLWy=g@mail.gmail.com>
References: <A8DBD659-57C6-4C7C-8F16-E5B790125BAB@demuc.de>
 <CA+JHcKRdws=_J24iOEaDQW3kOVnRdYBOH-M_VtO4B2xx8Eh+Jg@mail.gmail.com>
 <CAHazPT=teew1u3tyHHJ4JmRR7QXGQAX71w4yxK6Jfd1S+-Tmtw@mail.gmail.com>
 <F6F22FBD-3F64-4280-981E-E3BDAAC7A6CF@demuc.de> <CA+JHcKT5_jWAojhkpb+XsEkN5vYTDy+2OX7rTOvMwOCk51K=+A@mail.gmail.com>
 <CAHazPTkmM21Vco3ifjJ5GG8GwH=FRxK9ZcrYHujLcGbkuLWy=g@mail.gmail.com>
Message-ID: <CA+JHcKTY=CFgs4PKsCTuaqn=kCKpQU+Sw0BD4WXOF-b09yR6ZA@mail.gmail.com>

My preference would be to change the interface to be more functional (which
fits better in skimage, despite a few OO interfaces currently in the
library), so the code could change quite a bit from its present state. The
simplicity might remain, but even tiny PRs often require a lot of
formatting, new tests, and so forth.


On Tue, Jan 7, 2014 at 10:48 AM, Ronnie Ghose <ronnie.ghose at gmail.com>wrote:

> the code is actually very simple - it shouldn't be too much work. quite a
> lot of random boilerplate though
>
>
> On Mon, Jan 6, 2014 at 6:47 PM, Juan Nunez-Iglesias <jni.soma at gmail.com>wrote:
>
>> You should know as well as anybody that reviewing the PR will be a lot of
>> work! =) Again, if someone else volunteers, I'm happy for it to go ahead.
>> But certainly if we invite the PR, it should be reviewed quickly. We don't
>> want to invite someone and then have the PR languish in review.
>>
>>
>> On Tue, Jan 7, 2014 at 1:14 AM, Johannes Sch?nberger <jsch at demuc.de>wrote:
>>
>>> Yes, I definitely agree on all your points, but we could ask the author
>>> of the package if she/he is willing to do it?
>>>
>>> Johannes
>>>
>>> Am 05.01.2014 um 21:47 schrieb Ronnie Ghose <ronnie.ghose at gmail.com>:
>>>
>>> > + To Juan's Idea.. they look nice ... but I can't see intellectual
>>> applications? Maybe have a reference to them or the like, I don't know if
>>> we want to spend time maintaining them necessarily
>>> >
>>> >
>>> > On Sun, Jan 5, 2014 at 9:45 PM, Juan Nunez-Iglesias <
>>> jni.soma at gmail.com> wrote:
>>> > I'm ambivalent. They are cool and would be nice for publicity, but
>>> let's not forget that it's scikit-image, and these filters have
>>> questionable scientific use (at least that I can think of ? I've been shown
>>> more than once to lack imagination! =). In addition, the object-based
>>> implementation wouldn't fit very well with skimage's more functional
>>> interface.
>>> >
>>> > I wouldn't be opposed to including them but I also would not want to
>>> spend my time on them.
>>> >
>>> > Juan.
>>> >
>>> >
>>> >
>>> > On Mon, Jan 6, 2014 at 12:11 PM, Johannes Sch?nberger <jsch at demuc.de>
>>> wrote:
>>> > Hi everyone,
>>> >
>>> > Interesting and those filters could be incorporated into scikit-image
>>> in my opinion:
>>> >
>>> >         http://jason2506.github.io/imfilter/
>>> >
>>> > What do others think?
>>> >
>>> > --
>>> > 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.
>>>
>>> --
>>> 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.
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>>
>
>  --
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From deshpande.jaidev at gmail.com  Tue Jan  7 08:59:16 2014
From: deshpande.jaidev at gmail.com (Jaidev Deshpande)
Date: Tue, 7 Jan 2014 19:29:16 +0530
Subject: Raw & Central Moments
In-Reply-To: <337523AF-1446-454E-9BF6-6007F0C1287E@demuc.de>
References: <CAB=suEnvQCZ_pQ9amj_MfJ=VbN+ZJ5gJeFkVcqahjid4efqa6A@mail.gmail.com>
 <337523AF-1446-454E-9BF6-6007F0C1287E@demuc.de>
Message-ID: <CAB=suEkk09p0w862oZiOx-xvbhXYiBnEPMn8ONe1LqMe+vzACA@mail.gmail.com>

On Tue, Jan 7, 2014 at 12:18 AM, Johannes Sch?nberger <jsch at demuc.de> wrote:

> Hi,
>
> instead of:
>
> > x_bar, y_bar = props.centroid
>
> it must be:
>
> > y_bar, x_bar = props.centroid
>


Oh, silly mistake. Thanks a lot.


>
> Hope that helps?
>
> Johannes
>
> Am 06.01.2014 um 13:11 schrieb Jaidev Deshpande <
> deshpande.jaidev at gmail.com>:
>
> > Hi all,
> >
> > According to the wikipedia page on image moments, central moments and
> raw moments are related as in this link:
> http://en.wikipedia.org/wiki/Image_moment#Central_moments
> >
> > I?ve been trying to examine these relationships using the
> skimage.measure module.
> >
> > I created an ellipse image as per the measure region properties example (
> http://scikit-image.org/docs/dev/auto_examples/plot_regionprops.html#example-plot-regionprops-py)
> and rotated it.
> >
> > Then I ran the following script:
> >
> > from skimage.measure import regionprops, moments, moments_central
> > from skimage.morphology import label
> >
> > props = regionprops(image) # where `image` is the rotated ellipse
> > x_bar, y_bar = props.centroid
> >
> > raw_moments = moments(image)
> > central_moments = moments_central(image, x_bar, y_bar)
> >
> > Now according to the wikipedia page, central_moments[2,0] should be
> equal to:
> > raw_moments[2,0] - x_bar * raw_moments[1,0]
> >
> > But that?s not working out. In fact, the value yielded by the above
> formula is much larger than what skimage says it should be.
> >
> > What am I missing?
> >
> > Thanks!
> >
> > --
> > 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.
> > 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.
>



-- 
JD
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From stefan at sun.ac.za  Wed Jan  8 19:33:44 2014
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 9 Jan 2014 01:33:44 +0100
Subject: Image filters
In-Reply-To: <84A6EF14-7B95-44EC-B342-4F4ED6324E7C@demuc.de>
References: <A8DBD659-57C6-4C7C-8F16-E5B790125BAB@demuc.de>
 <CA+JHcKRdws=_J24iOEaDQW3kOVnRdYBOH-M_VtO4B2xx8Eh+Jg@mail.gmail.com>
 <CAHazPT=teew1u3tyHHJ4JmRR7QXGQAX71w4yxK6Jfd1S+-Tmtw@mail.gmail.com>
 <F6F22FBD-3F64-4280-981E-E3BDAAC7A6CF@demuc.de> <CA+JHcKT5_jWAojhkpb+XsEkN5vYTDy+2OX7rTOvMwOCk51K=+A@mail.gmail.com>
 <CAHazPTkmM21Vco3ifjJ5GG8GwH=FRxK9ZcrYHujLcGbkuLWy=g@mail.gmail.com> <84A6EF14-7B95-44EC-B342-4F4ED6324E7C@demuc.de>
Message-ID: <CABDkGQkDDTAhcW9JoefsizshQhpH3Qtsg6EWUfxvatkj-cDP1w@mail.gmail.com>

There are a lot of interesting algorithms related to "artsy" kind of
things, e.g. colorization, Picasso-fication, etc.  Perhaps
``skimage.effects``?


From stefan at sun.ac.za  Wed Jan  8 19:35:28 2014
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 9 Jan 2014 01:35:28 +0100
Subject: incoherent face orientation in marching cubes
In-Reply-To: <0e23eadd-9bdc-41bf-8e90-f0c0bfed2422@googlegroups.com>
References: <008f5bbb-a5d7-4243-9f79-770e0503ce96@googlegroups.com> <0e23eadd-9bdc-41bf-8e90-f0c0bfed2422@googlegroups.com>
Message-ID: <CABDkGQkLvB=ysuAj00RHrH7BM=Ddit0tUbn8D-2NtxUgug15-Q@mail.gmail.com>

Josh, you said you had some ideas on how to add this--could you expand?


From silvertrumpet999 at gmail.com  Thu Jan  9 19:51:56 2014
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Thu, 9 Jan 2014 16:51:56 -0800 (PST)
Subject: incoherent face orientation in marching cubes
In-Reply-To: <CABDkGQkLvB=ysuAj00RHrH7BM=Ddit0tUbn8D-2NtxUgug15-Q@mail.gmail.com>
References: <008f5bbb-a5d7-4243-9f79-770e0503ce96@googlegroups.com> <0e23eadd-9bdc-41bf-8e90-f0c0bfed2422@googlegroups.com>
 <CABDkGQkLvB=ysuAj00RHrH7BM=Ddit0tUbn8D-2NtxUgug15-Q@mail.gmail.com>
Message-ID: <6cff6466-4eb1-4c33-ac3b-67652839ced3@googlegroups.com>

Calculate the gradient for each face, normalize it, and orient the face 
counterclockwise around the descent of said gradient vector.

It would require some pretty heavy modification, but might be worth it.

On the other hand, you could potentially hack in a fix (depends on how the 
STL package works) much easier by making the output double sided. A 
double-sided mesh has each face twice, covering both orientations This way 
you'd just append `faces` to itself, reverse indexing to flip the 
orientation of each face, e.g.

``` python
import numpy as np
from skimage.measure import marching_cubes

verts, faces = marching_cubes(vol, value)

faces = np.concatenate((faces, faces[:, -1], axis=0)

# Remainder of STL export code for faces here
```

Which would be *far, far* simpler and less computationally intense than 
dealing with the gradients...

Would you mind trying this quick fix, Janto?


On Wednesday, January 8, 2014 6:35:28 PM UTC-6, Stefan van der Walt wrote:
>
> Josh, you said you had some ideas on how to add this--could you expand? 
>
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From jni.soma at gmail.com  Thu Jan  9 21:18:45 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Fri, 10 Jan 2014 13:18:45 +1100
Subject: incoherent face orientation in marching cubes
In-Reply-To: <6cff6466-4eb1-4c33-ac3b-67652839ced3@googlegroups.com>
References: <008f5bbb-a5d7-4243-9f79-770e0503ce96@googlegroups.com>
 <0e23eadd-9bdc-41bf-8e90-f0c0bfed2422@googlegroups.com> <CABDkGQkLvB=ysuAj00RHrH7BM=Ddit0tUbn8D-2NtxUgug15-Q@mail.gmail.com>
 <6cff6466-4eb1-4c33-ac3b-67652839ced3@googlegroups.com>
Message-ID: <CA+JHcKS18XeQfKfimp4tnZ2GzbYqmaygwxVe8R+JNEv9fCRxpA@mail.gmail.com>

I think you mean

faces = np.concatenate((faces, faces[:, ::-1]), axis=0)

=)


On Fri, Jan 10, 2014 at 11:51 AM, Josh Warner <silvertrumpet999 at gmail.com>wrote:

> Calculate the gradient for each face, normalize it, and orient the face
> counterclockwise around the descent of said gradient vector.
>
> It would require some pretty heavy modification, but might be worth it.
>
> On the other hand, you could potentially hack in a fix (depends on how the
> STL package works) much easier by making the output double sided. A
> double-sided mesh has each face twice, covering both orientations This way
> you'd just append `faces` to itself, reverse indexing to flip the
> orientation of each face, e.g.
>
> ``` python
> import numpy as np
> from skimage.measure import marching_cubes
>
> verts, faces = marching_cubes(vol, value)
>
> faces = np.concatenate((faces, faces[:, -1], axis=0)
>
> # Remainder of STL export code for faces here
> ```
>
> Which would be *far, far* simpler and less computationally intense than
> dealing with the gradients...
>
> Would you mind trying this quick fix, Janto?
>
>
>
> On Wednesday, January 8, 2014 6:35:28 PM UTC-6, Stefan van der Walt wrote:
>>
>> Josh, you said you had some ideas on how to add this--could you expand?
>>
>  --
> 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 jsch at demuc.de  Sun Jan 12 20:18:10 2014
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Sun, 12 Jan 2014 20:18:10 -0500
Subject: Image filters
In-Reply-To: <CABDkGQkDDTAhcW9JoefsizshQhpH3Qtsg6EWUfxvatkj-cDP1w@mail.gmail.com>
References: <A8DBD659-57C6-4C7C-8F16-E5B790125BAB@demuc.de> <CA+JHcKRdws=_J24iOEaDQW3kOVnRdYBOH-M_VtO4B2xx8Eh+Jg@mail.gmail.com> <CAHazPT=teew1u3tyHHJ4JmRR7QXGQAX71w4yxK6Jfd1S+-Tmtw@mail.gmail.com> <F6F22FBD-3F64-4280-981E-E3BDAAC7A6CF@demuc.de> <CA+JHcKT5_jWAojhkpb+XsEkN5vYTDy+2OX7rTOvMwOCk51K=+A@mail.gmail.com> <CAHazPTkmM21Vco3ifjJ5GG8GwH=FRxK9ZcrYHujLcGbkuLWy=g@mail.gmail.com> <84A6EF14-7B95-44EC-B342-4F4ED6324E7C@demuc.de> <CABDkGQkDDTAhcW9JoefsizshQhpH3Qtsg6EWUfxvatkj-cDP1w@mail.gmail.com>
Message-ID: <AFB5B030-E778-4AC4-9684-1907C1B83434@demuc.de>

+1 for skimage.effects
On Jan 8, 2014, at 19:33, St?fan van der Walt <stefan at sun.ac.za> wrote:

> There are a lot of interesting algorithms related to "artsy" kind of
> things, e.g. colorization, Picasso-fication, etc.  Perhaps
> ``skimage.effects``?
> 
> -- 
> 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 jantod at gmail.com  Mon Jan 13 02:10:46 2014
From: jantod at gmail.com (Janto Dreijer)
Date: Sun, 12 Jan 2014 23:10:46 -0800 (PST)
Subject: incoherent face orientation in marching cubes
In-Reply-To: <6cff6466-4eb1-4c33-ac3b-67652839ced3@googlegroups.com>
References: <008f5bbb-a5d7-4243-9f79-770e0503ce96@googlegroups.com> <0e23eadd-9bdc-41bf-8e90-f0c0bfed2422@googlegroups.com>
 <CABDkGQkLvB=ysuAj00RHrH7BM=Ddit0tUbn8D-2NtxUgug15-Q@mail.gmail.com>
 <6cff6466-4eb1-4c33-ac3b-67652839ced3@googlegroups.com>
Message-ID: <c58b29da-f048-4a4d-8b27-e8a2c291b686@googlegroups.com>

Thanks Josh,

Unfortunately I need a single sided mesh. The resulting STL will be passed 
to constructive solid geometry code which needs to know which side is 
inside/outside.

