From joel.bernier at gmail.com  Mon Dec  1 17:01:00 2014
From: joel.bernier at gmail.com (Joel Bernier)
Date: Mon, 1 Dec 2014 14:01:00 -0800 (PST)
Subject: 3d blob detection
In-Reply-To: <CA+JHcKQJyWic3wF1oEXs7AABc2FzOocVjgxUfUC_RF24RNkRPA@mail.gmail.com>
References: <b413c132-e44f-48cc-b7c3-df8b41e653a5@googlegroups.com> <CAA48SF9bEZFf0yjzmm9x5657aBFGoxvRhNqBrhmKC1G6bd_ciA@mail.gmail.com>
 <CA+JHcKQJyWic3wF1oEXs7AABc2FzOocVjgxUfUC_RF24RNkRPA@mail.gmail.com>
Message-ID: <6736739c-a13f-4a67-a17c-4f0b7a87fc81@googlegroups.com>

Thanks Juan!

On Wednesday, November 26, 2014 3:57:04 PM UTC-8, Juan Nunez-Iglesias wrote:
>
> Hi Joel,
>
> I'm the self-appointed Guardian of the of the Dimensions here at 
> scikit-image. =) This is a good idea and I will pop it near the top of the 
> list for conversion to 3D. Of course, pull requests are very welcome! If 
> you would like to try your hand at it, I'm happy to help you through any 
> hairy bits. =)
>
> Juan.
>
> On Thu, Nov 27, 2014 at 5:42 AM, Thomas Caswell <tcas... at gmail.com 
> <javascript:>> wrote:
>
>> It might be worth having a look at 
>> https://github.com/soft-matter/trackpy/pull/162
>>
>>
>> On Wed Nov 26 2014 at 1:34:54 PM Joel Bernier <joel.b... at gmail.com 
>> <javascript:>> wrote:
>>
>>> Any hope of modifying some of the tools in skimage.feature (say 
>>> blob_log() 
>>> <http://scikit-image.org/docs/dev/api/skimage.feature.html#skimage.feature.blob_log>) 
>>> to handle 3d images?  I have a good application in the really of 
>>> processing X-rya diffraction data?
>>>
>>> -J
>>>
>>> -- 
>>> You received this message because you are subscribed to the Google 
>>> Groups "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send 
>>> an email to scikit-image... at googlegroups.com <javascript:>.
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>  -- 
>> You received this message because you are subscribed to the Google Groups 
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an 
>> email to scikit-image... at googlegroups.com <javascript:>.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>
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From julien.derr at gmail.com  Thu Dec  4 13:05:32 2014
From: julien.derr at gmail.com (Julien Derr)
Date: Thu, 4 Dec 2014 10:05:32 -0800 (PST)
Subject: Is there a problem with the function points_in_poly ?
  measure.points_in_poly
Message-ID: <520bf57d-5ac7-4d25-b16f-e3c33915fabe@googlegroups.com>

Hi everyone, 

I would like to use the function points_in_poly to test if the point x,y is 
in the contour cont2
x=0 y=0, but I have the problem with any value of x and y:

skimage.measure.points_in_poly(np.array([x,y]),cont2)  where cont2 is a 
contour of type  array :
but I get the following error:  "IndexError: invalid index"

it is a little obscure for me, is there a problem with this function, or is 
it me who don't know how to apply it ?

thanks a lot!

Julien




cont2        ndarray    7879x2: 15758 elems, type `float64`, 126064 bytes 
(123 kb)

In [12]: skimage.measure.points_in_poly(np.array([0,0]),cont2)
---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
/home/julien/Dropbox/density_seiche/<ipython-input-12-2271d0f2b0ba> in 
<module>()
----> 1 skimage.measure.points_in_poly(np.array([0,0]),cont2)

/usr/local/lib/python2.7/dist-packages/scikit_image-0.11dev-py2.7-linux-x86_64.egg/skimage/measure/_pnpoly.so 
in skimage.measure._pnpoly.points_in_poly (skimage/measure/_pnpoly.c:2397)()

IndexError: invalid index

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From stefan at sun.ac.za  Thu Dec  4 06:06:12 2014
From: stefan at sun.ac.za (Stefan van der Walt)
Date: Thu, 04 Dec 2014 13:06:12 +0200
Subject: scikit-image v0.11 sprint, 12--14 December
Message-ID: <87zjb34qu3.fsf@sun.ac.za>

Hi everyone

On the weekend of 12 to 14 December, we'll be sprinting to release the
next version of scikit-image.  Since we're spread out all over the
world, from Australia to the US, we'll do tag teams as necessary.

No matter your level of expertise, we can use your help!

In preparation, I'll be triaging tickets for the 0.11 milestone, which
you can find here:

https://github.com/scikit-image/scikit-image/milestones/0.11

The event will be coordinated via HipChat:

https://skimage.hipchat.com (sign-in required, full history)
http://www.hipchat.com/gVXougY5x (no sign-in required, no history)

I look forward to seeing you there!

Regards
St?fan


From fboulogne at sciunto.org  Thu Dec  4 13:12:23 2014
From: fboulogne at sciunto.org (=?UTF-8?B?RnJhbsOnb2lzIEJvdWxvZ25l?=)
Date: Thu, 04 Dec 2014 13:12:23 -0500
Subject: Is there a problem with the function points_in_poly ? measure.points_in_poly
In-Reply-To: <520bf57d-5ac7-4d25-b16f-e3c33915fabe@googlegroups.com>
References: <520bf57d-5ac7-4d25-b16f-e3c33915fabe@googlegroups.com>
Message-ID: <5480A407.5040809@sciunto.org>

Le 04/12/2014 13:05, Julien Derr a ?crit :
> Hi everyone,
>
> I would like to use the function points_in_poly to test if the point
> x,y is in the contour cont2
> x=0 y=0, but I have the problem with any value of x and y:
>
> skimage.measure.points_in_poly(np.array([x,y]),cont2)  where cont2 is
> a contour of type  array :
> but I get the following error:  "IndexError: invalid index"
>
> it is a little obscure for me, is there a problem with this function,
> or is it me who don't know how to apply it ?
>


Hi Julien,

Could you provide a minimal example with data to reproduce the error?

-- 
Fran?ois Boulogne.
http://www.sciunto.org
GPG: 32D5F22F



From jsch at demuc.de  Thu Dec  4 13:19:07 2014
From: jsch at demuc.de (Johannes Schoenberger)
Date: Thu, 4 Dec 2014 13:19:07 -0500
Subject: Is there a problem with the function points_in_poly ? measure.points_in_poly
In-Reply-To: <520bf57d-5ac7-4d25-b16f-e3c33915fabe@googlegroups.com>
References: <520bf57d-5ac7-4d25-b16f-e3c33915fabe@googlegroups.com>
Message-ID: <6299280B-3BDD-407C-A4BE-21504099122E@demuc.de>

The docs say `points` must be a (N, 2) array. You pass a (2, ) array.

Make it: ``skimage.measure.points_in_poly(np.array([[0,0]]),cont2)``

> On Dec 4, 2014, at 1:05 PM, Julien Derr <julien.derr at gmail.com> wrote:
> 
> Hi everyone, 
> 
> I would like to use the function points_in_poly to test if the point x,y is in the contour cont2
> x=0 y=0, but I have the problem with any value of x and y:
> 
> skimage.measure.points_in_poly(np.array([x,y]),cont2)  where cont2 is a contour of type  array :
> but I get the following error:  "IndexError: invalid index"
> 
> it is a little obscure for me, is there a problem with this function, or is it me who don't know how to apply it ?
> 
> thanks a lot!
> 
> Julien
> 
> 
> 
> 
> cont2        ndarray    7879x2: 15758 elems, type `float64`, 126064 bytes (123 kb)
> 
> In [12]: skimage.measure.points_in_poly(np.array([0,0]),cont2)
> ---------------------------------------------------------------------------
> IndexError                                Traceback (most recent call last)
> /home/julien/Dropbox/density_seiche/<ipython-input-12-2271d0f2b0ba> in <module>()
> ----> 1 skimage.measure.points_in_poly(np.array([0,0]),cont2)
> 
> /usr/local/lib/python2.7/dist-packages/scikit_image-0.11dev-py2.7-linux-x86_64.egg/skimage/measure/_pnpoly.so in skimage.measure._pnpoly.points_in_poly (skimage/measure/_pnpoly.c:2397)()
> 
> IndexError: invalid index
> 
> 
> -- 
> 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/d/optout.



From stefan at sun.ac.za  Thu Dec  4 07:07:46 2014
From: stefan at sun.ac.za (Stefan van der Walt)
Date: Thu, 04 Dec 2014 14:07:46 +0200
Subject: Image warping using transform.PolynomialTransform: crazy results
In-Reply-To: <133fea57-5306-428a-8812-350eefdcd5e0@googlegroups.com>
References: <133fea57-5306-428a-8812-350eefdcd5e0@googlegroups.com>
Message-ID: <87sigv4nzh.fsf@sun.ac.za>

Hi Herv?

On 2014-11-18 13:21:34, Herve Bouy <hervebouy at gmail.com> wrote:
> Here is my problem. I have a greyscale image with some curved lines.
> I want to transform it so the lines become straight.
>
> <https://lh3.googleusercontent.com/-l7PV-L6ZCek/VGsf6aKWYpI/AAAAAAAABSk/Pae2VGzGThY/s1600/test2.png>
>
> So I measure the position of the lines at regular intervals (in the 
> attached file source_test2.csv)
>
> And compute the desired positions after transformation (in the attached 
> file destination_test2.csv)

I had a look at your input CSV files, but I cannot quite match the
coordinates given there to what is happening in the image.  Can you
provide some insight?

Regards
St?fan


From willemolding at gmail.com  Thu Dec  4 18:08:04 2014
From: willemolding at gmail.com (Willem Olding)
Date: Thu, 4 Dec 2014 15:08:04 -0800 (PST)
Subject: Local GLCM features
Message-ID: <59431232-3b1d-441d-8963-54368394e882@googlegroups.com>

Hi,
The scikit-image implementation of GLCM computes the grey level 
co-occurrence matrix for entire images or image patches. For some image 
labeling problems it is preferred to calculate GLCM features for each 
individual pixel using a sliding window approach as described in 
http://www.fp.ucalgary.ca/mhallbey/texture_calculations.htm. This approach 
can be implemented in scikit-image using a combination of view_as_windows, 
greycomatrix and greycoprops although I found it to be too slow for 
practical use. 