Could your suggestion of looking at the volume field's gradient be done 
after running marching_cubes? It might be simpler than extending the 
internals of marching_cube.
Then again, I'm working with a binary input volume. So I don't really have 
a gradient...

Regards
Janto

On Friday, January 10, 2014 2:51:56 AM UTC+2, Josh Warner wrote:
>
> Calculate the gradient for each face, normalize it, and orient the face 
> counterclockwise around the descent of said gradient vector.
>
> It would require some pretty heavy modification, but might be worth it.
>
> On the other hand, you could potentially hack in a fix (depends on how the 
> STL package works) much easier by making the output double sided. A 
> double-sided mesh has each face twice, covering both orientations This way 
> you'd just append `faces` to itself, reverse indexing to flip the 
> orientation of each face, e.g.
>
> ``` python
> import numpy as np
> from skimage.measure import marching_cubes
>
> verts, faces = marching_cubes(vol, value)
>
> faces = np.concatenate((faces, faces[:, -1], axis=0)
>
> # Remainder of STL export code for faces here
> ```
>
> Which would be *far, far* simpler and less computationally intense than 
> dealing with the gradients...
>
> Would you mind trying this quick fix, Janto?
>
>
> On Wednesday, January 8, 2014 6:35:28 PM UTC-6, Stefan van der Walt wrote:
>>
>> Josh, you said you had some ideas on how to add this--could you expand? 
>>
>
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From stefan at sun.ac.za  Tue Jan 14 10:16:35 2014
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 14 Jan 2014 16:16:35 +0100
Subject: 3D Template matching
Message-ID: <CABDkGQnOZ29AUo=9jK_WbAUJZjgmfb_+Jvv1U7NN91DB+V5i2A@mail.gmail.com>

Hey everyone,

Just a heads-up that 3D template matching is now available as a side-effect of

https://github.com/scikit-image/scikit-image/pull/847

Thanks, Johannes!

St?fan


From silvertrumpet999 at gmail.com  Wed Jan 15 15:38:49 2014
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Wed, 15 Jan 2014 12:38:49 -0800 (PST)
Subject: incoherent face orientation in marching cubes
In-Reply-To: <c58b29da-f048-4a4d-8b27-e8a2c291b686@googlegroups.com>
References: <008f5bbb-a5d7-4243-9f79-770e0503ce96@googlegroups.com> <0e23eadd-9bdc-41bf-8e90-f0c0bfed2422@googlegroups.com>
 <CABDkGQkLvB=ysuAj00RHrH7BM=Ddit0tUbn8D-2NtxUgug15-Q@mail.gmail.com>
 <6cff6466-4eb1-4c33-ac3b-67652839ced3@googlegroups.com>
 <c58b29da-f048-4a4d-8b27-e8a2c291b686@googlegroups.com>
Message-ID: <2529c4f4-6ca6-4e8b-bbc5-a8a87f6dca27@googlegroups.com>

I think you're right, this could be done in post. And I believe "gradient" 
in this case should work even for binary input.

I'm keen to work on this, but have some deadlines which will keep me busy 
until at least next week.

Regards,
Josh

On Monday, January 13, 2014 1:10:46 AM UTC-6, Janto Dreijer wrote:
>
> Thanks Josh,
>
> Unfortunately I need a single sided mesh. The resulting STL will be passed 
> to constructive solid geometry code which needs to know which side is 
> inside/outside.
>
> Could your suggestion of looking at the volume field's gradient be done 
> after running marching_cubes? It might be simpler than extending the 
> internals of marching_cube.
> Then again, I'm working with a binary input volume. So I don't really have 
> a gradient...
>
> Regards
> Janto
>
> On Friday, January 10, 2014 2:51:56 AM UTC+2, Josh Warner wrote:
>>
>> Calculate the gradient for each face, normalize it, and orient the face 
>> counterclockwise around the descent of said gradient vector.
>>
>> It would require some pretty heavy modification, but might be worth it.
>>
>> On the other hand, you could potentially hack in a fix (depends on how 
>> the STL package works) much easier by making the output double sided. A 
>> double-sided mesh has each face twice, covering both orientations This way 
>> you'd just append `faces` to itself, reverse indexing to flip the 
>> orientation of each face, e.g.
>>
>> ``` python
>> import numpy as np
>> from skimage.measure import marching_cubes
>>
>> verts, faces = marching_cubes(vol, value)
>>
>> faces = np.concatenate((faces, faces[:, -1], axis=0)
>>
>> # Remainder of STL export code for faces here
>> ```
>>
>> Which would be *far, far* simpler and less computationally intense than 
>> dealing with the gradients...
>>
>> Would you mind trying this quick fix, Janto?
>>
>>
>> On Wednesday, January 8, 2014 6:35:28 PM UTC-6, Stefan van der Walt wrote:
>>>
>>> Josh, you said you had some ideas on how to add this--could you expand? 
>>>
>>
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From jsch at demuc.de  Sat Jan 18 02:12:34 2014
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Sat, 18 Jan 2014 02:12:34 -0500
Subject: scikit-image paper
In-Reply-To: <CAEym_HqD3DWpnfEcr8rXq_=zhatHHgfrkeakz_dN8zKCDaA2uQ@mail.gmail.com>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com> <CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com> <CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com> <CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com> <bf9ff28b-cb0a-4f18-9184-34679c31dbe8@googlegroups.com> <CAEym_Hpj8X2E9aw-Z37Am_2hJouci0eY4zUi=cP1b13bjmg5JA@mail.gmail.com> <CAEym_HqMxaNb9KspKeC9KivcuQnFxw0bTqjxaWPut=G9bvt0DQ@mail.gmail.com> <CABDkGQnS51Zb=63QSHoz6U8=MYuVWML_PCnOomvrMn2gSdk1=w@mail.gmail.com> <CAEym_HqD3DWpnfEcr8rXq_=zhatHHgfrkeakz_dN8zKCDaA2uQ@mail.gmail.com>
Message-ID: <900F93A6-208D-418E-A873-CF3535707F94@demuc.de>

Ping to all involved people. what's the status in this project?


From stefan at sun.ac.za  Sat Jan 18 04:30:25 2014
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sat, 18 Jan 2014 10:30:25 +0100
Subject: scikit-image paper
In-Reply-To: <900F93A6-208D-418E-A873-CF3535707F94@demuc.de>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com>
	<CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com>
	<CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com>
	<CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com>
	<bf9ff28b-cb0a-4f18-9184-34679c31dbe8@googlegroups.com>
	<CAEym_Hpj8X2E9aw-Z37Am_2hJouci0eY4zUi=cP1b13bjmg5JA@mail.gmail.com>
	<CAEym_HqMxaNb9KspKeC9KivcuQnFxw0bTqjxaWPut=G9bvt0DQ@mail.gmail.com>
	<CABDkGQnS51Zb=63QSHoz6U8=MYuVWML_PCnOomvrMn2gSdk1=w@mail.gmail.com>
	<CAEym_HqD3DWpnfEcr8rXq_=zhatHHgfrkeakz_dN8zKCDaA2uQ@mail.gmail.com>
	<900F93A6-208D-418E-A873-CF3535707F94@demuc.de>
Message-ID: <CABDkGQkhcoYzniy0bidoFvha7mVPcP1kTRJjqdZTPUf8PCGJbQ@mail.gmail.com>

Johannes, sorry for the delay on this; the paper is a top priority for me,
and I should have quite a bit of time to work on this starting Sunday
evening.
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From jsch at demuc.de  Sat Jan 18 11:24:08 2014
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Sat, 18 Jan 2014 11:24:08 -0500
Subject: scikit-image paper
In-Reply-To: <CABDkGQkhcoYzniy0bidoFvha7mVPcP1kTRJjqdZTPUf8PCGJbQ@mail.gmail.com>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com> <CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com> <CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com> <CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com> <bf9ff28b-cb0a-4f18-9184-34679c31dbe8@googlegroups.com> <CAEym_Hpj8X2E9aw-Z37Am_2hJouci0eY4zUi=cP1b13bjmg5JA@mail.gmail.com> <CAEym_HqMxaNb9KspKeC9KivcuQnFxw0bTqjxaWPut=G9bvt0DQ@mail.gmail.com> <CABDkGQnS51Zb=63QSHoz6U8=MYuVWML_PCnOomvrMn2gSdk1=w@mail.gmail.com> <CAEym_HqD3DWpnfEcr8rXq_=zhatHHgfrkeakz_dN8zKCDaA2uQ@mail.gmail.com> <900F93A6-208D-418E-A873-CF3535707F94@demuc.de> <CABDkGQkhcoYzniy0bidoFvha7mVPcP1kTRJjqdZTPUf8PCGJbQ@mail.gmail.com>
Message-ID: <58CA473E-BA50-4998-8F5F-781D617E01F5@demuc.de>

Good to hear.

Let me know how to improve the Development section and I could certainly contribute another example - not sure how many examples we want to include?

On Jan 18, 2014, at 4:30, St?fan van der Walt <stefan at sun.ac.za> wrote:

> Johannes, sorry for the delay on this; the paper is a top priority for me, and I should have quite a bit of time to work on this starting Sunday evening.
> 
> 
> -- 
> 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 jsch at demuc.de  Sat Jan 18 22:24:52 2014
From: jsch at demuc.de (=?ISO-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Sat, 18 Jan 2014 22:24:52 -0500
Subject: scikit-image paper
In-Reply-To: <CA+JHcKRPfwrR09+QqmiVgrh=m4Hrg8AhswOPKMzxNmWHM3o=9g@mail.gmail.com>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com>
	<CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com>
	<CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com>
	<CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com>
	<bf9ff28b-cb0a-4f18-9184-34679c31dbe8@googlegroups.com>
	<CAEym_Hpj8X2E9aw-Z37Am_2hJouci0eY4zUi=cP1b13bjmg5JA@mail.gmail.com>
	<CAEym_HqMxaNb9KspKeC9KivcuQnFxw0bTqjxaWPut=G9bvt0DQ@mail.gmail.com>
	<CABDkGQnS51Zb=63QSHoz6U8=MYuVWML_PCnOomvrMn2gSdk1=w@mail.gmail.com>
	<CAEym_HqD3DWpnfEcr8rXq_=zhatHHgfrkeakz_dN8zKCDaA2uQ@mail.gmail.com>
	<900F93A6-208D-418E-A873-CF3535707F94@demuc.de>
	<CABDkGQkhcoYzniy0bidoFvha7mVPcP1kTRJjqdZTPUf8PCGJbQ@mail.gmail.com>
	<58CA473E-BA50-4998-8F5F-781D617E01F5@demuc.de>
	<CA+JHcKRPfwrR09+QqmiVgrh=m4Hrg8AhswOPKMzxNmWHM3o=9g@mail.gmail.com>
Message-ID: <CAFTxfL=VV62-HiDWLaeLBUR_1RBp1eK8FQwF=NJrqeJ+nv1FEw@mail.gmail.com>

@Juan That'd be great :-)

On Sat, Jan 18, 2014 at 9:28 PM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> Thanks for the ping, Johannes! I myself dropped the ball on this but ready
> to pick it up again!
>
>
> On Sun, Jan 19, 2014 at 3:24 AM, Johannes Sch?nberger <jsch at demuc.de> wrote:
>>
>> Good to hear.
>>
>> Let me know how to improve the Development section and I could certainly
>> contribute another example - not sure how many examples we want to include?
>>
>> On Jan 18, 2014, at 4:30, St?fan van der Walt <stefan at sun.ac.za> wrote:
>>
>> > Johannes, sorry for the delay on this; the paper is a top priority for
>> > me, and I should have quite a bit of time to work on this starting Sunday
>> > evening.
>> >
>> >
>> > --
>> > 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
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From aaaagrawal at gmail.com  Sun Jan 19 08:05:20 2014
From: aaaagrawal at gmail.com (Ankit Agrawal)
Date: Sun, 19 Jan 2014 05:05:20 -0800 (PST)
Subject: Review of PR : FAST and ORB
Message-ID: <4b5baa86-a419-4035-b9bb-94b50bd778d5@googlegroups.com>

Hi all,

       The FAST and ORB pull request<https://github.com/scikit-image/scikit-image/pull/834>needs a final round of review. Johannes is done with some crucial design 
changes on the original PR<https://github.com/scikit-image/scikit-image/pull/699>. 
Please review it if you have some time. This might sound pretty lame, but 
merging this PR will motivate me to complete the work on FREAK descriptor<https://github.com/scikit-image/scikit-image/pull/729>. 
Thank you.


Regards,
Ankit.
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From jsch at demuc.de  Sun Jan 19 09:45:01 2014
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Sun, 19 Jan 2014 09:45:01 -0500
Subject: Review of PR : FAST and ORB
In-Reply-To: <4b5baa86-a419-4035-b9bb-94b50bd778d5@googlegroups.com>
References: <4b5baa86-a419-4035-b9bb-94b50bd778d5@googlegroups.com>
Message-ID: <1B63B1E5-DC49-443C-85AC-2DED7815A7D7@demuc.de>

Hi Ankit,

Sorry, that this PR takes so long, but it is a rather large change.

I made some (in my opinion final) changes, to also follow the estimator convention as discussed here: https://github.com/scikit-image/scikit-image/pull/840

This was basically the one thing I was waiting for and from my side we are good to merge now.

Johannes

On Jan 19, 2014, at 8:05, Ankit Agrawal <aaaagrawal at gmail.com> wrote:

> Hi all,
> 
>        The FAST and ORB pull request needs a final round of review. Johannes is done with some crucial design changes on the original PR. Please review it if you have some time. This might sound pretty lame, but merging this PR will motivate me to complete the work on FREAK descriptor. Thank you.
> 
> 
> Regards,
> Ankit.
> 
> -- 
> 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 jni.soma at gmail.com  Sat Jan 18 21:28:01 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Sun, 19 Jan 2014 13:28:01 +1100
Subject: scikit-image paper
In-Reply-To: <58CA473E-BA50-4998-8F5F-781D617E01F5@demuc.de>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com>
 <CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com>
 <CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com>
 <CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com>
 <bf9ff28b-cb0a-4f18-9184-34679c31dbe8@googlegroups.com> <CAEym_Hpj8X2E9aw-Z37Am_2hJouci0eY4zUi=cP1b13bjmg5JA@mail.gmail.com>
 <CAEym_HqMxaNb9KspKeC9KivcuQnFxw0bTqjxaWPut=G9bvt0DQ@mail.gmail.com>
 <CABDkGQnS51Zb=63QSHoz6U8=MYuVWML_PCnOomvrMn2gSdk1=w@mail.gmail.com>
 <CAEym_HqD3DWpnfEcr8rXq_=zhatHHgfrkeakz_dN8zKCDaA2uQ@mail.gmail.com>
 <900F93A6-208D-418E-A873-CF3535707F94@demuc.de> <CABDkGQkhcoYzniy0bidoFvha7mVPcP1kTRJjqdZTPUf8PCGJbQ@mail.gmail.com>
 <58CA473E-BA50-4998-8F5F-781D617E01F5@demuc.de>
Message-ID: <CA+JHcKRPfwrR09+QqmiVgrh=m4Hrg8AhswOPKMzxNmWHM3o=9g@mail.gmail.com>

Thanks for the ping, Johannes! I myself dropped the ball on this but ready
to pick it up again!


On Sun, Jan 19, 2014 at 3:24 AM, Johannes Sch?nberger <jsch at demuc.de> wrote:

> Good to hear.
>
> Let me know how to improve the Development section and I could certainly
> contribute another example - not sure how many examples we want to include?
>
> On Jan 18, 2014, at 4:30, St?fan van der Walt <stefan at sun.ac.za> wrote:
>
> > Johannes, sorry for the delay on this; the paper is a top priority for
> me, and I should have quite a bit of time to work on this starting Sunday
> evening.
> >
> >
> > --
> > 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.
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From ralf.gommers at gmail.com  Tue Jan 21 01:06:39 2014
From: ralf.gommers at gmail.com (Ralf Gommers)
Date: Tue, 21 Jan 2014 07:06:39 +0100
Subject: Help with Travis
In-Reply-To: <CA+JHcKRuEhTKmv3qUYU4YmPhjR_8YQA3gYQkCV7c3YchaqPH7A@mail.gmail.com>
References: <CA+JHcKRuEhTKmv3qUYU4YmPhjR_8YQA3gYQkCV7c3YchaqPH7A@mail.gmail.com>
Message-ID: <CABL7CQhfFAyQo8JENsAspe-pJVU74YmvEsD-y24qmqm5bsAbjg@mail.gmail.com>

On Tue, Jan 21, 2014 at 2:00 AM, Juan Nunez-Iglesias <jni.soma at gmail.com>wrote:

> Hi guys,
>
> A bit off-topic but I hope someone will be able to help trivially...
>
> I'm trying to run Travis on my own gala repository (you might remember
> gala from my scipy2012 talk, when it was called ray). It appeared to be
> working fine, but actually it's giving me a little green dot when in fact a
> bunch of tests are failing!
>
> https://travis-ci.org/jni/gala/builds/16860892
>

Last line: "Done. Your build exited with 0."

>
> Here's the corresponding .travis.yml file:
>
> https://github.com/jni/gala/blob/tree-agglo/.travis.yml
>
> What am I doing wrong? How can I make it so the test failures result in
> build failures?
>

You need your test script to have a nonzero exit status. You also need to
run all your tests from a single script for that to work properly. You
could copy and adapt
https://github.com/scipy/scipy/blob/master/runtests.pyfor your
project.

Cheers,
Ralf



> Thanks,
>
> 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 jjhelmus at gmail.com  Tue Jan 21 10:55:37 2014
From: jjhelmus at gmail.com (Jonathan Helmus)
Date: Tue, 21 Jan 2014 09:55:37 -0600
Subject: Help with Travis
In-Reply-To: <CABL7CQhfFAyQo8JENsAspe-pJVU74YmvEsD-y24qmqm5bsAbjg@mail.gmail.com>
References: <CA+JHcKRuEhTKmv3qUYU4YmPhjR_8YQA3gYQkCV7c3YchaqPH7A@mail.gmail.com> <CABL7CQhfFAyQo8JENsAspe-pJVU74YmvEsD-y24qmqm5bsAbjg@mail.gmail.com>
Message-ID: <52DE9879.4080003@gmail.com>

Juan,

     You also might want to look into using a testing framework such as 
nose (https://nose.readthedocs.org/en/latest/) for running your unit 
tests.  A number of scientific python packages use this package 
including scikit-image.  If you name the file and functions/classes 
containing your unit tests correctly, nose will automatically collect 
and run your tests. In addition, you can use the handy nosetests command 
which will set the exit value correctly.  If you look at the .travis.yml 
file for scikits-image you will see that on line 66 nosetests is used to 
run runs the unit tests.  This same method is used in many other 
scientific python packages

Cheers,

     - Jonathan

On 01/21/2014 12:06 AM, Ralf Gommers wrote:
>
>
>
> On Tue, Jan 21, 2014 at 2:00 AM, Juan Nunez-Iglesias 
> <jni.soma at gmail.com <mailto:jni.soma at gmail.com>> wrote:
>
>     Hi guys,
>
>     A bit off-topic but I hope someone will be able to help trivially...
>
>     I'm trying to run Travis on my own gala repository (you might
>     remember gala from my scipy2012 talk, when it was called ray). It
>     appeared to be working fine, but actually it's giving me a little
>     green dot when in fact a bunch of tests are failing!
>
>     https://travis-ci.org/jni/gala/builds/16860892
>
>
> Last line:"Done. Your build exited with 0."
>
>
>     Here's the corresponding .travis.yml file:
>
>     https://github.com/jni/gala/blob/tree-agglo/.travis.yml
>
>     What am I doing wrong? How can I make it so the test failures
>     result in build failures?
>
>
> You need your test script to have a nonzero exit status. You also need 
> to run all your tests from a single script for that to work properly. 
> You could copy and adapt 
> https://github.com/scipy/scipy/blob/master/runtests.py for your project.
>
> Cheers,
> Ralf
>
>
>
>     Thanks,
>
>     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
>     <mailto:scikit-image%2Bunsubscribe 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 jni.soma at gmail.com  Mon Jan 20 20:00:08 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Tue, 21 Jan 2014 12:00:08 +1100
Subject: Help with Travis
Message-ID: <CA+JHcKRuEhTKmv3qUYU4YmPhjR_8YQA3gYQkCV7c3YchaqPH7A@mail.gmail.com>

Hi guys,

A bit off-topic but I hope someone will be able to help trivially...

I'm trying to run Travis on my own gala repository (you might remember gala
from my scipy2012 talk, when it was called ray). It appeared to be working
fine, but actually it's giving me a little green dot when in fact a bunch
of tests are failing!

https://travis-ci.org/jni/gala/builds/16860892

Here's the corresponding .travis.yml file:

https://github.com/jni/gala/blob/tree-agglo/.travis.yml

What am I doing wrong? How can I make it so the test failures result in
build failures?

Thanks,

Juan.
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From stefan at sun.ac.za  Tue Jan 21 08:01:15 2014
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 21 Jan 2014 14:01:15 +0100
Subject: Access to PowerPC platform
Message-ID: <CABDkGQk5nVvqe9xq0fJ2Y2N4jGkmzrEAR3ux9iLvSetoxbU9Hg@mail.gmail.com>

Hi,

Does anyone have access to a PowerPC machine?  It would be helpful to
have a backtrace on the following error in FreeImage:

https://buildd.debian.org/status/fetch.php?pkg=skimage&arch=powerpc&ver=0.9.3-3&stamp=1390024125&file=log

Thanks
St?fan


From jni.soma at gmail.com  Tue Jan 21 16:52:13 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Wed, 22 Jan 2014 08:52:13 +1100
Subject: Help with Travis
In-Reply-To: <52DE9879.4080003@gmail.com>
References: <CA+JHcKRuEhTKmv3qUYU4YmPhjR_8YQA3gYQkCV7c3YchaqPH7A@mail.gmail.com>
 <CABL7CQhfFAyQo8JENsAspe-pJVU74YmvEsD-y24qmqm5bsAbjg@mail.gmail.com> <52DE9879.4080003@gmail.com>
Message-ID: <CA+JHcKTdn3WNXtJO4m6dZ3Q9GhNrMvr4yqTYyNkzyJhVmxOb_Q@mail.gmail.com>

Ralf, Jonathan,

Thanks for your help ? the exit code was indeed the problem, and nosetests
the solution. Running the test files with python -m nose or just nosetests
indeed resolved the problem. (Though not the running-from-a-single-file
problem... But I can deal with that later. This will at least tell me what
the first test to fail is. =)

Thanks!

Juan.



On Wed, Jan 22, 2014 at 2:55 AM, Jonathan Helmus <jjhelmus at gmail.com> wrote:

>  Juan,
>
>     You also might want to look into using a testing framework such as
> nose (https://nose.readthedocs.org/en/latest/) for running your unit
> tests.  A number of scientific python packages use this package including
> scikit-image.  If you name the file and functions/classes containing your
> unit tests correctly, nose will automatically collect and run your tests.
> In addition, you can use the handy nosetests command which will set the
> exit value correctly.  If you look at the .travis.yml file for
> scikits-image you will see that on line 66 nosetests is used to run runs
> the unit tests.  This same method is used in many other scientific python
> packages
>
> Cheers,
>
>     - Jonathan
>
>
> On 01/21/2014 12:06 AM, Ralf Gommers wrote:
>
>
>
>
> On Tue, Jan 21, 2014 at 2:00 AM, Juan Nunez-Iglesias <jni.soma at gmail.com>wrote:
>
>> Hi guys,
>>
>>  A bit off-topic but I hope someone will be able to help trivially...
>>
>>  I'm trying to run Travis on my own gala repository (you might remember
>> gala from my scipy2012 talk, when it was called ray). It appeared to be
>> working fine, but actually it's giving me a little green dot when in fact a
>> bunch of tests are failing!
>>
>>  https://travis-ci.org/jni/gala/builds/16860892
>>
>
>  Last line: "Done. Your build exited with 0."
>
>>
>>  Here's the corresponding .travis.yml file:
>>
>>  https://github.com/jni/gala/blob/tree-agglo/.travis.yml
>>
>>  What am I doing wrong? How can I make it so the test failures result in
>> build failures?
>>
>
>  You need your test script to have a nonzero exit status. You also need
> to run all your tests from a single script for that to work properly. You
> could copy and adapt
> https://github.com/scipy/scipy/blob/master/runtests.py for your project.
>
> Cheers,
> Ralf
>
>
>
>>  Thanks,
>>
>>  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.
>>
>
>  --
> 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 mt at matttrent.com  Wed Jan 22 21:37:14 2014
From: mt at matttrent.com (Matthew Trentacoste)
Date: Wed, 22 Jan 2014 18:37:14 -0800
Subject: Non-local means denoising
In-Reply-To: <CABDkGQkGe+b3a+XJFeSROm1p1vUGEx+_pajCEMmwcGa43EgbWA@mail.gmail.com>
References: <CABDkGQkGe+b3a+XJFeSROm1p1vUGEx+_pajCEMmwcGa43EgbWA@mail.gmail.com>
Message-ID: <CAJU8MvRG8ix2RWZcFCJjDu0KxxEByZONnQcPicaXVV5cbRmXMQ@mail.gmail.com>

I've looked at the paper a bit.  That might actually be up my alley.  Let
me reread and get back to you.


On Wed, Jan 22, 2014 at 5:05 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> Hi all,
>
> Has anyone taken a look at non-local means denoising?  It would make
> for a good PR.
>
> 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.
>



-- 

[  matthew m trentacoste                                     ]
[                                                            ]
[  mt at matttrent.com                                          ]
[  http://matttrent.com                                      ]
[  twitter: @matttrent                                       ]
[  +1.415.326.3226                                           ]
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From stefan at sun.ac.za  Wed Jan 22 20:05:04 2014
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 23 Jan 2014 02:05:04 +0100
Subject: Non-local means denoising
Message-ID: <CABDkGQkGe+b3a+XJFeSROm1p1vUGEx+_pajCEMmwcGa43EgbWA@mail.gmail.com>

Hi all,

Has anyone taken a look at non-local means denoising?  It would make
for a good PR.