To overcome this I extended scikit-image with a function that performs the 
sliding window as fast cython code. It takes an image, distance, angle and 
window size and generates a texture image with the GLCM 
features ['mean','variance','contrast','dissimilarity','homogeneity','ASM','entropy','correlation'] 
calculated at every pixel. 

Would this be something people are interested in including as part of 
scikit-image?
Regards,
Willem
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From jni.soma at gmail.com  Thu Dec  4 21:02:47 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Thu, 04 Dec 2014 18:02:47 -0800 (PST)
Subject: Permalinks embedded on mailing list messages
Message-ID: <1417744967624.45f4b1e1@Nodemailer>

Does anyone know of a way to get these? My current workflow involves Googling for the skimage mailing list, finding the right link (it's not the top hit), hunting down the right message, and then two clicks and a copy-paste to get the link.


Nabble provides them by default (much as GitHub does), and they are very useful, since mailing list messages are often quite shareable. I'd even advocate moving to Nabble if there's no way to do this.
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From jni.soma at gmail.com  Thu Dec  4 21:24:13 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Thu, 04 Dec 2014 18:24:13 -0800 (PST)
Subject: scikit-image v0.11 sprint, 12--14 December
In-Reply-To: <87zjb34qu3.fsf@sun.ac.za>
References: <87zjb34qu3.fsf@sun.ac.za>
Message-ID: <1417746253642.141eb216@Nodemailer>

skimage.hipchat.com currently redirects to www.hipchat.com? Anyone having better luck?




I'm also not impressed that they apparently don't allow hyphenated last names.

On Thu, Dec 4, 2014 at 10:06 PM, Stefan van der Walt <stefan at sun.ac.za>
wrote:

> Hi everyone
> On the weekend of 12 to 14 December, we'll be sprinting to release the
> next version of scikit-image.  Since we're spread out all over the
> world, from Australia to the US, we'll do tag teams as necessary.
> No matter your level of expertise, we can use your help!
> In preparation, I'll be triaging tickets for the 0.11 milestone, which
> you can find here:
> https://github.com/scikit-image/scikit-image/milestones/0.11
> The event will be coordinated via HipChat:
> https://skimage.hipchat.com (sign-in required, full history)
> http://www.hipchat.com/gVXougY5x (no sign-in required, no history)
> I look forward to seeing you there!
> 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/d/optout.
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From julien.derr at gmail.com  Thu Dec  4 13:25:50 2014
From: julien.derr at gmail.com (Julien Derr)
Date: Thu, 4 Dec 2014 19:25:50 +0100
Subject: Is there a problem with the function points_in_poly ? measure.points_in_poly
In-Reply-To: <6299280B-3BDD-407C-A4BE-21504099122E@demuc.de>
References: <520bf57d-5ac7-4d25-b16f-e3c33915fabe@googlegroups.com> <6299280B-3BDD-407C-A4BE-21504099122E@demuc.de>
Message-ID: <CAOUdFY6Tyidv79Po+itCR5QYHfLtmxdB=ETrcknxiQz7Jf1j+Q@mail.gmail.com>

Thanks to both of you for your quick reply!  and yes Johannes, you are
right!! it works the way you say!

sorry for bothering you for this mistake of mine! I am not very good at
convention, I thought my array was a (1,2) (1 line and two columns, so N=1)
bu I think I understand now!

thanks!


On Thu, Dec 4, 2014 at 7:19 PM, Johannes Schoenberger <jsch at demuc.de> wrote:

> The docs say `points` must be a (N, 2) array. You pass a (2, ) array.
>
> Make it: ``skimage.measure.points_in_poly(np.array([[0,0]]),cont2)``
>
> > On Dec 4, 2014, at 1:05 PM, Julien Derr <julien.derr at gmail.com> wrote:
> >
> > Hi everyone,
> >
> > I would like to use the function points_in_poly to test if the point x,y
> is in the contour cont2
> > x=0 y=0, but I have the problem with any value of x and y:
> >
> > skimage.measure.points_in_poly(np.array([x,y]),cont2)  where cont2 is a
> contour of type  array :
> > but I get the following error:  "IndexError: invalid index"
> >
> > it is a little obscure for me, is there a problem with this function, or
> is it me who don't know how to apply it ?
> >
> > thanks a lot!
> >
> > Julien
> >
> >
> >
> >
> > cont2        ndarray    7879x2: 15758 elems, type `float64`, 126064
> bytes (123 kb)
> >
> > In [12]: skimage.measure.points_in_poly(np.array([0,0]),cont2)
> >
> ---------------------------------------------------------------------------
> > IndexError                                Traceback (most recent call
> last)
> > /home/julien/Dropbox/density_seiche/<ipython-input-12-2271d0f2b0ba> in
> <module>()
> > ----> 1 skimage.measure.points_in_poly(np.array([0,0]),cont2)
> >
> >
> /usr/local/lib/python2.7/dist-packages/scikit_image-0.11dev-py2.7-linux-x86_64.egg/skimage/measure/_pnpoly.so
> in skimage.measure._pnpoly.points_in_poly (skimage/measure/_pnpoly.c:2397)()
> >
> > IndexError: invalid index
> >
> >
> > --
> > 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/d/optout.
>
> --
> 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/44_uNlLqqhE/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From stefan at sun.ac.za  Fri Dec  5 07:53:03 2014
From: stefan at sun.ac.za (Stefan van der Walt)
Date: Fri, 05 Dec 2014 14:53:03 +0200
Subject: Permalinks embedded on mailing list messages
In-Reply-To: <1417744967624.45f4b1e1@Nodemailer>
References: <1417744967624.45f4b1e1@Nodemailer>
Message-ID: <87vblqtg0g.fsf@sun.ac.za>

Hi Juan

On 2014-12-05 04:02:47, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> Does anyone know of a way to get these? My current workflow involves
> Googling for the skimage mailing list, finding the right link (it's
> not the top hit), hunting down the right message, and then two clicks
> and a copy-paste to get the link.

Unfortunately, it looks like this is almost impossible.  We should
consider moving our forum, but I also cannot find a way to export Google
Groups data, which is a bit distressing.  Any tips appreciated.

St?fan


From jni.soma at gmail.com  Fri Dec  5 20:01:04 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Fri, 05 Dec 2014 17:01:04 -0800 (PST)
Subject: Permalinks embedded on mailing list messages
In-Reply-To: <87vblqtg0g.fsf@sun.ac.za>
References: <87vblqtg0g.fsf@sun.ac.za>
Message-ID: <1417827664422.112d502b@Nodemailer>

Holy moly! What happened to Google's "Data Liberation Front"? I guess this illustrates just how neglected GGroups is.




I'm assuming your Googling skills are at least as good as mine, but this is the best I could come up with in a short time:


http://saturnboy.com/2010/03/scraping-google-groups/




I don't read PHP, but the code looks simple, and might be correspondingly simple to port to Python. Uploading to a new service (e.g. Nabble) might not be trivial, though. =\

On Fri, Dec 5, 2014 at 11:53 PM, Stefan van der Walt <stefan at sun.ac.za>
wrote:

> Hi Juan
> On 2014-12-05 04:02:47, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
>> Does anyone know of a way to get these? My current workflow involves
>> Googling for the skimage mailing list, finding the right link (it's
>> not the top hit), hunting down the right message, and then two clicks
>> and a copy-paste to get the link.
> Unfortunately, it looks like this is almost impossible.  We should
> consider moving our forum, but I also cannot find a way to export Google
> Groups data, which is a bit distressing.  Any tips appreciated.
> 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/d/optout.
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From steven.silvester at gmail.com  Fri Dec  5 22:34:00 2014
From: steven.silvester at gmail.com (Steven Silvester)
Date: Fri, 5 Dec 2014 19:34:00 -0800 (PST)
Subject: scikit-image v0.11 sprint, 12--14 December
In-Reply-To: <87zjb34qu3.fsf@sun.ac.za>
References: <87zjb34qu3.fsf@sun.ac.za>
Message-ID: <0d3b06ef-cfce-414f-9bda-a353d24a50bb@googlegroups.com>

I had the same problem.  I'm logged in to Hipchat through another project 
and I just get redirected to it.

- Steve

On Thursday, December 4, 2014 5:06:16 AM UTC-6, Stefan van der Walt wrote:
>
> Hi everyone 
>
> On the weekend of 12 to 14 December, we'll be sprinting to release the 
> next version of scikit-image.  Since we're spread out all over the 
> world, from Australia to the US, we'll do tag teams as necessary. 
>
> No matter your level of expertise, we can use your help! 
>
> In preparation, I'll be triaging tickets for the 0.11 milestone, which 
> you can find here: 
>
> https://github.com/scikit-image/scikit-image/milestones/0.11 
>
> The event will be coordinated via HipChat: 
>
> https://skimage.hipchat.com (sign-in required, full history) 
> http://www.hipchat.com/gVXougY5x (no sign-in required, no history) 
>
> I look forward to seeing you there! 
>
> Regards 
> St?fan 
>
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From jni.soma at gmail.com  Sat Dec  6 08:49:01 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Sat, 06 Dec 2014 05:49:01 -0800 (PST)
Subject: scikit-image v0.11 sprint, 12--14 December
In-Reply-To: <CAHaFxPw44+TwRarenUD-V29ShsEqWQt7WK_s1MQYCw2JhGEg5A@mail.gmail.com>
References: <CAHaFxPw44+TwRarenUD-V29ShsEqWQt7WK_s1MQYCw2JhGEg5A@mail.gmail.com>
Message-ID: <1417873740744.9e139c73@Nodemailer>

If you log in as guest, and then click on the signup link at the top, it should work. At least that worked for me, but I didn't have a pre-existing HipChat account, so YMMV. At any rate, St?fan and I are having a nice chat on gitter, so we might stick with that anyway. =)

On Sat, Dec 6, 2014 at 11:55 PM, Steven Silvester
<steven.silvester at gmail.com> wrote:

> The problem persists...but I *can* log in as a guest.
> On Sat, Dec 6, 2014 at 4:10 AM, Stefan van der Walt <stefan at sun.ac.za>
> wrote:
>> Hi Steven
>>
>> On 2014-12-06 05:34:00, Steven Silvester <steven.silvester at gmail.com>
>> wrote:
>> > I had the same problem.  I'm logged in to Hipchat through another project
>> > and I just get redirected to it.
>>
>> Please try the following link and let me know:
>>
>> https://skimage.hipchat.com/chat
>>
>> St?fan
>>
>> --
>> You received this message because you are subscribed to a topic in the
>> Google Groups "scikit-image" group.
>> To unsubscribe from this topic, visit
>> https://groups.google.com/d/topic/scikit-image/KtnLZJEV54Y/unsubscribe.
>> To unsubscribe from this group and all its topics, send an email to
>> scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
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From steven.silvester at gmail.com  Sat Dec  6 07:55:46 2014
From: steven.silvester at gmail.com (Steven Silvester)
Date: Sat, 6 Dec 2014 06:55:46 -0600
Subject: scikit-image v0.11 sprint, 12--14 December
In-Reply-To: <87fvctt7fw.fsf@sun.ac.za>
References: <87zjb34qu3.fsf@sun.ac.za>
	<0d3b06ef-cfce-414f-9bda-a353d24a50bb@googlegroups.com>
	<87fvctt7fw.fsf@sun.ac.za>
Message-ID: <CAHaFxPw44+TwRarenUD-V29ShsEqWQt7WK_s1MQYCw2JhGEg5A@mail.gmail.com>

The problem persists...but I *can* log in as a guest.