St?fan


From kevin.keraudren at googlemail.com  Thu Jan 23 04:47:44 2014
From: kevin.keraudren at googlemail.com (Kevin Keraudren)
Date: Thu, 23 Jan 2014 09:47:44 +0000
Subject: Non-local means denoising
In-Reply-To: <CAJU8MvRG8ix2RWZcFCJjDu0KxxEByZONnQcPicaXVV5cbRmXMQ@mail.gmail.com>
References: <CABDkGQkGe+b3a+XJFeSROm1p1vUGEx+_pajCEMmwcGa43EgbWA@mail.gmail.com> <CAJU8MvRG8ix2RWZcFCJjDu0KxxEByZONnQcPicaXVV5cbRmXMQ@mail.gmail.com>
Message-ID: <52E0E540.6090309@googlemail.com>

Hi,

Here are some implementations of Non-Local Means Denoising you might be 
interested in for reference/comparison:

Image Processing On Line Journal (Antoni Buades, Bartomeu Coll, and 
Jean-Michel Morel):
http://www.ipol.im/pub/art/2011/bcm_nlm/

Pierrick Coup??'s website:
https://sites.google.com/site/pierrickcoupe/softwares/denoising-for-medical-imaging/mri-denoising

ITK implementation in the Baby Brain Toolkit, from Fran??ois Rousseau:
https://github.com/rousseau/fbrain/blob/master/Code/Denoising/btkNLMTool.txx

The first one provides an online demo, is easy to wrap in cython, but is 
only 2D whereas the two others handle 3D images.

Kind regards,

Kevin


Le 23/01/2014 02:37, Matthew Trentacoste a ??crit :
> I've looked at the paper a bit.  That might actually be up my alley. 
>  Let me reread and get back to you.
>
>
> On Wed, Jan 22, 2014 at 5:05 PM, St??fan van der Walt <stefan at sun.ac.za 
> <mailto:stefan at sun.ac.za>> wrote:
>
>     Hi all,
>
>     Has anyone taken a look at non-local means denoising?  It would make
>     for a good PR.
>
>     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
>     <mailto:scikit-image%2Bunsubscribe at googlegroups.com>.
>     For more options, visit https://groups.google.com/groups/opt_out.
>
>
>
>
> -- 
>
> [  matthew m trentacoste                                     ]
> [                                                            ]
> [ mt at matttrent.com <mailto:mt at matttrent.com>                ]
> [ http://matttrent.com                ]
> [  twitter: @matttrent                                       ]
> [  +1.415.326.3226                                           ]
> -- 
> 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 Jan 23 06:55:03 2014
From: stefan at sun.ac.za (=?iso-8859-1?Q?St=E9fan?= van der Walt)
Date: Thu, 23 Jan 2014 12:55:03 +0100
Subject: Non-local means denoising
In-Reply-To: <52E0E540.6090309@googlemail.com>
References: <CABDkGQkGe+b3a+XJFeSROm1p1vUGEx+_pajCEMmwcGa43EgbWA@mail.gmail.com>
 <CAJU8MvRG8ix2RWZcFCJjDu0KxxEByZONnQcPicaXVV5cbRmXMQ@mail.gmail.com>
 <52E0E540.6090309@googlemail.com>
Message-ID: <20140123115503.GB16463@gmail.com>

Hi Kevin

On Thu, 23 Jan 2014 09:47:44 +0000, Kevin Keraudren wrote:
> Here are some implementations of Non-Local Means Denoising you might
> be interested in for reference/comparison:

Thanks for these informative links.  Are you interested in working on nlmeans,
or do you know of someone who would be able to help us review the code once it
is written?

Thanks
St??fan


From kevin.keraudren at googlemail.com  Thu Jan 23 10:48:41 2014
From: kevin.keraudren at googlemail.com (Kevin Keraudren)
Date: Thu, 23 Jan 2014 15:48:41 +0000
Subject: Non-local means denoising
In-Reply-To: <20140123115503.GB16463@gmail.com>
References: <CABDkGQkGe+b3a+XJFeSROm1p1vUGEx+_pajCEMmwcGa43EgbWA@mail.gmail.com> <CAJU8MvRG8ix2RWZcFCJjDu0KxxEByZONnQcPicaXVV5cbRmXMQ@mail.gmail.com> <52E0E540.6090309@googlemail.com> <20140123115503.GB16463@gmail.com>
Message-ID: <52E139D9.9000102@googlemail.com>

I just listed these implementations as I recently searched for a C++ 
implementation.
Unfortunately, I cannot volunteer to work on this and I do not know 
anyone who already worked on this topic...
Kind regards,
Kevin



Le 23/01/2014 11:55, St??fan van der Walt a ??crit :
> Hi Kevin
>
> On Thu, 23 Jan 2014 09:47:44 +0000, Kevin Keraudren wrote:
>> Here are some implementations of Non-Local Means Denoising you might
>> be interested in for reference/comparison:
> Thanks for these informative links.  Are you interested in working on nlmeans,
> or do you know of someone who would be able to help us review the code once it
> is written?
>
> Thanks
> St??fan
>



From emmanuelle.gouillart at nsup.org  Thu Jan 23 11:26:59 2014
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Thu, 23 Jan 2014 17:26:59 +0100
Subject: Non-local means denoising
In-Reply-To: <52E139D9.9000102@googlemail.com>
References: <CABDkGQkGe+b3a+XJFeSROm1p1vUGEx+_pajCEMmwcGa43EgbWA@mail.gmail.com>
 <CAJU8MvRG8ix2RWZcFCJjDu0KxxEByZONnQcPicaXVV5cbRmXMQ@mail.gmail.com>
 <52E0E540.6090309@googlemail.com>
 <20140123115503.GB16463@gmail.com>
 <52E139D9.9000102@googlemail.com>
Message-ID: <20140123162659.GA29205@phare.normalesup.org>

Hi,

it happens that I have an implementation of NL-means (implemented in C +
cython). I have to clean it a little and then I can send it to the list.
It would actually be interesting to convert it to pure Cython for further
maintanability.

Cheers,
Emmanuelle

On Thu, Jan 23, 2014 at 03:48:41PM +0000, Kevin Keraudren wrote:
> I just listed these implementations as I recently searched for a C++
> implementation.
> Unfortunately, I cannot volunteer to work on this and I do not know
> anyone who already worked on this topic...
> Kind regards,
> Kevin



> Le 23/01/2014 11:55, St??fan van der Walt a ??crit :
> >Hi Kevin

> >On Thu, 23 Jan 2014 09:47:44 +0000, Kevin Keraudren wrote:
> >>Here are some implementations of Non-Local Means Denoising you might
> >>be interested in for reference/comparison:
> >Thanks for these informative links.  Are you interested in working on nlmeans,
> >or do you know of someone who would be able to help us review the code once it
> >is written?

> >Thanks
> >St??fan


From jni.soma at gmail.com  Thu Jan 23 19:46:19 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Fri, 24 Jan 2014 11:46:19 +1100
Subject: Non-local means denoising
In-Reply-To: <20140123162659.GA29205@phare.normalesup.org>
References: <CABDkGQkGe+b3a+XJFeSROm1p1vUGEx+_pajCEMmwcGa43EgbWA@mail.gmail.com>
 <CAJU8MvRG8ix2RWZcFCJjDu0KxxEByZONnQcPicaXVV5cbRmXMQ@mail.gmail.com>
 <52E0E540.6090309@googlemail.com> <20140123115503.GB16463@gmail.com>
 <52E139D9.9000102@googlemail.com> <20140123162659.GA29205@phare.normalesup.org>
Message-ID: <CA+JHcKQtwBRjjKD3wacGvoQ3hbDAf9BZZXVpofeG-kT8vD96xg@mail.gmail.com>

Haha, hi Emmanuelle, long time no see! ;) I think your interjection in this
thread is rather priceless. =D Is your implementation 3D? Either way, if
you submit a WIP PR, I might be tempted to use some cycles to help out. =)



On Fri, Jan 24, 2014 at 3:26 AM, Emmanuelle Gouillart <
emmanuelle.gouillart at nsup.org> wrote:

> Hi,
>
> it happens that I have an implementation of NL-means (implemented in C +
> cython). I have to clean it a little and then I can send it to the list.
> It would actually be interesting to convert it to pure Cython for further
> maintanability.
>
> Cheers,
> Emmanuelle
>
> On Thu, Jan 23, 2014 at 03:48:41PM +0000, Kevin Keraudren wrote:
> > I just listed these implementations as I recently searched for a C++
> > implementation.
> > Unfortunately, I cannot volunteer to work on this and I do not know
> > anyone who already worked on this topic...
> > Kind regards,
> > Kevin
>
>
>
> > Le 23/01/2014 11:55, St?fan van der Walt a ?crit :
> > >Hi Kevin
>
> > >On Thu, 23 Jan 2014 09:47:44 +0000, Kevin Keraudren wrote:
> > >>Here are some implementations of Non-Local Means Denoising you might
> > >>be interested in for reference/comparison:
> > >Thanks for these informative links.  Are you interested in working on
> nlmeans,
> > >or do you know of someone who would be able to help us review the code
> once it
> > >is written?
>
> > >Thanks
> > >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 fboulogne at sciunto.org  Fri Jan 24 17:57:17 2014
From: fboulogne at sciunto.org (=?ISO-8859-1?Q?Fran=E7ois_Boulogne?=)
Date: Fri, 24 Jan 2014 17:57:17 -0500
Subject: scikit-image paper
In-Reply-To: <CAFTxfL=VV62-HiDWLaeLBUR_1RBp1eK8FQwF=NJrqeJ+nv1FEw@mail.gmail.com>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com>	<CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com>	<CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com>	<CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com>	<bf9ff28b-cb0a-4f18-9184-34679c31dbe8@googlegroups.com>	<CAEym_Hpj8X2E9aw-Z37Am_2hJouci0eY4zUi=cP1b13bjmg5JA@mail.gmail.com>	<CAEym_HqMxaNb9KspKeC9KivcuQnFxw0bTqjxaWPut=G9bvt0DQ@mail.gmail.com>	<CABDkGQnS51Zb=63QSHoz6U8=MYuVWML_PCnOomvrMn2gSdk1=w@mail.gmail.com>	<CAEym_HqD3DWpnfEcr8rXq_=zhatHHgfrkeakz_dN8zKCDaA2uQ@mail.gmail.com>	<900F93A6-208D-418E-A873-CF3535707F94@demuc.de>	<CABDkGQkhcoYzniy0bidoFvha7mVPcP1kTRJjqdZTPUf8PCGJbQ@mail.gmail.com>	<58CA473E-BA50-4998-8F5F-781D617E01F5@demuc.de>	<CA+JHcKRPfwrR09+QqmiVgrh=m4Hrg8AhswOPKMzxNmWHM3o=9g@mail.gmail.com> <CAFTxfL=VV62-HiDWLaeLBUR_1RBp1eK8FQwF=NJrqeJ+nv1FEw@mail.gmail.com>
Message-ID: <52E2EFCD.5020000@sciunto.org>

Hi,

I think we should decide where and how we write codes, in the text with
a snippet style and/or at the end with a full code.
I don't know how it depends on the journal where you want to submit the
paper. Have you reached a consensus about that?

Thank you.
Best.

-- 
Fran?ois Boulogne.
http://www.sciunto.org
GPG fingerprint: 25F6 C971 4875 A6C1 EDD1  75C8 1AA7 216E 32D5 F22F



From stefan at sun.ac.za  Fri Jan 24 19:01:39 2014
From: stefan at sun.ac.za (=?iso-8859-1?Q?St=E9fan?= van der Walt)
Date: Sat, 25 Jan 2014 01:01:39 +0100
Subject: scikit-image paper
In-Reply-To: <52E2EFCD.5020000@sciunto.org>
References: <CAEym_Hpj8X2E9aw-Z37Am_2hJouci0eY4zUi=cP1b13bjmg5JA@mail.gmail.com>
 <CAEym_HqMxaNb9KspKeC9KivcuQnFxw0bTqjxaWPut=G9bvt0DQ@mail.gmail.com>
 <CABDkGQnS51Zb=63QSHoz6U8=MYuVWML_PCnOomvrMn2gSdk1=w@mail.gmail.com>
 <CAEym_HqD3DWpnfEcr8rXq_=zhatHHgfrkeakz_dN8zKCDaA2uQ@mail.gmail.com>
 <900F93A6-208D-418E-A873-CF3535707F94@demuc.de>
 <CABDkGQkhcoYzniy0bidoFvha7mVPcP1kTRJjqdZTPUf8PCGJbQ@mail.gmail.com>
 <58CA473E-BA50-4998-8F5F-781D617E01F5@demuc.de>
 <CA+JHcKRPfwrR09+QqmiVgrh=m4Hrg8AhswOPKMzxNmWHM3o=9g@mail.gmail.com>
 <CAFTxfL=VV62-HiDWLaeLBUR_1RBp1eK8FQwF=NJrqeJ+nv1FEw@mail.gmail.com>
 <52E2EFCD.5020000@sciunto.org>
Message-ID: <20140125000139.GC23850@gmail.com>

On Fri, 24 Jan 2014 17:57:17 -0500, Fran??ois Boulogne wrote:
> I think we should decide where and how we write codes, in the text with
> a snippet style and/or at the end with a full code.
> I don't know how it depends on the journal where you want to submit the
> paper. Have you reached a consensus about that?

If you want to show something specific, e.g. the simplicity of building a
pipeline, for which you need just 3-5 lines of code, then it should probably
go inline.  If it is a longer snippet, attach it at the end or perhaps think
whether it should be included at all.

We can very easily write an IPython notebook and simply reference that from
the paper for examples.

St??fan



From emmanuelle.gouillart at nsup.org  Sat Jan 25 06:23:07 2014
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Sat, 25 Jan 2014 12:23:07 +0100
Subject: Non-local means denoising
In-Reply-To: <CA+JHcKQtwBRjjKD3wacGvoQ3hbDAf9BZZXVpofeG-kT8vD96xg@mail.gmail.com>
References: <CABDkGQkGe+b3a+XJFeSROm1p1vUGEx+_pajCEMmwcGa43EgbWA@mail.gmail.com>
 <CAJU8MvRG8ix2RWZcFCJjDu0KxxEByZONnQcPicaXVV5cbRmXMQ@mail.gmail.com>
 <52E0E540.6090309@googlemail.com>
 <20140123115503.GB16463@gmail.com>
 <52E139D9.9000102@googlemail.com>
 <20140123162659.GA29205@phare.normalesup.org>
 <CA+JHcKQtwBRjjKD3wacGvoQ3hbDAf9BZZXVpofeG-kT8vD96xg@mail.gmail.com>
Message-ID: <20140125112307.GA26044@phare.normalesup.org>

Hi Juan,

yes, it's been a long time :-) (I took a new job in September and it's
been pretty hectic since then!).

My implementation is indeed 3-D. I'll start working on a PR this week-end
then! For 3-D images the code is pretty slow due to the large size of the
data, but I also have a pycuda + cuda implementation written by my PhD
student William. You'll tell me if you're interested!

Cheers,
Emmanuelle

On Fri, Jan 24, 2014 at 11:46:19AM +1100, Juan Nunez-Iglesias wrote:
> Haha, hi Emmanuelle, long time no see! ;) I think your interjection in this
> thread is rather priceless. =D Is your implementation 3D? Either way, if you
> submit a WIP PR, I might be tempted to use some cycles to help out. =)



> On Fri, Jan 24, 2014 at 3:26 AM, Emmanuelle Gouillart <
> emmanuelle.gouillart at nsup.org> wrote:

>     Hi,

>     it happens that I have an implementation of NL-means (implemented in C +
>     cython). I have to clean it a little and then I can send it to the list.
>     It would actually be interesting to convert it to pure Cython for further
>     maintanability.

>     Cheers,
>     Emmanuelle

>     On Thu, Jan 23, 2014 at 03:48:41PM +0000, Kevin Keraudren wrote:
>     > I just listed these implementations as I recently searched for a C++
>     > implementation.
>     > Unfortunately, I cannot volunteer to work on this and I do not know
>     > anyone who already worked on this topic...
>     > Kind regards,
>     > Kevin



>     > Le 23/01/2014 11:55, St??fan van der Walt a ??crit :
>     > >Hi Kevin

>     > >On Thu, 23 Jan 2014 09:47:44 +0000, Kevin Keraudren wrote:
>     > >>Here are some implementations of Non-Local Means Denoising you might
>     > >>be interested in for reference/comparison:
>     > >Thanks for these informative links. ??Are you interested in working on
>     nlmeans,
>     > >or do you know of someone who would be able to help us review the code
>     once it
>     > >is written?

>     > >Thanks
>     > >St??fan


From emmanuelle.gouillart at nsup.org  Sat Jan 25 08:19:26 2014
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Sat, 25 Jan 2014 14:19:26 +0100
Subject: Non-local means denoising
In-Reply-To: <CA+JHcKSVZ1RuQqsOwOkj2OcDugt_qJ-jrO8Rj_gywzvMGC+crg@mail.gmail.com>
References: <CABDkGQkGe+b3a+XJFeSROm1p1vUGEx+_pajCEMmwcGa43EgbWA@mail.gmail.com>
 <CAJU8MvRG8ix2RWZcFCJjDu0KxxEByZONnQcPicaXVV5cbRmXMQ@mail.gmail.com>
 <52E0E540.6090309@googlemail.com>
 <20140123115503.GB16463@gmail.com>
 <52E139D9.9000102@googlemail.com>
 <20140123162659.GA29205@phare.normalesup.org>
 <CA+JHcKQtwBRjjKD3wacGvoQ3hbDAf9BZZXVpofeG-kT8vD96xg@mail.gmail.com>
 <20140125112307.GA26044@phare.normalesup.org>
 <CA+JHcKSVZ1RuQqsOwOkj2OcDugt_qJ-jrO8Rj_gywzvMGC+crg@mail.gmail.com>
Message-ID: <20140125131926.GB26044@phare.normalesup.org>


> I'm personally very interested, yes! Regarding scikit-image, I'm not sure
> whether St??fan would be happy to go down the GPU route (and CUDA more
> specifically), but my feeling is that a very large chunk of scientific
> computing is going in that direction, so it would be good to have at least an
> optional dependency there...

Sorry, I must have been unclear; I was not suggesting to include the CUDA
code in scikit-image, I don't think cuda is mature and flexible enough
yet to allow for an easily maintanable + cross-platform integration in
scikit-image. However since I know that you work with large data, I
could put this pycuda code in another repository so that it could be used
by other people than my team.

Emma


From stefan at sun.ac.za  Sat Jan 25 13:44:25 2014
From: stefan at sun.ac.za (=?iso-8859-1?Q?St=E9fan?= van der Walt)
Date: Sat, 25 Jan 2014 19:44:25 +0100
Subject: Non-local means denoising
In-Reply-To: <CA+JHcKSVZ1RuQqsOwOkj2OcDugt_qJ-jrO8Rj_gywzvMGC+crg@mail.gmail.com>
References: <CABDkGQkGe+b3a+XJFeSROm1p1vUGEx+_pajCEMmwcGa43EgbWA@mail.gmail.com>
 <CAJU8MvRG8ix2RWZcFCJjDu0KxxEByZONnQcPicaXVV5cbRmXMQ@mail.gmail.com>
 <52E0E540.6090309@googlemail.com>
 <20140123115503.GB16463@gmail.com>
 <52E139D9.9000102@googlemail.com>
 <20140123162659.GA29205@phare.normalesup.org>
 <CA+JHcKQtwBRjjKD3wacGvoQ3hbDAf9BZZXVpofeG-kT8vD96xg@mail.gmail.com>
 <20140125112307.GA26044@phare.normalesup.org>
 <CA+JHcKSVZ1RuQqsOwOkj2OcDugt_qJ-jrO8Rj_gywzvMGC+crg@mail.gmail.com>
Message-ID: <20140125184425.GA26658@gmail.com>

On Sat, 25 Jan 2014 23:49:29 +1100, Juan Nunez-Iglesias wrote:
> I'm personally very interested, yes! Regarding scikit-image, I'm not sure
> whether St??fan would be happy to go down the GPU route (and CUDA more
> specifically), but my feeling is that a very large chunk of scientific
> computing is going in that direction, so it would be good to have at least
> an optional dependency there...

We've considered this before (recall discussions about multiple backends), but
in the end found that it is not viable to maintain multiple implementations of
the same code (at least not for our small team).

I am putting my bets on tools like Numba, Parakeet, etc. to save us from
Python's slowness.

St??fan



From jni.soma at gmail.com  Sat Jan 25 07:49:29 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Sat, 25 Jan 2014 23:49:29 +1100
Subject: Non-local means denoising
In-Reply-To: <20140125112307.GA26044@phare.normalesup.org>
References: <CABDkGQkGe+b3a+XJFeSROm1p1vUGEx+_pajCEMmwcGa43EgbWA@mail.gmail.com>
 <CAJU8MvRG8ix2RWZcFCJjDu0KxxEByZONnQcPicaXVV5cbRmXMQ@mail.gmail.com>
 <52E0E540.6090309@googlemail.com> <20140123115503.GB16463@gmail.com>
 <52E139D9.9000102@googlemail.com> <20140123162659.GA29205@phare.normalesup.org>
 <CA+JHcKQtwBRjjKD3wacGvoQ3hbDAf9BZZXVpofeG-kT8vD96xg@mail.gmail.com> <20140125112307.GA26044@phare.normalesup.org>
Message-ID: <CA+JHcKSVZ1RuQqsOwOkj2OcDugt_qJ-jrO8Rj_gywzvMGC+crg@mail.gmail.com>

Ah, cool, congratulations on the new position then!

I'm personally very interested, yes! Regarding scikit-image, I'm not sure
whether St?fan would be happy to go down the GPU route (and CUDA more
specifically), but my feeling is that a very large chunk of scientific
computing is going in that direction, so it would be good to have at least
an optional dependency there...

Juan.



On Sat, Jan 25, 2014 at 10:23 PM, Emmanuelle Gouillart <
emmanuelle.gouillart at nsup.org> wrote:

> Hi Juan,
>
> yes, it's been a long time :-) (I took a new job in September and it's
> been pretty hectic since then!).
>
> My implementation is indeed 3-D. I'll start working on a PR this week-end
> then! For 3-D images the code is pretty slow due to the large size of the
> data, but I also have a pycuda + cuda implementation written by my PhD
> student William. You'll tell me if you're interested!
>
> Cheers,
> Emmanuelle
>
> On Fri, Jan 24, 2014 at 11:46:19AM +1100, Juan Nunez-Iglesias wrote:
> > Haha, hi Emmanuelle, long time no see! ;) I think your interjection in
> this
> > thread is rather priceless. =D Is your implementation 3D? Either way, if
> you
> > submit a WIP PR, I might be tempted to use some cycles to help out. =)
>
>
>
> > On Fri, Jan 24, 2014 at 3:26 AM, Emmanuelle Gouillart <
> > emmanuelle.gouillart at nsup.org> wrote:
>
> >     Hi,
>
> >     it happens that I have an implementation of NL-means (implemented in
> C +
> >     cython). I have to clean it a little and then I can send it to the
> list.
> >     It would actually be interesting to convert it to pure Cython for
> further
> >     maintanability.
>
> >     Cheers,
> >     Emmanuelle
>
> >     On Thu, Jan 23, 2014 at 03:48:41PM +0000, Kevin Keraudren wrote:
> >     > I just listed these implementations as I recently searched for a
> C++
> >     > implementation.
> >     > Unfortunately, I cannot volunteer to work on this and I do not know
> >     > anyone who already worked on this topic...
> >     > Kind regards,
> >     > Kevin
>
>
>
> >     > Le 23/01/2014 11:55, St?fan van der Walt a ?crit :
> >     > >Hi Kevin
>
> >     > >On Thu, 23 Jan 2014 09:47:44 +0000, Kevin Keraudren wrote:
> >     > >>Here are some implementations of Non-Local Means Denoising you
> might
> >     > >>be interested in for reference/comparison:
> >     > >Thanks for these informative links.  Are you interested in
> working on
> >     nlmeans,
> >     > >or do you know of someone who would be able to help us review the
> code
> >     once it
> >     > >is written?
>
> >     > >Thanks
> >     > >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  Sat Jan 25 19:01:49 2014
From: stefan at sun.ac.za (=?iso-8859-1?Q?St=E9fan?= van der Walt)
Date: Sun, 26 Jan 2014 01:01:49 +0100
Subject: Non-local means denoising
In-Reply-To: <CA+JHcKQkL6-e=UWCx1RqkkmkVzJt9nD1XC2RORFDd_cdTc+VGA@mail.gmail.com>
References: <CAJU8MvRG8ix2RWZcFCJjDu0KxxEByZONnQcPicaXVV5cbRmXMQ@mail.gmail.com>
 <52E0E540.6090309@googlemail.com>
 <20140123115503.GB16463@gmail.com>
 <52E139D9.9000102@googlemail.com>
 <20140123162659.GA29205@phare.normalesup.org>
 <CA+JHcKQtwBRjjKD3wacGvoQ3hbDAf9BZZXVpofeG-kT8vD96xg@mail.gmail.com>
 <20140125112307.GA26044@phare.normalesup.org>
 <CA+JHcKSVZ1RuQqsOwOkj2OcDugt_qJ-jrO8Rj_gywzvMGC+crg@mail.gmail.com>
 <20140125184425.GA26658@gmail.com>
 <CA+JHcKQkL6-e=UWCx1RqkkmkVzJt9nD1XC2RORFDd_cdTc+VGA@mail.gmail.com>
Message-ID: <20140126000149.GA29586@gmail.com>

On Sun, 26 Jan 2014 10:52:46 +1100, Juan Nunez-Iglesias wrote:
> I do remember these, but it's a worthwhile conversation to bring up every
> so often as tools mature and more people contribute. To be honest I know
> next to nothing about CUDA and GPU programming, I just see the success
> stories fly by. =)

Those are the only stories people like to tell, but they forget to mention
that GPU implementations often need to be tweaked for each platform--and
tweaks can be fairly extensive, including buffer and pool sizes, algorithm
configurations etc.  It is not the kind of complication I would like to deal
with--but, like you say, it is good to evaluate this from time to time.