On Sat, Dec 6, 2014 at 4:10 AM, Stefan van der Walt <stefan at sun.ac.za>
wrote:

> Hi Steven
>
> On 2014-12-06 05:34:00, Steven Silvester <steven.silvester at gmail.com>
> wrote:
> > I had the same problem.  I'm logged in to Hipchat through another project
> > and I just get redirected to it.
>
> Please try the following link and let me know:
>
> https://skimage.hipchat.com/chat
>
> St?fan
>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "scikit-image" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/scikit-image/KtnLZJEV54Y/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From steven.silvester at gmail.com  Sat Dec  6 10:07:00 2014
From: steven.silvester at gmail.com (Steven Silvester)
Date: Sat, 6 Dec 2014 07:07:00 -0800 (PST)
Subject: scikit-image v0.11 sprint, 12--14 December
In-Reply-To: <87zjb34qu3.fsf@sun.ac.za>
References: <87zjb34qu3.fsf@sun.ac.za>
Message-ID: <7e3943f5-3389-4139-97e5-a36398b32fad@googlegroups.com>

I tried creating a separate account, with the team name 'skimage', and I 
get this error message: "This Team Name is already in use. If your team is 
already using HipChat, please ask the group admin for an invite."

- Steve

On Thursday, December 4, 2014 5:06:16 AM UTC-6, Stefan van der Walt wrote:
>
> Hi everyone 
>
> On the weekend of 12 to 14 December, we'll be sprinting to release the 
> next version of scikit-image.  Since we're spread out all over the 
> world, from Australia to the US, we'll do tag teams as necessary. 
>
> No matter your level of expertise, we can use your help! 
>
> In preparation, I'll be triaging tickets for the 0.11 milestone, which 
> you can find here: 
>
> https://github.com/scikit-image/scikit-image/milestones/0.11 
>
> The event will be coordinated via HipChat: 
>
> https://skimage.hipchat.com (sign-in required, full history) 
> http://www.hipchat.com/gVXougY5x (no sign-in required, no history) 
>
> I look forward to seeing you there! 
>
> Regards 
> St?fan 
>
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From stefan at sun.ac.za  Sat Dec  6 05:10:27 2014
From: stefan at sun.ac.za (Stefan van der Walt)
Date: Sat, 06 Dec 2014 12:10:27 +0200
Subject: scikit-image v0.11 sprint, 12--14 December
In-Reply-To: <0d3b06ef-cfce-414f-9bda-a353d24a50bb@googlegroups.com>
References: <87zjb34qu3.fsf@sun.ac.za> <0d3b06ef-cfce-414f-9bda-a353d24a50bb@googlegroups.com>
Message-ID: <87fvctt7fw.fsf@sun.ac.za>

Hi Steven

On 2014-12-06 05:34:00, Steven Silvester <steven.silvester at gmail.com> wrote:
> I had the same problem.  I'm logged in to Hipchat through another project 
> and I just get redirected to it.

Please try the following link and let me know:

https://skimage.hipchat.com/chat

St?fan


From stefan at sun.ac.za  Sat Dec  6 07:15:56 2014
From: stefan at sun.ac.za (Stefan van der Walt)
Date: Sat, 06 Dec 2014 14:15:56 +0200
Subject: scikit-image v0.11 sprint, 12--14 December
In-Reply-To: <87zjb34qu3.fsf@sun.ac.za>
References: <87zjb34qu3.fsf@sun.ac.za>
Message-ID: <87egsdt1mr.fsf@sun.ac.za>

On 2014-12-04 13:06:12, Stefan van der Walt <stefan at sun.ac.za> wrote:
> The event will be coordinated via HipChat:
>
> https://skimage.hipchat.com (sign-in required, full history)
> http://www.hipchat.com/gVXougY5x (no sign-in required, no history)

Folks have voted with their virtual feet, and I see we already have a
assembly at:

https://gitter.im/scikit-image/scikit-image

(Gitter authenticates via GitHub, which is much easier it seems)

So, let's make this the meeting point for the sprint.

Thanks
St?fan


From stefan at sun.ac.za  Sat Dec  6 10:09:08 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Sat, 6 Dec 2014 17:09:08 +0200
Subject: scikit-image v0.11 sprint, 12--14 December
In-Reply-To: <7e3943f5-3389-4139-97e5-a36398b32fad@googlegroups.com>
References: <87zjb34qu3.fsf@sun.ac.za> <7e3943f5-3389-4139-97e5-a36398b32fad@googlegroups.com>
Message-ID: <CABDkGQnpbjYun5fpm9Dug73ByZ5qugFV-qrDayz7HpfknvjeMg@mail.gmail.com>

On Sat, Dec 6, 2014 at 5:07 PM, Steven Silvester
<steven.silvester at gmail.com> wrote:
> I tried creating a separate account, with the team name 'skimage', and I get
> this error message: "This Team Name is already in use. If your team is
> already using HipChat, please ask the group admin for an invite."

We'll be using the Gitter chatroom for the sprint.

St?fan


From jni.soma at gmail.com  Sun Dec  7 18:00:56 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Sun, 07 Dec 2014 15:00:56 -0800 (PST)
Subject: Travis-wheels fix?
Message-ID: <1417993256117.cc5d57fd@Nodemailer>

A bunch of Travis errors are being caused (apparently) by travis-wheels.scikit-image.org not responding. I haven't been following the discussion closely, but my question is, do we need to get rid of it for the Travis build so that we can have a stable build system at the sprint? Or do we perhaps want to add a condition to use regular pip builds if travis-wheels is unavailable?
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From hughesadam87 at gmail.com  Sun Dec  7 19:11:25 2014
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Sun, 7 Dec 2014 16:11:25 -0800 (PST)
Subject: How do you keep documentation so nice?
Message-ID: <1de0c5cc-d13a-4ec4-91e1-06f48836e439@googlegroups.com>

Hi,

I've been working with sphinx api-doc for autogenerating some documentation 
for a package, and the output is a farcry from the nice, super-slick layout 
that scikit-image has.  I saw that on the bottom of your page, the docs are 
built with sphinx and bootstrap.  Is the source code for the documentation 
available for perusing by chance?  I'd love to get some insights on how you 
keep your page so nice and tidy!
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From jni.soma at gmail.com  Sun Dec  7 19:17:43 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Sun, 07 Dec 2014 16:17:43 -0800 (PST)
Subject: How do you keep documentation so nice?
In-Reply-To: <CAMHV+dC9CaxdThPhSkgqiv1pu0qRxyhsTuOoBmkYVzTcppT+Ow@mail.gmail.com>
References: <CAMHV+dC9CaxdThPhSkgqiv1pu0qRxyhsTuOoBmkYVzTcppT+Ow@mail.gmail.com>
Message-ID: <1417997863187.a64bc4ca@Nodemailer>

Hahaha it's not that dumb! I personally have tried to dive into the doc build process a few times but have found it quite opaque, so I wouldn't mind if St?fan and/or Tony elaborated a bit here about the build system! =)




But as to drawing inspiration, I'm pretty sure it's all BSD, which means you can draw even a bit more than that! =)

On Mon, Dec 8, 2014 at 11:14 AM, Adam Hughes <hughesadam87 at gmail.com>
wrote:

> I'm dumb.  It's clearly right there on your github page in "docs".  Geez.
> It's ok if I draw inspiration from you guys, right?
> On Sun, Dec 7, 2014 at 7:11 PM, Adam Hughes <hughesadam87 at gmail.com> wrote:
>> Hi,
>>
>> I've been working with sphinx api-doc for autogenerating some
>> documentation for a package, and the output is a farcry from the nice,
>> super-slick layout that scikit-image has.  I saw that on the bottom of your
>> page, the docs are built with sphinx and bootstrap.  Is the source code for
>> the documentation available for perusing by chance?  I'd love to get some
>> insights on how you keep your page so nice and tidy!
>>
>> --
>> 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/k5K6_vanZVI/unsubscribe.
>> To unsubscribe from this group and all its topics, send an email to
>> scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
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From hughesadam87 at gmail.com  Sun Dec  7 19:14:50 2014
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Sun, 7 Dec 2014 19:14:50 -0500
Subject: How do you keep documentation so nice?
In-Reply-To: <1de0c5cc-d13a-4ec4-91e1-06f48836e439@googlegroups.com>
References: <1de0c5cc-d13a-4ec4-91e1-06f48836e439@googlegroups.com>
Message-ID: <CAMHV+dC9CaxdThPhSkgqiv1pu0qRxyhsTuOoBmkYVzTcppT+Ow@mail.gmail.com>

I'm dumb.  It's clearly right there on your github page in "docs".  Geez.

It's ok if I draw inspiration from you guys, right?

On Sun, Dec 7, 2014 at 7:11 PM, Adam Hughes <hughesadam87 at gmail.com> wrote:

> Hi,
>
> I've been working with sphinx api-doc for autogenerating some
> documentation for a package, and the output is a farcry from the nice,
> super-slick layout that scikit-image has.  I saw that on the bottom of your
> page, the docs are built with sphinx and bootstrap.  Is the source code for
> the documentation available for perusing by chance?  I'd love to get some
> insights on how you keep your page so nice and tidy!
>
> --
> 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/k5K6_vanZVI/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From hughesadam87 at gmail.com  Sun Dec  7 19:22:29 2014
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Sun, 7 Dec 2014 19:22:29 -0500
Subject: How do you keep documentation so nice?
In-Reply-To: <1417997863187.a64bc4ca@Nodemailer>
References: <CAMHV+dC9CaxdThPhSkgqiv1pu0qRxyhsTuOoBmkYVzTcppT+Ow@mail.gmail.com>
	<1417997863187.a64bc4ca@Nodemailer>
Message-ID: <CAMHV+dB9SzY7w-8+zf_QXbk8p9k3LBu5JPJ079FcV0N2ccxA=A@mail.gmail.com>

Thanks Juan.  It's funny, but I feel like writing documents is 10 times
harder than writing software

On Sun, Dec 7, 2014 at 7:17 PM, Juan Nunez-Iglesias <jni.soma at gmail.com>
wrote:

> Hahaha it's not that dumb! I personally have tried to dive into the doc
> build process a few times but have found it quite opaque, so I wouldn't
> mind if St?fan and/or Tony elaborated a bit here about the build system! =)
>
> But as to drawing inspiration, I'm pretty sure it's all BSD, which means
> you can draw even a bit more than that! =)
>
>
>
>
> On Mon, Dec 8, 2014 at 11:14 AM, Adam Hughes <hughesadam87 at gmail.com>
> wrote:
>
>>  I'm dumb.  It's clearly right there on your github page in "docs".
>> Geez.
>>
>> It's ok if I draw inspiration from you guys, right?
>>
>> On Sun, Dec 7, 2014 at 7:11 PM, Adam Hughes <hughesadam87 at gmail.com>
>> wrote:
>>
>>> Hi,
>>>
>>> I've been working with sphinx api-doc for autogenerating some
>>> documentation for a package, and the output is a farcry from the nice,
>>> super-slick layout that scikit-image has.  I saw that on the bottom of your
>>> page, the docs are built with sphinx and bootstrap.  Is the source code for
>>> the documentation available for perusing by chance?  I'd love to get some
>>> insights on how you keep your page so nice and tidy!
>>>
>>> --
>>> 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/k5K6_vanZVI/unsubscribe.
>>> To unsubscribe from this group and all its topics, send an email to
>>> scikit-image+unsubscribe at googlegroups.com.
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>
>>  --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>  --
> 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/k5K6_vanZVI/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From jjhelmus at gmail.com  Mon Dec  8 11:38:06 2014
From: jjhelmus at gmail.com (Jonathan Helmus)
Date: Mon, 08 Dec 2014 10:38:06 -0600
Subject: Travis-wheels fix?
In-Reply-To: <1417993256117.cc5d57fd@Nodemailer>
References: <1417993256117.cc5d57fd@Nodemailer>
Message-ID: <5485D3EE.9080901@gmail.com>

On 12/07/2014 05:00 PM, Juan Nunez-Iglesias wrote:
> A bunch of Travis errors are being caused (apparently) by 
> travis-wheels.scikit-image.org not responding. I haven't been 
> following the discussion closely, but my question is, do we need to 
> get rid of it for the Travis build so that we can have a stable build 
> system at the sprint? Or do we perhaps want to add a condition to use 
> regular pip builds if travis-wheels is unavailable?
>
>
> -- 
> 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+unsubscribe at googlegroups.com>.
> For more options, visit https://groups.google.com/d/optout.


We know have http://wheels.scipy.org/ which has OS-X and Linux wheels 
for many SciPy stack modules. http://travis-wheels.scikit-image.org/ 
still responds for me and seems to have more files than the scipy.org 
domain.  Github issue #1057 is where we are discussing the wheels, 
Windows CI, and related topic, 
https://github.com/scikit-image/scikit-image/pull/1057.  If there are 
files you need at either site I can add them easily.

Cheers,

     - Jonathan Helmus
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From jni.soma at gmail.com  Mon Dec  8 19:29:34 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Mon, 08 Dec 2014 16:29:34 -0800 (PST)
Subject: Travis-wheels fix?
In-Reply-To: <5485D3EE.9080901@gmail.com>
References: <5485D3EE.9080901@gmail.com>
Message-ID: <1418084973674.c801790a@Nodemailer>

Hey Jonathan,




I'm not suggesting that travis-wheels is unresponsive all the time or missing files. I'm just saying that many (~30% guesstimate) builds have been failing because of a travis-wheels.scikit-image.org error. There is clearly a problem with uptime or with response time. I don't have any files that I need. Steven is the architect of the present build system (thanks Steven! =) so he'll know best how to deal with this.




Juan.

On Tue, Dec 9, 2014 at 3:38 AM, Jonathan Helmus <jjhelmus at gmail.com>
wrote:

> On 12/07/2014 05:00 PM, Juan Nunez-Iglesias wrote:
>> A bunch of Travis errors are being caused (apparently) by 
>> travis-wheels.scikit-image.org not responding. I haven't been 
>> following the discussion closely, but my question is, do we need to 
>> get rid of it for the Travis build so that we can have a stable build 
>> system at the sprint? Or do we perhaps want to add a condition to use 
>> regular pip builds if travis-wheels is unavailable?
>>
>>
>> -- 
>> 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+unsubscribe at googlegroups.com>.
>> For more options, visit https://groups.google.com/d/optout.
> We know have http://wheels.scipy.org/ which has OS-X and Linux wheels 
> for many SciPy stack modules. http://travis-wheels.scikit-image.org/ 
> still responds for me and seems to have more files than the scipy.org 
> domain.  Github issue #1057 is where we are discussing the wheels, 
> Windows CI, and related topic, 
> https://github.com/scikit-image/scikit-image/pull/1057.  If there are 
> files you need at either site I can add them easily.
> Cheers,
>      - Jonathan Helmus
> -- 
> 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/d/optout.
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From hughesadam87 at gmail.com  Mon Dec  8 18:40:27 2014
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Mon, 8 Dec 2014 18:40:27 -0500
Subject: How do you keep documentation so nice?
In-Reply-To: <CAMHV+dB9SzY7w-8+zf_QXbk8p9k3LBu5JPJ079FcV0N2ccxA=A@mail.gmail.com>
References: <CAMHV+dC9CaxdThPhSkgqiv1pu0qRxyhsTuOoBmkYVzTcppT+Ow@mail.gmail.com>
	<1417997863187.a64bc4ca@Nodemailer>
	<CAMHV+dB9SzY7w-8+zf_QXbk8p9k3LBu5JPJ079FcV0N2ccxA=A@mail.gmail.com>
Message-ID: <CAMHV+dAXJAP-3R_mbtqFF=Znez9wtq7U1ND98S0-ATXngcOc-Q@mail.gmail.com>

I really am impressed by this plt2rst.py module for autogenerating example
documentation!

I've been trying to implement it just to test it out and think I have it
setup right in terms of placement in my docs directory, I made an example
plot_test.py file in examples, but I'm confused on how to actually use the
plt2rst.py module.  Consider this line from that file:

    def setup(app):
        app.connect('builder-inited', generate_example_galleries)

        app.add_config_value('plot2rst_paths',
                         ('../examples', 'auto_examples'), True

When/how is this ever called?  The examples themselves don't use these
directives; so when is this found?

When I build in my make file, no auto_examples.html file is ever created in
my build directory.  So I'm thinking I'm not using this correctly.  Is
there another step besides just doing make build?


On Sun, Dec 7, 2014 at 7:22 PM, Adam Hughes <hughesadam87 at gmail.com> wrote:

> Thanks Juan.  It's funny, but I feel like writing documents is 10 times
> harder than writing software
>
> On Sun, Dec 7, 2014 at 7:17 PM, Juan Nunez-Iglesias <jni.soma at gmail.com>
> wrote:
>
>> Hahaha it's not that dumb! I personally have tried to dive into the doc
>> build process a few times but have found it quite opaque, so I wouldn't
>> mind if St?fan and/or Tony elaborated a bit here about the build system! =)
>>
>> But as to drawing inspiration, I'm pretty sure it's all BSD, which means
>> you can draw even a bit more than that! =)
>>
>>
>>
>>
>> On Mon, Dec 8, 2014 at 11:14 AM, Adam Hughes <hughesadam87 at gmail.com>
>> wrote:
>>
>>>  I'm dumb.  It's clearly right there on your github page in "docs".
>>> Geez.
>>>
>>> It's ok if I draw inspiration from you guys, right?
>>>
>>> On Sun, Dec 7, 2014 at 7:11 PM, Adam Hughes <hughesadam87 at gmail.com>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> I've been working with sphinx api-doc for autogenerating some
>>>> documentation for a package, and the output is a farcry from the nice,
>>>> super-slick layout that scikit-image has.  I saw that on the bottom of your
>>>> page, the docs are built with sphinx and bootstrap.  Is the source code for
>>>> the documentation available for perusing by chance?  I'd love to get some
>>>> insights on how you keep your page so nice and tidy!
>>>>
>>>> --
>>>> 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/k5K6_vanZVI/unsubscribe.
>>>> To unsubscribe from this group and all its topics, send an email to
>>>> scikit-image+unsubscribe at googlegroups.com.
>>>> For more options, visit https://groups.google.com/d/optout.
>>>>
>>>
>>>  --
>>> You received this message because you are subscribed to the Google
>>> Groups "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>
>>  --
>> 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/k5K6_vanZVI/unsubscribe.
>> To unsubscribe from this group and all its topics, send an email to
>> scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>
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From steven.silvester at gmail.com  Mon Dec  8 21:41:41 2014
From: steven.silvester at gmail.com (Steven Silvester)
Date: Mon, 8 Dec 2014 18:41:41 -0800 (PST)
Subject: Travis-wheels fix?
In-Reply-To: <1417993256117.cc5d57fd@Nodemailer>
References: <1417993256117.cc5d57fd@Nodemailer>
Message-ID: <75b9e8e1-9f90-46bf-b54e-8205de75064b@googlegroups.com>

Juan,  

I'm not sure what is causing the recent failures.  We have been using the 
new travis-wheels site for over a month:  
https://github.com/scikit-image/scikit-image/commit/b6f775a7cf8c775d89e8fe203cd2e0f874be5965.  
Perhaps the rackspace server is having some trouble.