St??fan



From jni.soma at gmail.com  Sat Jan 25 09:53:20 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Sun, 26 Jan 2014 01:53:20 +1100
Subject: Non-local means denoising
In-Reply-To: <20140125131926.GB26044@phare.normalesup.org>
References: <CABDkGQkGe+b3a+XJFeSROm1p1vUGEx+_pajCEMmwcGa43EgbWA@mail.gmail.com>
 <CAJU8MvRG8ix2RWZcFCJjDu0KxxEByZONnQcPicaXVV5cbRmXMQ@mail.gmail.com>
 <52E0E540.6090309@googlemail.com> <20140123115503.GB16463@gmail.com>
 <52E139D9.9000102@googlemail.com> <20140123162659.GA29205@phare.normalesup.org>
 <CA+JHcKQtwBRjjKD3wacGvoQ3hbDAf9BZZXVpofeG-kT8vD96xg@mail.gmail.com>
 <20140125112307.GA26044@phare.normalesup.org> <CA+JHcKSVZ1RuQqsOwOkj2OcDugt_qJ-jrO8Rj_gywzvMGC+crg@mail.gmail.com>
 <20140125131926.GB26044@phare.normalesup.org>
Message-ID: <CA+JHcKRUnAAdcAtmxX9MnYX2ysrPcg_TeTK64V4mtH-aT7mtbQ@mail.gmail.com>

On Sun, Jan 26, 2014 at 12:19 AM, Emmanuelle Gouillart <
emmanuelle.gouillart at nsup.org> wrote:
>
> Sorry, I must have been unclear;


You actually weren't, I just took a leap. =)


> However since I know that you work with large data, I
> could put this pycuda code in another repository so that it could be used
> by other people than my team.
>

That would be excellent! =)

Juan.
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From google at terre-adelie.org  Sun Jan 26 02:22:11 2014
From: google at terre-adelie.org (Jerome Kieffer)
Date: Sun, 26 Jan 2014 08:22:11 +0100
Subject: Non-local means denoising
In-Reply-To: <20140126000149.GA29586@gmail.com>
References: <CAJU8MvRG8ix2RWZcFCJjDu0KxxEByZONnQcPicaXVV5cbRmXMQ@mail.gmail.com>
	<52E0E540.6090309@googlemail.com>
	<20140123115503.GB16463@gmail.com>
	<52E139D9.9000102@googlemail.com>
	<20140123162659.GA29205@phare.normalesup.org>
	<CA+JHcKQtwBRjjKD3wacGvoQ3hbDAf9BZZXVpofeG-kT8vD96xg@mail.gmail.com>
	<20140125112307.GA26044@phare.normalesup.org>
	<CA+JHcKSVZ1RuQqsOwOkj2OcDugt_qJ-jrO8Rj_gywzvMGC+crg@mail.gmail.com>
	<20140125184425.GA26658@gmail.com>
	<CA+JHcKQkL6-e=UWCx1RqkkmkVzJt9nD1XC2RORFDd_cdTc+VGA@mail.gmail.com>
	<20140126000149.GA29586@gmail.com>
Message-ID: <20140126082211.074920da.google@terre-adelie.org>

On Sun, 26 Jan 2014 01:01:49 +0100
St?fan van der Walt <stefan at sun.ac.za> wrote:

> On Sun, 26 Jan 2014 10:52:46 +1100, Juan Nunez-Iglesias wrote:
> > I do remember these, but it's a worthwhile conversation to bring up every
> > so often as tools mature and more people contribute. To be honest I know
> > next to nothing about CUDA and GPU programming, I just see the success
> > stories fly by. =)
> 
> Those are the only stories people like to tell, but they forget to mention
> that GPU implementations often need to be tweaked for each platform--and
> tweaks can be fairly extensive, including buffer and pool sizes, algorithm
> configurations etc.  It is not the kind of complication I would like to deal
> with--but, like you say, it is good to evaluate this from time to time.

Hi Stefan,

While I can confirm that best performances can only got with optimized
kernels, our OpenCL implementation of SIFT is able to chose the right
implementation on runtime depending on the architecture and on the
compute-capabilities of the selected device ... 

Moreover, devices are becoming more and more clever (since Fermi, there
is a memory cache !)

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


From stefan at sun.ac.za  Sun Jan 26 03:06:49 2014
From: stefan at sun.ac.za (=?iso-8859-1?Q?St=E9fan?= van der Walt)
Date: Sun, 26 Jan 2014 09:06:49 +0100
Subject: Non-local means denoising
In-Reply-To: <20140126082211.074920da.google@terre-adelie.org>
References: <20140123115503.GB16463@gmail.com>
 <52E139D9.9000102@googlemail.com>
 <20140123162659.GA29205@phare.normalesup.org>
 <CA+JHcKQtwBRjjKD3wacGvoQ3hbDAf9BZZXVpofeG-kT8vD96xg@mail.gmail.com>
 <20140125112307.GA26044@phare.normalesup.org>
 <CA+JHcKSVZ1RuQqsOwOkj2OcDugt_qJ-jrO8Rj_gywzvMGC+crg@mail.gmail.com>
 <20140125184425.GA26658@gmail.com>
 <CA+JHcKQkL6-e=UWCx1RqkkmkVzJt9nD1XC2RORFDd_cdTc+VGA@mail.gmail.com>
 <20140126000149.GA29586@gmail.com>
 <20140126082211.074920da.google@terre-adelie.org>
Message-ID: <20140126080649.GA31520@gmail.com>

On Sun, 26 Jan 2014 08:22:11 +0100, Jerome Kieffer wrote:
> While I can confirm that best performances can only got with optimized
> kernels, our OpenCL implementation of SIFT is able to chose the right
> implementation on runtime depending on the architecture and on the
> compute-capabilities of the selected device ... 

As with any technology, you require the appropriate technicians for
maintenance.  We do not have particularly strong GPU abilities in our group,
and I don't like the idea of "outsourcing" scikit-image maintenance until the
developers can all catch up.

St??fan


From jni.soma at gmail.com  Sat Jan 25 18:52:46 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Sun, 26 Jan 2014 10:52:46 +1100
Subject: Non-local means denoising
In-Reply-To: <20140125184425.GA26658@gmail.com>
References: <CABDkGQkGe+b3a+XJFeSROm1p1vUGEx+_pajCEMmwcGa43EgbWA@mail.gmail.com>
 <CAJU8MvRG8ix2RWZcFCJjDu0KxxEByZONnQcPicaXVV5cbRmXMQ@mail.gmail.com>
 <52E0E540.6090309@googlemail.com> <20140123115503.GB16463@gmail.com>
 <52E139D9.9000102@googlemail.com> <20140123162659.GA29205@phare.normalesup.org>
 <CA+JHcKQtwBRjjKD3wacGvoQ3hbDAf9BZZXVpofeG-kT8vD96xg@mail.gmail.com>
 <20140125112307.GA26044@phare.normalesup.org> <CA+JHcKSVZ1RuQqsOwOkj2OcDugt_qJ-jrO8Rj_gywzvMGC+crg@mail.gmail.com>
 <20140125184425.GA26658@gmail.com>
Message-ID: <CA+JHcKQkL6-e=UWCx1RqkkmkVzJt9nD1XC2RORFDd_cdTc+VGA@mail.gmail.com>

On Sun, Jan 26, 2014 at 5:44 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> We've considered this before (recall discussions about multiple backends),
> but
>  in the end found that it is not viable to maintain multiple
> implementations of
> the same code (at least not for our small team).
>

I do remember these, but it's a worthwhile conversation to bring up every
so often as tools mature and more people contribute. To be honest I know
next to nothing about CUDA and GPU programming, I just see the success
stories fly by. =)

I am putting my bets on tools like Numba, Parakeet, etc. to save us from
> Python's slowness.
>

Yeah these are pretty exciting. =)

Juan.
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From jsch at demuc.de  Mon Jan 27 09:54:17 2014
From: jsch at demuc.de (=?ISO-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Mon, 27 Jan 2014 09:54:17 -0500
Subject: imsave PIL quality for JPGs
Message-ID: <CAFTxfLmnuqmT1ad7sh23ZxbtTpvjb4jdJtn=WCXEGpSX87U=jA@mail.gmail.com>

Hi everyone,

Does anyone know how to set the quality of JPG images (the PIL plugin
does not expose the "quality" parameter)? Is there another plugin that
lets one adjust it?

Thanks, Johannes


From jsch at demuc.de  Mon Jan 27 10:03:50 2014
From: jsch at demuc.de (=?ISO-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Mon, 27 Jan 2014 10:03:50 -0500
Subject: imsave PIL quality for JPGs
In-Reply-To: <20140127150023.GC14839@gmail.com>
References: <CAFTxfLmnuqmT1ad7sh23ZxbtTpvjb4jdJtn=WCXEGpSX87U=jA@mail.gmail.com>
	<20140127150023.GC14839@gmail.com>
Message-ID: <CAFTxfLk5F15HdToZ_VZG4daHF5Ppa2f5w2GZKR=UKJ9EN1cP5A@mail.gmail.com>

Great, thanks a lot!

On Mon, Jan 27, 2014 at 10:00 AM, St?fan van der Walt <stefan at sun.ac.za> wrote:
> On Mon, 27 Jan 2014 09:54:17 -0500, Johannes Sch?nberger wrote:
>> Does anyone know how to set the quality of JPG images (the PIL plugin
>> does not expose the "quality" parameter)? Is there another plugin that
>> lets one adjust it?
>
> A bit arcane, but here goes:
>
> from skimage.io._plugins import freeimage_plugin
> freeimage_plugin.write(array, filename, flags=freeimage_plugin.IO_FLAGS.JPEG_QUALITYSUPERB)
>
> 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.


From stefan at sun.ac.za  Mon Jan 27 05:24:48 2014
From: stefan at sun.ac.za (=?iso-8859-1?Q?St=E9fan?= van der Walt)
Date: Mon, 27 Jan 2014 11:24:48 +0100
Subject: Access to an OSX machine
Message-ID: <20140127102448.GB11711@gmail.com>

Hi everyone

In trying to solve [0], we need access to OSX.  Does someone have a server we
can use for testing?

Thanks,
St??fan

[0] https://github.com/scikit-image/scikit-image/issues/835



From hughesadam87 at gmail.com  Mon Jan 27 15:53:49 2014
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Mon, 27 Jan 2014 12:53:49 -0800 (PST)
Subject: scikit-image paper
In-Reply-To: <20140125000139.GC23850@gmail.com>
References: <CAEym_Hpj8X2E9aw-Z37Am_2hJouci0eY4zUi=cP1b13bjmg5JA@mail.gmail.com>
 <CAEym_HqMxaNb9KspKeC9KivcuQnFxw0bTqjxaWPut=G9bvt0DQ@mail.gmail.com>
 <CABDkGQnS51Zb=63QSHoz6U8=MYuVWML_PCnOomvrMn2gSdk1=w@mail.gmail.com>
 <CAEym_HqD3DWpnfEcr8rXq_=zhatHHgfrkeakz_dN8zKCDaA2uQ@mail.gmail.com>
 <900F93A6-208D-418E-A873-CF3535707F94@demuc.de>
 <CABDkGQkhcoYzniy0bidoFvha7mVPcP1kTRJjqdZTPUf8PCGJbQ@mail.gmail.com>
 <58CA473E-BA50-4998-8F5F-781D617E01F5@demuc.de>
 <CA+JHcKRPfwrR09+QqmiVgrh=m4Hrg8AhswOPKMzxNmWHM3o=9g@mail.gmail.com>
 <CAFTxfL=VV62-HiDWLaeLBUR_1RBp1eK8FQwF=NJrqeJ+nv1FEw@mail.gmail.com>
 <52E2EFCD.5020000@sciunto.org>
 <20140125000139.GC23850@gmail.com>
Message-ID: <20cc63c8-2ebf-4c64-a9de-184afe5d5042@googlegroups.com>

Hi guys,

Just a curiosity following up on the notebook question:  Is there a 
standard practice to submitting journal articles with iPython notebooks? 
 We were looking to do the same with a few papers in our lab and wondered 
if this was common yet, if there were guidelines set forth by the journals 
to this regard, and if only certain journals accepted notebook as 
accompanying materials.

On Friday, January 24, 2014 7:01:39 PM UTC-5, Stefan van der Walt wrote:
>
> On Fri, 24 Jan 2014 17:57:17 -0500, Fran?ois Boulogne wrote: 
> > I think we should decide where and how we write codes, in the text with 
> > a snippet style and/or at the end with a full code. 
> > I don't know how it depends on the journal where you want to submit the 
> > paper. Have you reached a consensus about that? 
>
> If you want to show something specific, e.g. the simplicity of building a 
> pipeline, for which you need just 3-5 lines of code, then it should 
> probably 
> go inline.  If it is a longer snippet, attach it at the end or perhaps 
> think 
> whether it should be included at all. 
>
> We can very easily write an IPython notebook and simply reference that 
> from 
> the paper for examples. 
>
> St?fan 
>
>
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From stefan at sun.ac.za  Mon Jan 27 10:00:23 2014
From: stefan at sun.ac.za (=?iso-8859-1?Q?St=E9fan?= van der Walt)
Date: Mon, 27 Jan 2014 16:00:23 +0100
Subject: imsave PIL quality for JPGs
In-Reply-To: <CAFTxfLmnuqmT1ad7sh23ZxbtTpvjb4jdJtn=WCXEGpSX87U=jA@mail.gmail.com>
References: <CAFTxfLmnuqmT1ad7sh23ZxbtTpvjb4jdJtn=WCXEGpSX87U=jA@mail.gmail.com>
Message-ID: <20140127150023.GC14839@gmail.com>

On Mon, 27 Jan 2014 09:54:17 -0500, Johannes Sch??nberger wrote:
> Does anyone know how to set the quality of JPG images (the PIL plugin
> does not expose the "quality" parameter)? Is there another plugin that
> lets one adjust it?