- Steve

On Sunday, December 7, 2014 5:00:58 PM UTC-6, Juan Nunez-Iglesias wrote:
>
>  A bunch of Travis errors are being caused (apparently) by 
> travis-wheels.scikit-image.org not responding. I haven't been following 
> the discussion closely, but my question is, do we need to get rid of it for 
> the Travis build so that we can have a stable build system at the sprint? 
> Or do we perhaps want to add a condition to use regular pip builds if 
> travis-wheels is unavailable?
>
>
>  
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From tsyu80 at gmail.com  Mon Dec  8 21:12:17 2014
From: tsyu80 at gmail.com (Tony Yu)
Date: Mon, 8 Dec 2014 20:12:17 -0600
Subject: How do you keep documentation so nice?
In-Reply-To: <CAMHV+dAXJAP-3R_mbtqFF=Znez9wtq7U1ND98S0-ATXngcOc-Q@mail.gmail.com>
References: <CAMHV+dC9CaxdThPhSkgqiv1pu0qRxyhsTuOoBmkYVzTcppT+Ow@mail.gmail.com>
 <1417997863187.a64bc4ca@Nodemailer> <CAMHV+dB9SzY7w-8+zf_QXbk8p9k3LBu5JPJ079FcV0N2ccxA=A@mail.gmail.com>
 <CAMHV+dAXJAP-3R_mbtqFF=Znez9wtq7U1ND98S0-ATXngcOc-Q@mail.gmail.com>
Message-ID: <CAEym_HpRoyKUjsPt9m7zr1CA2=WuOtG09i==0AaNFk7ky7Qgsw@mail.gmail.com>

Hi Adam!

On Mon, Dec 8, 2014 at 5:40 PM, Adam Hughes <hughesadam87 at gmail.com> wrote:

> I really am impressed by this plt2rst.py module for autogenerating example
> documentation!
>
> I've been trying to implement it just to test it out and think I have it
> setup right in terms of placement in my docs directory, I made an example
> plot_test.py file in examples, but I'm confused on how to actually use the
> plt2rst.py module.  Consider this line from that file:
>
>     def setup(app):
>         app.connect('builder-inited', generate_example_galleries)
>
>         app.add_config_value('plot2rst_paths',
>                          ('../examples', 'auto_examples'), True
>
> When/how is this ever called?  The examples themselves don't use these
> directives; so when is this found?
>

This plotting code is partially my fault, so I'll try to explain based on
memory. I should say, though, that I adapted this code from an older
version in the `scikit-image` docs, which took it from `scikit-learn`
(which may have taken it from nipy or some other project). That is to say,
I don't completely understand all the things. ;)

This particular `setup(app)` function is run as part of the Sphinx
infrastructure (see http://sphinx-doc.org/extdev/tutorial.html).


> When I build in my make file, no auto_examples.html file is ever created
> in my build directory.  So I'm thinking I'm not using this correctly.  Is
> there another step besides just doing make build?
>

There's a bit of documentation written up here:

https://github.com/tonysyu/mpltools/blob/master/doc/source/getting_started.rst#plot2rst-sphinx-extension

One possible hang-up is that examples are expected to start with `plot_`
and an `index.rst` file is required in gallery directories.

I haven't looked at this in a while, but if you have any more questions, I
can try to dig into the code a bit to try to remember what's going on.

Cheers!
-Tony
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From claiborne.morton at gmail.com  Tue Dec  9 14:58:43 2014
From: claiborne.morton at gmail.com (Claiborne Morton)
Date: Tue, 9 Dec 2014 11:58:43 -0800 (PST)
Subject: Help with shape descriptors
Message-ID: <892d6e2e-6a60-4e9f-91ae-bf6d5ec8f9ae@googlegroups.com>

Hello Scikit community, 

I'm looking for help using particle descriptors to identify sickle cells in 
the attached image. As you can see the sickle cells are the long, thin 
cells. I have two issues, the first is that in some cases the sickle cells 
are in contact with other healthy cells. I am trying to find a way of 
separating (or water-shedding) the cells so that each "particle" is 
actually one cell. The second issue is that I am dealing with is trying to 
find shape descriptors that will allow me to accurately distinguish the 
sickle cells from the healthy cells. 

I used an eccentricity filter on the original image to remove all of the 
cells with eccentricity less than 0.6. Making this any higher results in 
removal of sickle cells. What other descriptors might be used for further 
differentiation?

Thanks, Clay 
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From silvertrumpet999 at gmail.com  Tue Dec  9 16:08:50 2014
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Tue, 9 Dec 2014 13:08:50 -0800 (PST)
Subject: Help with shape descriptors
In-Reply-To: <892d6e2e-6a60-4e9f-91ae-bf6d5ec8f9ae@googlegroups.com>
References: <892d6e2e-6a60-4e9f-91ae-bf6d5ec8f9ae@googlegroups.com>
Message-ID: <e39d0cdf-fb53-4dab-8c9a-f1f1a10ff65d@googlegroups.com>

At first glance, regarding identifying RBCs from sickle cells:

You could do a binary fill holes operation and then subtract the previous 
image from the result - you'd have only the small "holes" evident inside 
normal RBC's shown in your example. Then remove any labeled regions in 
contact with those holes.

You'll probably have a few spurious ones left over, and this might 
accidentally remove a sickle cell here or there (can't see any in the 
example, but I'm sure it's possible). However, with minimal tweaking this 
would remove most normal RBCs from the thresholded image shown.

Speaking in the abstract sans example code, here, but it seems like you 
could get pretty far this way. 


I'll let someone else chime in about separating cells in contact. 

Josh 


On Tuesday, December 9, 2014 1:58:43 PM UTC-6, Claiborne Morton wrote:
>
> Hello Scikit community, 
>
> I'm looking for help using particle descriptors to identify sickle cells 
> in the attached image. As you can see the sickle cells are the long, thin 
> cells. I have two issues, the first is that in some cases the sickle cells 
> are in contact with other healthy cells. I am trying to find a way of 
> separating (or water-shedding) the cells so that each "particle" is 
> actually one cell. The second issue is that I am dealing with is trying to 
> find shape descriptors that will allow me to accurately distinguish the 
> sickle cells from the healthy cells. 
>
> I used an eccentricity filter on the original image to remove all of the 
> cells with eccentricity less than 0.6. Making this any higher results in 
> removal of sickle cells. What other descriptors might be used for further 
> differentiation?
>
> Thanks, Clay 
>
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From jni.soma at gmail.com  Tue Dec  9 17:43:24 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Tue, 09 Dec 2014 14:43:24 -0800 (PST)
Subject: Help with shape descriptors
In-Reply-To: <892d6e2e-6a60-4e9f-91ae-bf6d5ec8f9ae@googlegroups.com>
References: <892d6e2e-6a60-4e9f-91ae-bf6d5ec8f9ae@googlegroups.com>
Message-ID: <1418165003869.5f9ec185@Nodemailer>

Hey Clay,




Application is everything. =) Depending on your downstream question, one approach might be preferred over another. If your goal is to count normal vs sickle cells, *and* you want to do so often, you could:




- use regionprops to get *a lot* of features from your data. There's eccentricity but that'll pick up those clumps of normal cells. You can also compute Euler number (the number of holes in a shape), area, and maybe solidity.?

- then run the regions through clustering in scikit-learn. I think you'll get clusters corresponding to sickle cells, normal cells, clumps of 2 normal cells, clumps of a normal and a sickle cell, etc.

- then count based on the number of regions in each cluster times the number of cells corresponding to that cluster.




Of course this might be too complicated... But simpler approaches will probably have a significant error rate (as you have noticed).




Juan.

On Wed, Dec 10, 2014 at 7:01 AM, Claiborne Morton
<claiborne.morton at gmail.com> wrote:

> Hello Scikit community, 
> I'm looking for help using particle descriptors to identify sickle cells in 
> the attached image. As you can see the sickle cells are the long, thin 
> cells. I have two issues, the first is that in some cases the sickle cells 
> are in contact with other healthy cells. I am trying to find a way of 
> separating (or water-shedding) the cells so that each "particle" is 
> actually one cell. The second issue is that I am dealing with is trying to 
> find shape descriptors that will allow me to accurately distinguish the 
> sickle cells from the healthy cells. 
> I used an eccentricity filter on the original image to remove all of the 
> cells with eccentricity less than 0.6. Making this any higher results in 
> removal of sickle cells. What other descriptors might be used for further 
> differentiation?
> Thanks, Clay 
> -- 
> 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/d/optout.
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From hughesadam87 at gmail.com  Tue Dec  9 14:57:06 2014
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Tue, 9 Dec 2014 14:57:06 -0500
Subject: How do you keep documentation so nice?
In-Reply-To: <8761dkyd2p.fsf@sun.ac.za>
References: <CAMHV+dC9CaxdThPhSkgqiv1pu0qRxyhsTuOoBmkYVzTcppT+Ow@mail.gmail.com>
	<1417997863187.a64bc4ca@Nodemailer>
	<CAMHV+dB9SzY7w-8+zf_QXbk8p9k3LBu5JPJ079FcV0N2ccxA=A@mail.gmail.com>
	<CAMHV+dAXJAP-3R_mbtqFF=Znez9wtq7U1ND98S0-ATXngcOc-Q@mail.gmail.com>
	<CAEym_HpRoyKUjsPt9m7zr1CA2=WuOtG09i==0AaNFk7ky7Qgsw@mail.gmail.com>
	<8761dkyd2p.fsf@sun.ac.za>
Message-ID: <CAMHV+dDT83bD_uvP2gHbc0StGf2FtM374mhO5L+FCXpA=amneA@mail.gmail.com>

Thanks Tony and Stefan for the resources, I will start working on them now.