A bit arcane, but here goes:

from skimage.io._plugins import freeimage_plugin
freeimage_plugin.write(array, filename, flags=freeimage_plugin.IO_FLAGS.JPEG_QUALITYSUPERB)

St??fan



From deil.christoph at googlemail.com  Mon Jan 27 10:13:21 2014
From: deil.christoph at googlemail.com (Christoph Deil)
Date: Mon, 27 Jan 2014 16:13:21 +0100
Subject: Access to an OSX machine
In-Reply-To: <20140127102448.GB11711@gmail.com>
References: <20140127102448.GB11711@gmail.com>
Message-ID: <F4DBAD82-BAB8-440D-B07B-51954CC75DBF@gmail.com>


On 27 Jan 2014, at 11:24, St?fan van der Walt <stefan at sun.ac.za> wrote:

> Hi everyone
> 
> In trying to solve [0], we need access to OSX.  Does someone have a server we
> can use for testing?

Hi Stefan,

there is a numfocus-sponsored Mac at ci.scipy.org running the latest OS X 10.9 Mavericks.

I can make an account for ssh access for any Python open source tools developer for debugging / testing.

Please send me an email offline if you?d like an account and mention the username you?d like.

Christoph

> 
> Thanks,
> St?fan
> 
> [0] https://github.com/scikit-image/scikit-image/issues/835
> 
> -- 
> 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  Mon Jan 27 11:39:56 2014
From: stefan at sun.ac.za (=?iso-8859-1?Q?St=E9fan?= van der Walt)
Date: Mon, 27 Jan 2014 17:39:56 +0100
Subject: Access to an OSX machine
In-Reply-To: <F4DBAD82-BAB8-440D-B07B-51954CC75DBF@gmail.com>
References: <20140127102448.GB11711@gmail.com>
 <F4DBAD82-BAB8-440D-B07B-51954CC75DBF@gmail.com>
Message-ID: <20140127163956.GA17237@gmail.com>

Hi Christoph

On Mon, 27 Jan 2014 16:13:21 +0100, Christoph Deil wrote:
> there is a numfocus-sponsored Mac at ci.scipy.org running the latest OS X 10.9 Mavericks.
> 
> I can make an account for ssh access for any Python open source tools developer for debugging / testing.

That would be great--thank you!

username: skimage

St??fan


From stefan at sun.ac.za  Mon Jan 27 18:03:19 2014
From: stefan at sun.ac.za (=?iso-8859-1?Q?St=E9fan?= van der Walt)
Date: Tue, 28 Jan 2014 00:03:19 +0100
Subject: scikit-image paper
In-Reply-To: <20cc63c8-2ebf-4c64-a9de-184afe5d5042@googlegroups.com>
References: <CABDkGQnS51Zb=63QSHoz6U8=MYuVWML_PCnOomvrMn2gSdk1=w@mail.gmail.com>
 <CAEym_HqD3DWpnfEcr8rXq_=zhatHHgfrkeakz_dN8zKCDaA2uQ@mail.gmail.com>
 <900F93A6-208D-418E-A873-CF3535707F94@demuc.de>
 <CABDkGQkhcoYzniy0bidoFvha7mVPcP1kTRJjqdZTPUf8PCGJbQ@mail.gmail.com>
 <58CA473E-BA50-4998-8F5F-781D617E01F5@demuc.de>
 <CA+JHcKRPfwrR09+QqmiVgrh=m4Hrg8AhswOPKMzxNmWHM3o=9g@mail.gmail.com>
 <CAFTxfL=VV62-HiDWLaeLBUR_1RBp1eK8FQwF=NJrqeJ+nv1FEw@mail.gmail.com>
 <52E2EFCD.5020000@sciunto.org>
 <20140125000139.GC23850@gmail.com>
 <20cc63c8-2ebf-4c64-a9de-184afe5d5042@googlegroups.com>
Message-ID: <20140127230319.GA22634@gmail.com>

Hi Adam

On Mon, 27 Jan 2014 12:53:49 -0800, Adam Hughes wrote:
> Just a curiosity following up on the notebook question:  Is there a 
> standard practice to submitting journal articles with iPython notebooks? 
>  We were looking to do the same with a few papers in our lab and wondered 
> if this was common yet, if there were guidelines set forth by the journals 
> to this regard, and if only certain journals accepted notebook as 
> accompanying materials.

Perhaps have a chat to Konrad Hinsen about his ActivePapers project:

http://python.6.x6.nabble.com/Interfacing-ActivePapers-with-IPython-notebooks-td5044882.html

Regards
St??fan


From jsch at demuc.de  Tue Jan 28 07:32:20 2014
From: jsch at demuc.de (=?ISO-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Tue, 28 Jan 2014 07:32:20 -0500
Subject: Examples relicensing proposal
In-Reply-To: <CABDkGQnb4izF5WSsvnZ8UcgnZdtVR+MoD7vny9PKEZRwBBz_VA@mail.gmail.com>
References: <CABDkGQnb4izF5WSsvnZ8UcgnZdtVR+MoD7vny9PKEZRwBBz_VA@mail.gmail.com>
Message-ID: <CAFTxfLnvb9hHMCUPDgnNK5uOp2sTKJxC_oVv8aa_DrcFUC2r8A@mail.gmail.com>

Hi Stefan,

Basically I am OK with this, but doesn't that mean that we have to ask
every single person who ever contributed to the examples section for
permission?

What's the effort to include a small BSD license footnote to a slide
opposed to asking all these people and having two different licenses
in the project?

On Tue, Jan 28, 2014 at 6:51 AM, St?fan van der Walt <stefan at sun.ac.za> wrote:
> Hi, folks
>
> I just realised that having our examples licensed under BSD
> technically means that one has to display the license even in slide
> shows.  I'd like to make it as easy as possible for people to
> advertise our tools, so could we consider relicensing those as CC0?
>
> 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.
> For more options, visit https://groups.google.com/groups/opt_out.


From stefan at sun.ac.za  Tue Jan 28 06:51:56 2014
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 28 Jan 2014 12:51:56 +0100
Subject: Examples relicensing proposal
Message-ID: <CABDkGQnb4izF5WSsvnZ8UcgnZdtVR+MoD7vny9PKEZRwBBz_VA@mail.gmail.com>

Hi, folks

I just realised that having our examples licensed under BSD
technically means that one has to display the license even in slide
shows.  I'd like to make it as easy as possible for people to
advertise our tools, so could we consider relicensing those as CC0?

Regards
St?fan


From jturner at gemini.edu  Tue Jan 28 12:12:26 2014
From: jturner at gemini.edu (James Turner)
Date: Tue, 28 Jan 2014 14:12:26 -0300
Subject: Examples relicensing proposal
In-Reply-To: <CABDkGQnvCi01-0mQLqLZcbLWKkf2F8772yaC_kXWV0vGFHwAWw@mail.gmail.com>
References: <CABDkGQnb4izF5WSsvnZ8UcgnZdtVR+MoD7vny9PKEZRwBBz_VA@mail.gmail.com> <CAFTxfLnvb9hHMCUPDgnNK5uOp2sTKJxC_oVv8aa_DrcFUC2r8A@mail.gmail.com> <CA+JHcKTQMXqrHgT6Bc84SA1M22H3mXS1diihDP6gbMmF=Bx7Qw@mail.gmail.com> <CABDkGQnvCi01-0mQLqLZcbLWKkf2F8772yaC_kXWV0vGFHwAWw@mail.gmail.com>
Message-ID: <52E7E4FA.1020104@gemini.edu>

I suppose you could do like Google etc. and provide a means for
people to opt out if they don't like their contributions being
distributed under CC? I'm not sure how legally sound it is in
theory but I'd think it ought to pass any test of reasonableness
and it shifts the inertia to where it belongs :-).

Cheers,

James.


On 28/01/14 13:54, St??fan van der Walt wrote:
> On Tue, Jan 28, 2014 at 1:42 PM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
>> Having read CC0, I'd be ok with the examples being under that license. I'll
>> let you decide whether you prefer the dual-license complexity.
>
> I asked the scikit-learn folks as well, and they're saying something
> varying between "fair use" and "in the spirit of open source" , which
> I think comes down to "we don't really care".  Of course, I don't care
> either other than wanting to make sure people feel very free to use,
> modify and show our examples, without caring too much about the
> license.  They'll probably do that anyway...


From stefan at sun.ac.za  Tue Jan 28 11:54:47 2014
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 28 Jan 2014 17:54:47 +0100
Subject: Examples relicensing proposal
In-Reply-To: <CA+JHcKTQMXqrHgT6Bc84SA1M22H3mXS1diihDP6gbMmF=Bx7Qw@mail.gmail.com>
References: <CABDkGQnb4izF5WSsvnZ8UcgnZdtVR+MoD7vny9PKEZRwBBz_VA@mail.gmail.com>
 <CAFTxfLnvb9hHMCUPDgnNK5uOp2sTKJxC_oVv8aa_DrcFUC2r8A@mail.gmail.com> <CA+JHcKTQMXqrHgT6Bc84SA1M22H3mXS1diihDP6gbMmF=Bx7Qw@mail.gmail.com>
Message-ID: <CABDkGQnvCi01-0mQLqLZcbLWKkf2F8772yaC_kXWV0vGFHwAWw@mail.gmail.com>

On Tue, Jan 28, 2014 at 1:42 PM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> Having read CC0, I'd be ok with the examples being under that license. I'll
> let you decide whether you prefer the dual-license complexity.

I asked the scikit-learn folks as well, and they're saying something
varying between "fair use" and "in the spirit of open source" , which
I think comes down to "we don't really care".  Of course, I don't care
either other than wanting to make sure people feel very free to use,
modify and show our examples, without caring too much about the
license.  They'll probably do that anyway...

St?fan


From stefan at sun.ac.za  Tue Jan 28 12:18:29 2014
From: stefan at sun.ac.za (=?iso-8859-1?Q?St=E9fan?= van der Walt)
Date: Tue, 28 Jan 2014 18:18:29 +0100
Subject: Examples relicensing proposal
In-Reply-To: <52E7E4FA.1020104@gemini.edu>
References: <CABDkGQnb4izF5WSsvnZ8UcgnZdtVR+MoD7vny9PKEZRwBBz_VA@mail.gmail.com>
 <CAFTxfLnvb9hHMCUPDgnNK5uOp2sTKJxC_oVv8aa_DrcFUC2r8A@mail.gmail.com>
 <CA+JHcKTQMXqrHgT6Bc84SA1M22H3mXS1diihDP6gbMmF=Bx7Qw@mail.gmail.com>
 <CABDkGQnvCi01-0mQLqLZcbLWKkf2F8772yaC_kXWV0vGFHwAWw@mail.gmail.com>
 <52E7E4FA.1020104@gemini.edu>
Message-ID: <20140128171829.GG4803@gmail.com>

On Tue, 28 Jan 2014 14:12:26 -0300, James Turner wrote:
> I suppose you could do like Google etc. and provide a means for
> people to opt out if they don't like their contributions being
> distributed under CC? I'm not sure how legally sound it is in
> theory but I'd think it ought to pass any test of reasonableness
> and it shifts the inertia to where it belongs :-).

One can do that with future contributors, but there are those that already
contributed under terms of the BSD license.

I'm not sure how fluid the term "scikit-image team" is...

St??fan



From jni.soma at gmail.com  Tue Jan 28 07:42:50 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Tue, 28 Jan 2014 23:42:50 +1100
Subject: Examples relicensing proposal
In-Reply-To: <CAFTxfLnvb9hHMCUPDgnNK5uOp2sTKJxC_oVv8aa_DrcFUC2r8A@mail.gmail.com>
References: <CABDkGQnb4izF5WSsvnZ8UcgnZdtVR+MoD7vny9PKEZRwBBz_VA@mail.gmail.com>
 <CAFTxfLnvb9hHMCUPDgnNK5uOp2sTKJxC_oVv8aa_DrcFUC2r8A@mail.gmail.com>
Message-ID: <CA+JHcKTQMXqrHgT6Bc84SA1M22H3mXS1diihDP6gbMmF=Bx7Qw@mail.gmail.com>

Sheesh. Licensing is hard. =)

Having read CC0, I'd be ok with the examples being under that license. I'll
let you decide whether you prefer the dual-license complexity.

Juan.



On Tue, Jan 28, 2014 at 11:32 PM, Johannes Sch?nberger <jsch at demuc.de>wrote:

> Hi Stefan,
>
> Basically I am OK with this, but doesn't that mean that we have to ask
> every single person who ever contributed to the examples section for
> permission?
>
> What's the effort to include a small BSD license footnote to a slide
> opposed to asking all these people and having two different licenses
> in the project?
>
> On Tue, Jan 28, 2014 at 6:51 AM, St?fan van der Walt <stefan at sun.ac.za>
> wrote:
> > Hi, folks
> >
> > I just realised that having our examples licensed under BSD
> > technically means that one has to display the license even in slide
> > shows.  I'd like to make it as easy as possible for people to
> > advertise our tools, so could we consider relicensing those as CC0?
> >
> > 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.
> > 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.
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From jni.soma at gmail.com  Tue Jan 28 07:48:59 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Tue, 28 Jan 2014 23:48:59 +1100
Subject: scikit-image paper
In-Reply-To: <20140127230319.GA22634@gmail.com>
References: <CABDkGQnS51Zb=63QSHoz6U8=MYuVWML_PCnOomvrMn2gSdk1=w@mail.gmail.com>
 <CAEym_HqD3DWpnfEcr8rXq_=zhatHHgfrkeakz_dN8zKCDaA2uQ@mail.gmail.com>
 <900F93A6-208D-418E-A873-CF3535707F94@demuc.de> <CABDkGQkhcoYzniy0bidoFvha7mVPcP1kTRJjqdZTPUf8PCGJbQ@mail.gmail.com>
 <58CA473E-BA50-4998-8F5F-781D617E01F5@demuc.de> <CA+JHcKRPfwrR09+QqmiVgrh=m4Hrg8AhswOPKMzxNmWHM3o=9g@mail.gmail.com>
 <CAFTxfL=VV62-HiDWLaeLBUR_1RBp1eK8FQwF=NJrqeJ+nv1FEw@mail.gmail.com>
 <52E2EFCD.5020000@sciunto.org> <20140125000139.GC23850@gmail.com>
 <20cc63c8-2ebf-4c64-a9de-184afe5d5042@googlegroups.com> <20140127230319.GA22634@gmail.com>
Message-ID: <CA+JHcKSPD_8D2n_-TSWJYL4qvK4u44g3OV-BKCOfgniwOX4=8w@mail.gmail.com>

Hi all,

Although we need a paper before we need to find a home for it, I came
across this blog post from PeerJ, which appears to be moving up in the
world! Also, they apparently accept latex submissions, even if they don't
provide a template.
http://blog.peerj.com/post/74392709695/two-reviews-of-peerj

Just thought I'd add the journal to the pile.