On Tue, Dec 9, 2014 at 11:58 AM, Stefan van der Walt <stefan at sun.ac.za>
wrote:

> Hi Adam
>
> On 2014-12-09 04:12:17, Tony Yu <tsyu80 at gmail.com> wrote:
> >> I really am impressed by this plt2rst.py module for autogenerating
> example
> >> documentation!
>
> Also have a look at this project, which tries to unify the gallery
> builders of the different projects:
>
> https://github.com/sphinx-gallery/sphinx-gallery
>
> St?fan
>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "scikit-image" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/scikit-image/k5K6_vanZVI/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From hughesadam87 at gmail.com  Tue Dec  9 14:58:39 2014
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Tue, 9 Dec 2014 14:58:39 -0500
Subject: How do you keep documentation so nice?
In-Reply-To: <CAMHV+dDT83bD_uvP2gHbc0StGf2FtM374mhO5L+FCXpA=amneA@mail.gmail.com>
References: <CAMHV+dC9CaxdThPhSkgqiv1pu0qRxyhsTuOoBmkYVzTcppT+Ow@mail.gmail.com>
	<1417997863187.a64bc4ca@Nodemailer>
	<CAMHV+dB9SzY7w-8+zf_QXbk8p9k3LBu5JPJ079FcV0N2ccxA=A@mail.gmail.com>
	<CAMHV+dAXJAP-3R_mbtqFF=Znez9wtq7U1ND98S0-ATXngcOc-Q@mail.gmail.com>
	<CAEym_HpRoyKUjsPt9m7zr1CA2=WuOtG09i==0AaNFk7ky7Qgsw@mail.gmail.com>
	<8761dkyd2p.fsf@sun.ac.za>
	<CAMHV+dDT83bD_uvP2gHbc0StGf2FtM374mhO5L+FCXpA=amneA@mail.gmail.com>
Message-ID: <CAMHV+dDpzq4FNMjrwzGwxk22tdnqvNAsavK5JPYsk9hB4HTyzg@mail.gmail.com>

PS,

Tony, I don't see an index.rst file in scikit-images gallery.  You're
talking about this folder, yes?:

https://github.com/scikit-image/scikit-image/tree/master/doc/examples

On Tue, Dec 9, 2014 at 2:57 PM, Adam Hughes <hughesadam87 at gmail.com> wrote:

> Thanks Tony and Stefan for the resources, I will start working on them now.
>
> On Tue, Dec 9, 2014 at 11:58 AM, Stefan van der Walt <stefan at sun.ac.za>
> wrote:
>
>> Hi Adam
>>
>> On 2014-12-09 04:12:17, Tony Yu <tsyu80 at gmail.com> wrote:
>> >> I really am impressed by this plt2rst.py module for autogenerating
>> example
>> >> documentation!
>>
>> Also have a look at this project, which tries to unify the gallery
>> builders of the different projects:
>>
>> https://github.com/sphinx-gallery/sphinx-gallery
>>
>> St?fan
>>
>> --
>> You received this message because you are subscribed to a topic in the
>> Google Groups "scikit-image" group.
>> To unsubscribe from this topic, visit
>> https://groups.google.com/d/topic/scikit-image/k5K6_vanZVI/unsubscribe.
>> To unsubscribe from this group and all its topics, send an email to
>> scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>
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From jni.soma at gmail.com  Tue Dec  9 17:59:01 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Tue, 09 Dec 2014 14:59:01 -0800 (PST)
Subject: How do you keep documentation so nice?
In-Reply-To: <87tx14wivp.fsf@sun.ac.za>
References: <87tx14wivp.fsf@sun.ac.za>
Message-ID: <1418165940884.800f51a4@Nodemailer>

St?fan,




> I'm not sure how--that repo still looks to be fairly empty!




Huh??? You sent that link! LOL I was puzzled too but then saw the PR from the owner's "personal" fork of the repo, which I guess (no time to look at it yet) has a fair few resources.



> the rst files get compiled by Sphinx, during which the plots etc. get generated.



I don't actually understand the process of generating plots in the case of hand-written docs. E.g. this image embed by Emmanuelle:


https://github.com/scikit-image/scikit-image/blob/master/doc/source/user_guide/numpy_images.txt#L73




Is that generated from the code in the .rst file itself, or does she have to know (through non-automated means) that the auto-example produces the same image as is required in the rst?




Juan.
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From jni.soma at gmail.com  Mon Dec  8 23:27:33 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Tue, 9 Dec 2014 15:27:33 +1100
Subject: Travis-wheels fix?
In-Reply-To: <75b9e8e1-9f90-46bf-b54e-8205de75064b@googlegroups.com>
References: <1417993256117.cc5d57fd@Nodemailer> <75b9e8e1-9f90-46bf-b54e-8205de75064b@googlegroups.com>
Message-ID: <CA+JHcKR15W7FPEL6s4-6BrtaUGCe5bf7AQKJ=KjQer77tgCJLw@mail.gmail.com>

Ok no worries -- I just want to make sure that I'm not way off on what the
causes of the failures are... Sometimes Travis errors are misleading. Who's
running the actual server and do we have any logs about uptime?

On Tue, Dec 9, 2014 at 1:41 PM, Steven Silvester <steven.silvester at gmail.com
> wrote:

> Juan,
>
> I'm not sure what is causing the recent failures.  We have been using the
> new travis-wheels site for over a month:
> https://github.com/scikit-image/scikit-image/commit/b6f775a7cf8c775d89e8fe203cd2e0f874be5965.
> Perhaps the rackspace server is having some trouble.
>
>
> - Steve
>
> On Sunday, December 7, 2014 5:00:58 PM UTC-6, Juan Nunez-Iglesias wrote:
>>
>>  A bunch of Travis errors are being caused (apparently) by
>> travis-wheels.scikit-image.org not responding. I haven't been following
>> the discussion closely, but my question is, do we need to get rid of it for
>> the Travis build so that we can have a stable build system at the sprint?
>> Or do we perhaps want to add a condition to use regular pip builds if
>> travis-wheels is unavailable?
>>
>>
>>   --
> 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/d/optout.
>
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From jni.soma at gmail.com  Tue Dec  9 18:46:40 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Tue, 09 Dec 2014 15:46:40 -0800 (PST)
Subject: How do you keep documentation so nice?
In-Reply-To: <87oarcwhb8.fsf@sun.ac.za>
References: <87oarcwhb8.fsf@sun.ac.za>
Message-ID: <1418168800486.8d77c162@Nodemailer>

Thanks for all that. =)




> She "cheated" a bit and included an image from the gallery.




If I want to include my own non-gallery image, should I generate it manually, and if so, where should I put it?
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From hughesadam87 at gmail.com  Tue Dec  9 15:54:34 2014
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Tue, 9 Dec 2014 15:54:34 -0500
Subject: How do you keep documentation so nice?
In-Reply-To: <CAMHV+dDpzq4FNMjrwzGwxk22tdnqvNAsavK5JPYsk9hB4HTyzg@mail.gmail.com>
References: <CAMHV+dC9CaxdThPhSkgqiv1pu0qRxyhsTuOoBmkYVzTcppT+Ow@mail.gmail.com>
	<1417997863187.a64bc4ca@Nodemailer>
	<CAMHV+dB9SzY7w-8+zf_QXbk8p9k3LBu5JPJ079FcV0N2ccxA=A@mail.gmail.com>
	<CAMHV+dAXJAP-3R_mbtqFF=Znez9wtq7U1ND98S0-ATXngcOc-Q@mail.gmail.com>
	<CAEym_HpRoyKUjsPt9m7zr1CA2=WuOtG09i==0AaNFk7ky7Qgsw@mail.gmail.com>
	<8761dkyd2p.fsf@sun.ac.za>
	<CAMHV+dDT83bD_uvP2gHbc0StGf2FtM374mhO5L+FCXpA=amneA@mail.gmail.com>
	<CAMHV+dDpzq4FNMjrwzGwxk22tdnqvNAsavK5JPYsk9hB4HTyzg@mail.gmail.com>
Message-ID: <CAMHV+dANS8+z_1wnkv-+4wfNtr-sSPxcYVAxs+2woNZdKHvFaw@mail.gmail.com>

Nevermind guys, I was able to get it working through that sphinx-gallery
link that Stefan set.  Thanks for all of your help!  Really feels great to
see how nice a website can be created from just auto-docs.

On Tue, Dec 9, 2014 at 2:58 PM, Adam Hughes <hughesadam87 at gmail.com> wrote:

> PS,
>
> Tony, I don't see an index.rst file in scikit-images gallery.  You're
> talking about this folder, yes?:
>
> https://github.com/scikit-image/scikit-image/tree/master/doc/examples
>
> On Tue, Dec 9, 2014 at 2:57 PM, Adam Hughes <hughesadam87 at gmail.com>
> wrote:
>
>> Thanks Tony and Stefan for the resources, I will start working on them
>> now.
>>
>> On Tue, Dec 9, 2014 at 11:58 AM, Stefan van der Walt <stefan at sun.ac.za>
>> wrote:
>>
>>> Hi Adam
>>>
>>> On 2014-12-09 04:12:17, Tony Yu <tsyu80 at gmail.com> wrote:
>>> >> I really am impressed by this plt2rst.py module for autogenerating
>>> example
>>> >> documentation!
>>>
>>> Also have a look at this project, which tries to unify the gallery
>>> builders of the different projects:
>>>
>>> https://github.com/sphinx-gallery/sphinx-gallery
>>>
>>> St?fan
>>>
>>> --
>>> You received this message because you are subscribed to a topic in the
>>> Google Groups "scikit-image" group.
>>> To unsubscribe from this topic, visit
>>> https://groups.google.com/d/topic/scikit-image/k5K6_vanZVI/unsubscribe.
>>> To unsubscribe from this group and all its topics, send an email to
>>> scikit-image+unsubscribe at googlegroups.com.
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>
>>
>
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From steven.silvester at gmail.com  Tue Dec  9 17:02:20 2014
From: steven.silvester at gmail.com (Steven Silvester)
Date: Tue, 9 Dec 2014 16:02:20 -0600
Subject: Travis-wheels fix?
In-Reply-To: <CAH6Pt5osAD-aZ+_Oxpuvtp=9PGsb4rEjO=3wDd0bQ+xGAofQZQ@mail.gmail.com>
References: <1417993256117.cc5d57fd@Nodemailer>
	<75b9e8e1-9f90-46bf-b54e-8205de75064b@googlegroups.com>
	<CA+JHcKR15W7FPEL6s4-6BrtaUGCe5bf7AQKJ=KjQer77tgCJLw@mail.gmail.com>
	<CAH6Pt5osAD-aZ+_Oxpuvtp=9PGsb4rEjO=3wDd0bQ+xGAofQZQ@mail.gmail.com>
Message-ID: <CAHaFxPzxxDQjyZybja5YMoq4GzWO_GSY9tmOwVYaQE20cidpcg@mail.gmail.com>

I think I know what to do:  this line in `travis_setup.py` is causing it to
fail on retry:

`sh -e /etc/init.d/xvfb start`

I'll try moving that to `.travis.yml` and see if that clears it up.