Juan.



On Tue, Jan 28, 2014 at 10:03 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> Hi Adam
>
> On Mon, 27 Jan 2014 12:53:49 -0800, Adam Hughes wrote:
> > Just a curiosity following up on the notebook question:  Is there a
> > standard practice to submitting journal articles with iPython notebooks?
> >  We were looking to do the same with a few papers in our lab and wondered
> > if this was common yet, if there were guidelines set forth by the
> journals
> > to this regard, and if only certain journals accepted notebook as
> > accompanying materials.
>
> Perhaps have a chat to Konrad Hinsen about his ActivePapers project:
>
>
> http://python.6.x6.nabble.com/Interfacing-ActivePapers-with-IPython-notebooks-td5044882.html
>
> 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.
> For more options, visit https://groups.google.com/groups/opt_out.
>
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From jni.soma at gmail.com  Tue Jan 28 17:43:02 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Wed, 29 Jan 2014 09:43:02 +1100
Subject: scikit-image paper
In-Reply-To: <CA+JHcKSPD_8D2n_-TSWJYL4qvK4u44g3OV-BKCOfgniwOX4=8w@mail.gmail.com>
References: <CABDkGQnS51Zb=63QSHoz6U8=MYuVWML_PCnOomvrMn2gSdk1=w@mail.gmail.com>
 <CAEym_HqD3DWpnfEcr8rXq_=zhatHHgfrkeakz_dN8zKCDaA2uQ@mail.gmail.com>
 <900F93A6-208D-418E-A873-CF3535707F94@demuc.de> <CABDkGQkhcoYzniy0bidoFvha7mVPcP1kTRJjqdZTPUf8PCGJbQ@mail.gmail.com>
 <58CA473E-BA50-4998-8F5F-781D617E01F5@demuc.de> <CA+JHcKRPfwrR09+QqmiVgrh=m4Hrg8AhswOPKMzxNmWHM3o=9g@mail.gmail.com>
 <CAFTxfL=VV62-HiDWLaeLBUR_1RBp1eK8FQwF=NJrqeJ+nv1FEw@mail.gmail.com>
 <52E2EFCD.5020000@sciunto.org> <20140125000139.GC23850@gmail.com>
 <20cc63c8-2ebf-4c64-a9de-184afe5d5042@googlegroups.com> <20140127230319.GA22634@gmail.com>
 <CA+JHcKSPD_8D2n_-TSWJYL4qvK4u44g3OV-BKCOfgniwOX4=8w@mail.gmail.com>
Message-ID: <CA+JHcKTo1WWv77djs4GfC6wPimV9hWC1Q3eOsJHLpgq-sE+kVw@mail.gmail.com>

On Tue, Jan 28, 2014 at 11:48 PM, Juan Nunez-Iglesias <jni.soma at gmail.com>wrote:

> Also, they apparently accept latex submissions, even if they don't provide
> a template.
>

Aaaaand, on cue:
http://blog.peerj.com/post/74820148558/peerj-partners-with-writelatex
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From hughesadam87 at gmail.com  Thu Jan 30 03:10:30 2014
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Thu, 30 Jan 2014 03:10:30 -0500
Subject: Announcing an skimage-inspired project
Message-ID: <CAMHV+dB9nHTTBUD_-pceb_Qew0DVMsh9mU-b-=x6b-KoywKgWg@mail.gmail.com>

Hey everyone,

I have been working on a small project over the last month based on an idea
posted to the list last month:

https://groups.google.com/forum/#!topic/scikit-image/6LgfQLO4Jcc

In my research, we do a lot of processing of electron microscope images of
nanoparticles. While image processing is very simple in scikit-image (and
not-so-simple but still manageable when we were writing ImageJ Python
spaghetti code way back when), the post-processing always turned ad-hoc
once we started to quantify, manage and manipulate the segmented particles.
Simple masking worked to an extent, but got hard to juggle for all of the
various things we needed to do.

When I set out to tackle the "pattening/drawing" issue linked above, it
occurred to me that a fairly pythonic API for "managing particles" could be
adapted to particles returned by skimage.draw(), as well as
skimage.morphology.labels()/descriptors(). In other words, "particles" from
labeled images as well as "drawn particles" could be abstracted into a
single API. This was, in a sense, the key insight to motivate the pursuit,
and I think it paid off. The project is only possible because
skimage.draw/labels() are so intelligently built.

Except for maybe the gridding capabilities, all of the core structures are
built primarily to streamline common processing operations and are designed
to work for scikit-image, not in opposition to it. If any of the
descriptions of notebook tutorials suggest otherwise, please let me know so
that I may reword them.

Well, without further ado, here is the project, *pyparty.  *Thanks!

https://github.com/hugadams/pyparty

https://pypi.python.org/pypi
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From hughesadam87 at gmail.com  Thu Jan 30 13:48:54 2014
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Thu, 30 Jan 2014 10:48:54 -0800 (PST)
Subject: Announcing an skimage-inspired project
In-Reply-To: <20140130165859.GD16762@gmail.com>
References: <CAMHV+dB9nHTTBUD_-pceb_Qew0DVMsh9mU-b-=x6b-KoywKgWg@mail.gmail.com>
 <20140130165859.GD16762@gmail.com>
Message-ID: <9e2dda6b-74df-4876-86a1-d18981cb4f27@googlegroups.com>

Thanks Stefan.  Yes, the real world problems are always the tricky ones!

On Thursday, January 30, 2014 11:58:59 AM UTC-5, Stefan van der Walt wrote:
>
> Hi Adam 
>
> On Thu, 30 Jan 2014 03:10:30 -0500, Adam Hughes wrote: 
> > Well, without further ado, here is the project, *pyparty.  *Thanks! 
> > 
> > https://github.com/hugadams/pyparty 
>
> This looks great!  I can see you've put a lot of effort into it, 
> especially 
> those notebooks. 
>
> The only recommendation I can make is that you make your first example one 
> where you attack a real world particle problem. 
>
> Keep up the good work! 
>
> Cheers 
> St?fan 
>
>
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From stefan at sun.ac.za  Thu Jan 30 11:58:59 2014
From: stefan at sun.ac.za (=?iso-8859-1?Q?St=E9fan?= van der Walt)
Date: Thu, 30 Jan 2014 17:58:59 +0100
Subject: Announcing an skimage-inspired project
In-Reply-To: <CAMHV+dB9nHTTBUD_-pceb_Qew0DVMsh9mU-b-=x6b-KoywKgWg@mail.gmail.com>
References: <CAMHV+dB9nHTTBUD_-pceb_Qew0DVMsh9mU-b-=x6b-KoywKgWg@mail.gmail.com>
Message-ID: <20140130165859.GD16762@gmail.com>

Hi Adam

On Thu, 30 Jan 2014 03:10:30 -0500, Adam Hughes wrote:
> Well, without further ado, here is the project, *pyparty.  *Thanks!
> 
> https://github.com/hugadams/pyparty

This looks great!  I can see you've put a lot of effort into it, especially
those notebooks.

The only recommendation I can make is that you make your first example one
where you attack a real world particle problem.

Keep up the good work!

Cheers
St??fan



From aman.thakral at gmail.com  Fri Jan 31 17:15:58 2014
From: aman.thakral at gmail.com (Aman Thakral)
Date: Fri, 31 Jan 2014 14:15:58 -0800 (PST)
Subject: Help with using filter.rank.median
Message-ID: <065318cf-bbc0-4a2f-9ff3-98774934f6d2@googlegroups.com>

Hi all,

I'm currently trying to use a median filter on my data, an am getting an 
error that I can't seem to debug.

I'm taking the difference of two images (both numpy.float64), scaling them 
between -1 and 1, and trying to apply a median filter.  My image satisfies 
the conditions for being between -1 and 1 when I do the following test:

print diff.min()/dmax < -1.0 -> returns False  (LHS evals to -1.0)
print diff.max()/dmax > 1.0 -> returns False  (LHS evals to 0.663919388648)

The statement causing the error:

filtered = fltr.median(diff/dmax, selem)

where diff is my difference, and dmax is my scaling adjustment, selem is a 
disk of radius 2

This gives me the following traceback.

Traceback (most recent call last):

  File "/home/clustering.py", line 138, in image_ratio
    filtered = fltr.median(diff/dmax/2.+0.5, selem, mask=m.astype(np.bool))
  File 
"/usr/local/lib/python2.7/dist-packages/skimage/filter/rank/generic.py", 
line 369, in median
    out=out, mask=mask, shift_x=shift_x, shift_y=shift_y)
  File 
"/usr/local/lib/python2.7/dist-packages/skimage/filter/rank/generic.py", 
line 71, in _apply
    out_dtype)
  File 
"/usr/local/lib/python2.7/dist-packages/skimage/filter/rank/generic.py", 
line 34, in _handle_input
    image = img_as_ubyte(image)
  File "/usr/local/lib/python2.7/dist-packages/skimage/util/dtype.py", line 
358, in img_as_ubyte
    return convert(image, np.uint8, force_copy)
  File "/usr/local/lib/python2.7/dist-packages/skimage/util/dtype.py", line 
191, in convert
    raise ValueError("Images of type float must be between -1 and 1.")
ValueError: Images of type float must be between -1 and 1.

Has anyone else experienced this problem before? I tried searching in the 
groups, but couldn't find anything relevant.

Any help would be greatly appreciated!

Thanks,
Aman
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From jni.soma at gmail.com  Fri Jan 31 20:15:07 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Sat, 1 Feb 2014 12:15:07 +1100
Subject: Help with using filter.rank.median
In-Reply-To: <065318cf-bbc0-4a2f-9ff3-98774934f6d2@googlegroups.com>
References: <065318cf-bbc0-4a2f-9ff3-98774934f6d2@googlegroups.com>
Message-ID: <CA+JHcKTOtnKV7Ej9hh8TT+YncmKgO_=9V8MpCOcovyBGW0VPEg@mail.gmail.com>

Hi Aman,

Could you post a minimal example? I've tried the following and it seems to
work fine on my machine:

```python
>>> import numpy as np
>>> im = np.random.rand(5, 5)
>>> im[0, 0] = -1
>>> im[1, 1] = 1
>>> from skimage import morphology as mor, filter as fil
>>> selem = mor.disk(2)
>>> med = fil.rank.median(im, selem)
>>> med
array([[220, 220, 180, 216, 166],
       [220, 180, 216, 200, 200],
       [126, 180, 171, 180, 200],
       [119, 126, 155, 171, 216],
       [104, 119, 126, 171, 171]], dtype=uint8)
```

Also, please post the version of scikit-image you're using.

 But anyway, off the top of my head, no, I don't have any clear idea of
what's going wrong!

Juan.



On Sat, Feb 1, 2014 at 9:15 AM, Aman Thakral <aman.thakral at gmail.com> wrote:

> Hi all,
>
> I'm currently trying to use a median filter on my data, an am getting an
> error that I can't seem to debug.
>
> I'm taking the difference of two images (both numpy.float64), scaling them
> between -1 and 1, and trying to apply a median filter.  My image satisfies
> the conditions for being between -1 and 1 when I do the following test:
>
> print diff.min()/dmax < -1.0 -> returns False  (LHS evals to -1.0)
> print diff.max()/dmax > 1.0 -> returns False  (LHS evals to 0.663919388648)
>
> The statement causing the error:
>
> filtered = fltr.median(diff/dmax, selem)
>
> where diff is my difference, and dmax is my scaling adjustment, selem is a
> disk of radius 2
>
> This gives me the following traceback.
>
> Traceback (most recent call last):
>
>   File "/home/clustering.py", line 138, in image_ratio
>     filtered = fltr.median(diff/dmax/2.+0.5, selem, mask=m.astype(np.bool))
>   File
> "/usr/local/lib/python2.7/dist-packages/skimage/filter/rank/generic.py",
> line 369, in median
>     out=out, mask=mask, shift_x=shift_x, shift_y=shift_y)
>   File
> "/usr/local/lib/python2.7/dist-packages/skimage/filter/rank/generic.py",
> line 71, in _apply
>     out_dtype)
>   File
> "/usr/local/lib/python2.7/dist-packages/skimage/filter/rank/generic.py",
> line 34, in _handle_input
>     image = img_as_ubyte(image)
>   File "/usr/local/lib/python2.7/dist-packages/skimage/util/dtype.py",
> line 358, in img_as_ubyte
>     return convert(image, np.uint8, force_copy)
>   File "/usr/local/lib/python2.7/dist-packages/skimage/util/dtype.py",
> line 191, in convert
>     raise ValueError("Images of type float must be between -1 and 1.")
> ValueError: Images of type float must be between -1 and 1.
>
> Has anyone else experienced this problem before? I tried searching in the
> groups, but couldn't find anything relevant.
>
> Any help would be greatly appreciated!
>
> Thanks,
> Aman
>
> --
> 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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