On Tue, Dec 9, 2014 at 3:39 PM, Matthew Brett <matthew.brett at gmail.com>
wrote:

> I wonder if the directory listing is the problem?  Maybe we could try the
> latest github pip with the retry option?
>
> --
> 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/hCKQU-PSasM/unsubscribe.
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> For more options, visit https://groups.google.com/d/optout.
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From matthew.brett at gmail.com  Tue Dec  9 16:39:30 2014
From: matthew.brett at gmail.com (Matthew Brett)
Date: Tue, 9 Dec 2014 16:39:30 -0500
Subject: Travis-wheels fix?
In-Reply-To: <CA+JHcKR15W7FPEL6s4-6BrtaUGCe5bf7AQKJ=KjQer77tgCJLw@mail.gmail.com>
References: <1417993256117.cc5d57fd@Nodemailer>
	<75b9e8e1-9f90-46bf-b54e-8205de75064b@googlegroups.com>
	<CA+JHcKR15W7FPEL6s4-6BrtaUGCe5bf7AQKJ=KjQer77tgCJLw@mail.gmail.com>
Message-ID: <CAH6Pt5osAD-aZ+_Oxpuvtp=9PGsb4rEjO=3wDd0bQ+xGAofQZQ@mail.gmail.com>

I wonder if the directory listing is the problem?  Maybe we could try the
latest github pip with the retry option?
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From stefan at sun.ac.za  Tue Dec  9 11:58:54 2014
From: stefan at sun.ac.za (Stefan van der Walt)
Date: Tue, 09 Dec 2014 18:58:54 +0200
Subject: How do you keep documentation so nice?
In-Reply-To: <CAEym_HpRoyKUjsPt9m7zr1CA2=WuOtG09i==0AaNFk7ky7Qgsw@mail.gmail.com>
References: <CAMHV+dC9CaxdThPhSkgqiv1pu0qRxyhsTuOoBmkYVzTcppT+Ow@mail.gmail.com> <1417997863187.a64bc4ca@Nodemailer> <CAMHV+dB9SzY7w-8+zf_QXbk8p9k3LBu5JPJ079FcV0N2ccxA=A@mail.gmail.com> <CAMHV+dAXJAP-3R_mbtqFF=Znez9wtq7U1ND98S0-ATXngcOc-Q@mail.gmail.com> <CAEym_HpRoyKUjsPt9m7zr1CA2=WuOtG09i==0AaNFk7ky7Qgsw@mail.gmail.com>
Message-ID: <8761dkyd2p.fsf@sun.ac.za>

Hi Adam

On 2014-12-09 04:12:17, Tony Yu <tsyu80 at gmail.com> wrote:
>> I really am impressed by this plt2rst.py module for autogenerating example
>> documentation!

Also have a look at this project, which tries to unify the gallery
builders of the different projects:

https://github.com/sphinx-gallery/sphinx-gallery

St?fan


From hughesadam87 at gmail.com  Tue Dec  9 19:43:46 2014
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Tue, 9 Dec 2014 19:43:46 -0500
Subject: How do you keep documentation so nice?
In-Reply-To: <87bnncwekq.fsf@sun.ac.za>
References: <87oarcwhb8.fsf@sun.ac.za>
	<1418168800486.8d77c162@Nodemailer>
	<87bnncwekq.fsf@sun.ac.za>
Message-ID: <CAMHV+dAh9WDm+pnXir-BCSi4dumCF26o-d=KUcWTJRYU=9FhiA@mail.gmail.com>

Hey guys,

Thanks for all of your help!  Here is my working version:

http://hugadams.github.io/scikit-spectra/

Check out the IPython GUI video if you're interested.

On Tue, Dec 9, 2014 at 7:09 PM, Stefan van der Walt <stefan at sun.ac.za>
wrote:

> On 2014-12-10 01:46:40, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> > If I want to include my own non-gallery image, should I generate it
> > manually, and if so, where should I put it?
>
> In that case, you can use the "plot" directive (see `plot_directive.py`
> in the `doc/ext` directory.  Sorry that you have to pry all of this out
> of me--I am also rusty since I don't use it that often.
>
> St?fan
>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "scikit-image" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/scikit-image/k5K6_vanZVI/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From willemolding at gmail.com  Tue Dec  9 23:09:29 2014
From: willemolding at gmail.com (Willem Olding)
Date: Tue, 9 Dec 2014 20:09:29 -0800 (PST)
Subject: Local GLCM features
In-Reply-To: <877fy0we4p.fsf@sun.ac.za>
References: <59431232-3b1d-441d-8963-54368394e882@googlegroups.com>
 <877fy0we4p.fsf@sun.ac.za>
Message-ID: <a70fc2f5-2fae-4dde-b8f9-9e6bb16d44a3@googlegroups.com>

Great news.
I will tidy up my current code and post a pull request in the next couple 
of days.
Regards,
Willem
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From stefan at sun.ac.za  Tue Dec  9 17:31:14 2014
From: stefan at sun.ac.za (Stefan van der Walt)
Date: Wed, 10 Dec 2014 00:31:14 +0200
Subject: Help with shape descriptors
In-Reply-To: <892d6e2e-6a60-4e9f-91ae-bf6d5ec8f9ae@googlegroups.com>
References: <892d6e2e-6a60-4e9f-91ae-bf6d5ec8f9ae@googlegroups.com>
Message-ID: <87vblkwj4d.fsf@sun.ac.za>

Hi Clay

On 2014-12-09 21:58:43, Claiborne Morton <claiborne.morton at gmail.com> wrote:
> I used an eccentricity filter on the original image to remove all of the 
> cells with eccentricity less than 0.6. Making this any higher results in 
> removal of sickle cells. What other descriptors might be used for further 
> differentiation?

We don't have an implementation of this unfortunately, but you can also
try

"Partial shape recognition by sub-matrix matching for partial
matching guided image labeling" by Saber, Xu and Tekalp.

There is also a pull request (waiting for review) that implements Shape
Contexts by Malik et al.

St?fan


From stefan at sun.ac.za  Tue Dec  9 17:36:26 2014
From: stefan at sun.ac.za (Stefan van der Walt)
Date: Wed, 10 Dec 2014 00:36:26 +0200
Subject: How do you keep documentation so nice?
In-Reply-To: <CAMHV+dANS8+z_1wnkv-+4wfNtr-sSPxcYVAxs+2woNZdKHvFaw@mail.gmail.com>
References: <CAMHV+dC9CaxdThPhSkgqiv1pu0qRxyhsTuOoBmkYVzTcppT+Ow@mail.gmail.com> <1417997863187.a64bc4ca@Nodemailer> <CAMHV+dB9SzY7w-8+zf_QXbk8p9k3LBu5JPJ079FcV0N2ccxA=A@mail.gmail.com> <CAMHV+dAXJAP-3R_mbtqFF=Znez9wtq7U1ND98S0-ATXngcOc-Q@mail.gmail.com> <CAEym_HpRoyKUjsPt9m7zr1CA2=WuOtG09i==0AaNFk7ky7Qgsw@mail.gmail.com> <8761dkyd2p.fsf@sun.ac.za> <CAMHV+dDT83bD_uvP2gHbc0StGf2FtM374mhO5L+FCXpA=amneA@mail.gmail.com> <CAMHV+dDpzq4FNMjrwzGwxk22tdnqvNAsavK5JPYsk9hB4HTyzg@mail.gmail.com> <CAMHV+dANS8+z_1wnkv-+4wfNtr-sSPxcYVAxs+2woNZdKHvFaw@mail.gmail.com>
Message-ID: <87tx14wivp.fsf@sun.ac.za>

Hi Adam

On 2014-12-09 22:54:34, Adam Hughes <hughesadam87 at gmail.com> wrote:
> Nevermind guys, I was able to get it working through that sphinx-gallery
> link that Stefan set.

I'm not sure how--that repo still looks to be fairly empty!

The process is: we run tools that generates .rst files, the rst files
get compiled by Sphinx, during which the plots etc. get generated.  The
result is then pushed to a repository on GitHub.  Easiest way to
understand it is to run the script and examine the new files created.

St?fan


From stefan at sun.ac.za  Tue Dec  9 18:10:19 2014
From: stefan at sun.ac.za (Stefan van der Walt)
Date: Wed, 10 Dec 2014 01:10:19 +0200
Subject: How do you keep documentation so nice?
In-Reply-To: <1418165940884.800f51a4@Nodemailer>
References: <87tx14wivp.fsf@sun.ac.za> <1418165940884.800f51a4@Nodemailer>
Message-ID: <87oarcwhb8.fsf@sun.ac.za>

Hi Juan

On 2014-12-10 00:59:01, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> Huh??? You sent that link! LOL I was puzzled too but then saw the PR
> from the owner's "personal" fork of the repo, which I guess (no time
> to look at it yet) has a fair few resources.

This is where the project is supposed to be maintained--I am following
the discussions, and thought they just haven't committed any code.  Now
that I know differently I'll ask them to commit to that branch.

> I don't actually understand the process of generating plots in the case of hand-written docs. E.g. this image embed by Emmanuelle:
>
> https://github.com/scikit-image/scikit-image/blob/master/doc/source/user_guide/numpy_images.txt#L73

She "cheated" a bit and included an image from the gallery.

> Is that generated from the code in the .rst file itself, or does she
> have to know (through non-automated means) that the auto-example
> produces the same image as is required in the rst?

In this case, yes.

St?fan


From stefan at sun.ac.za  Tue Dec  9 18:26:36 2014
From: stefan at sun.ac.za (Stefan van der Walt)
Date: Wed, 10 Dec 2014 01:26:36 +0200
Subject: Permalinks embedded on mailing list messages
In-Reply-To: <1417827664422.112d502b@Nodemailer>
References: <87vblqtg0g.fsf@sun.ac.za> <1417827664422.112d502b@Nodemailer>
Message-ID: <87fvcowgk3.fsf@sun.ac.za>

Hi Juan

On 2014-12-06 03:01:04, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> Holy moly! What happened to Google's "Data Liberation Front"? I guess
> this illustrates just how neglected GGroups is.

If I understand [messages between the lines from my colleagues at
Google] correctly, Google Groups will be available on Google Takeout
sometime in the near-ish future.

Let's give it a while and see where it goes.

St?fan


From paalge at gmail.com  Wed Dec 10 05:05:19 2014
From: paalge at gmail.com (=?UTF-8?Q?P=C3=A5l_Gunnar_Ellingsen?=)
Date: Wed, 10 Dec 2014 02:05:19 -0800 (PST)
Subject: Number of bins in Entropy and Enhance_contrast for uint16
Message-ID: <79778062-f708-40ab-bd24-469616fe401b@googlegroups.com>

Hi

I'm new to using the scikit-image library, so if this question is silly 
please excuse me.

I'm trying to run contrast enhancement on thousands of  1000x1000 images of 
"numpy.uint16" type.
I'm expecting this to be very computationally expensive, something 
confirmed when running either entropy or enhance_contrast (from 

"skimage.filter.rank") with the warning:

"Bitdepth of 15 may result in bad rank filter performance due to large 
number of bins".
I'm wondering if it is possible to reduce the number of bins via an option?
I've tried to find such a keyword in the documentation and source code, but 
I haven't been able to find it.


Kind regards

P?l
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From stefan at sun.ac.za  Tue Dec  9 19:09:25 2014
From: stefan at sun.ac.za (Stefan van der Walt)
Date: Wed, 10 Dec 2014 02:09:25 +0200
Subject: How do you keep documentation so nice?
In-Reply-To: <1418168800486.8d77c162@Nodemailer>
References: <87oarcwhb8.fsf@sun.ac.za> <1418168800486.8d77c162@Nodemailer>
Message-ID: <87bnncwekq.fsf@sun.ac.za>

On 2014-12-10 01:46:40, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> If I want to include my own non-gallery image, should I generate it
> manually, and if so, where should I put it?

In that case, you can use the "plot" directive (see `plot_directive.py`
in the `doc/ext` directory.  Sorry that you have to pry all of this out
of me--I am also rusty since I don't use it that often.

St?fan


From stefan at sun.ac.za  Tue Dec  9 19:19:02 2014
From: stefan at sun.ac.za (Stefan van der Walt)
Date: Wed, 10 Dec 2014 02:19:02 +0200
Subject: Local GLCM features
In-Reply-To: <59431232-3b1d-441d-8963-54368394e882@googlegroups.com>
References: <59431232-3b1d-441d-8963-54368394e882@googlegroups.com>
Message-ID: <877fy0we4p.fsf@sun.ac.za>

Hi Willem

On 2014-12-05 01:08:04, Willem Olding <willemolding at gmail.com> wrote:
> To overcome this I extended scikit-image with a function that performs
> the sliding window as fast cython code. It takes an image, distance,
> angle and window size and generates a texture image with the GLCM
> features
> ['mean','variance','contrast','dissimilarity','homogeneity','ASM','entropy','correlation']
> calculated at every pixel.

We had a request for something very similar a while ago!  Also, I think
we need to think about the API for the current GLCM functionality--it
seems it is more natural to specify specific offsets, rather than the
current angle/radius.  What do you think?

> Would this be something people are interested in including as part of 
> scikit-image?

Absolutely!  Please file a pull request, and then we can work on it
there.

Regards
St?fan


From georgeshattab at gmail.com  Wed Dec 10 05:50:52 2014
From: georgeshattab at gmail.com (Georges H)
Date: Wed, 10 Dec 2014 02:50:52 -0800 (PST)
Subject: Help with shape descriptors
In-Reply-To: <892d6e2e-6a60-4e9f-91ae-bf6d5ec8f9ae@googlegroups.com>
References: <892d6e2e-6a60-4e9f-91ae-bf6d5ec8f9ae@googlegroups.com>
Message-ID: <194cfa3b-9fe9-422b-a783-3b30301f4fdb@googlegroups.com>

Segmentation using Watershed would work to differentiate all cells (or the 
seeded watershed).
Differentiating both shapes could be done using a mask for each by fitting 
it and then counting n fits.


On Tuesday, 9 December 2014 20:58:43 UTC+1, Claiborne Morton wrote:
>
> Hello Scikit community, 
>
> I'm looking for help using particle descriptors to identify sickle cells 
> in the attached image. As you can see the sickle cells are the long, thin 
> cells. I have two issues, the first is that in some cases the sickle cells 
> are in contact with other healthy cells. I am trying to find a way of 
> separating (or water-shedding) the cells so that each "particle" is 
> actually one cell. The second issue is that I am dealing with is trying to 
> find shape descriptors that will allow me to accurately distinguish the 
> sickle cells from the healthy cells. 
>
> I used an eccentricity filter on the original image to remove all of the 
> cells with eccentricity less than 0.6. Making this any higher results in 
> removal of sickle cells. What other descriptors might be used for further 
> differentiation?
>
> Thanks, Clay 
>
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From paalge at gmail.com  Wed Dec 10 07:17:33 2014
From: paalge at gmail.com (=?UTF-8?Q?P=C3=A5l_Gunnar_Ellingsen?=)
Date: Wed, 10 Dec 2014 04:17:33 -0800 (PST)
Subject: Number of bins in Entropy and Enhance_contrast for uint16
In-Reply-To: <87zjavvmqn.fsf@sun.ac.za>
References: <79778062-f708-40ab-bd24-469616fe401b@googlegroups.com>
 <87zjavvmqn.fsf@sun.ac.za>
Message-ID: <accdecce-678f-4963-9e0b-3b6778986b10@googlegroups.com>

Hi

Thank you for the quick answer.
I agree that converting it to uint8 will speed it up by a lot, and I have 
also tried this.
Though it also removes so much data from my 16 bit grayscale image, that 
the contrast I'm interesting in isn't there anymore.
This is the reason why I think that changing the binning from 1000 to 100 
or even 50, without changing the data type would be a better choice.

Kind regards

P?l



On Wednesday, 10 December 2014 11:10:48 UTC+1, Stefan van der Walt wrote:
>
> Hi P?l 
>
> On 2014-12-10 12:05:19, P?l Gunnar Ellingsen <paa... at gmail.com 
> <javascript:>> wrote: 
> > "Bitdepth of 15 may result in bad rank filter performance due to large 
> > number of bins". 
> > I'm wondering if it is possible to reduce the number of bins via an 
> option? 
> > I've tried to find such a keyword in the documentation and source code, 
> but 
> > I haven't been able to find it. 
>
> The easiest is to change the image dtype by using, e.g., 
>
> from skimage import img_as_ubyte 
> image8 = img_as_ubyte(image16) 
>
> The algorithm should run much faster on image8 than on image16. 
>
> Regards 
> St?fan 
>
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From hughesadam87 at gmail.com  Wed Dec 10 10:09:20 2014
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Wed, 10 Dec 2014 10:09:20 -0500
Subject: How do you keep documentation so nice?
In-Reply-To: <87k31zvjbr.fsf@sun.ac.za>
References: <87oarcwhb8.fsf@sun.ac.za>
	<1418168800486.8d77c162@Nodemailer>
	<87bnncwekq.fsf@sun.ac.za>
	<CAMHV+dAh9WDm+pnXir-BCSi4dumCF26o-d=KUcWTJRYU=9FhiA@mail.gmail.com>
	<87k31zvjbr.fsf@sun.ac.za>
Message-ID: <CAMHV+dBTXf+q2hER+45gEc_Pe8eqCynUoAbGfcbjA+S=RwPHeQ@mail.gmail.com>

Thanks Stefan.  Ya we were pretty surprised when dumping the mpld3 html
back into midel just happened to work and not break anything
On Dec 10, 2014 6:24 AM, "Stefan van der Walt" <stefan at sun.ac.za> wrote:

> Hi Adam
>
> On 2014-12-10 02:43:46, Adam Hughes <hughesadam87 at gmail.com> wrote:
> > http://hugadams.github.io/scikit-spectra/
>
> That is a very impressive notebook widget shown in the video!  I love
> how it interacts with mpl3d.
>
> St?fan
>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "scikit-image" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/scikit-image/k5K6_vanZVI/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From hughesadam87 at gmail.com  Wed Dec 10 10:16:13 2014
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Wed, 10 Dec 2014 10:16:13 -0500
Subject: How do you keep documentation so nice?
In-Reply-To: <CAMHV+dBTXf+q2hER+45gEc_Pe8eqCynUoAbGfcbjA+S=RwPHeQ@mail.gmail.com>
References: <87oarcwhb8.fsf@sun.ac.za>
	<1418168800486.8d77c162@Nodemailer>
	<87bnncwekq.fsf@sun.ac.za>
	<CAMHV+dAh9WDm+pnXir-BCSi4dumCF26o-d=KUcWTJRYU=9FhiA@mail.gmail.com>
	<87k31zvjbr.fsf@sun.ac.za>
	<CAMHV+dBTXf+q2hER+45gEc_Pe8eqCynUoAbGfcbjA+S=RwPHeQ@mail.gmail.com>
Message-ID: <CAMHV+dA248MbRwq1=xcpOX791ifS=m37MuRgDyJCOn-NtAN=zg@mail.gmail.com>

*model
On Dec 10, 2014 10:09 AM, "Adam Hughes" <hughesadam87 at gmail.com> wrote:

> Thanks Stefan.  Ya we were pretty surprised when dumping the mpld3 html
> back into midel just happened to work and not break anything
> On Dec 10, 2014 6:24 AM, "Stefan van der Walt" <stefan at sun.ac.za> wrote:
>
>> Hi Adam
>>
>> On 2014-12-10 02:43:46, Adam Hughes <hughesadam87 at gmail.com> wrote:
>> > http://hugadams.github.io/scikit-spectra/
>>
>> That is a very impressive notebook widget shown in the video!  I love
>> how it interacts with mpl3d.
>>
>> St?fan
>>
>> --
>> You received this message because you are subscribed to a topic in the
>> Google Groups "scikit-image" group.
>> To unsubscribe from this topic, visit
>> https://groups.google.com/d/topic/scikit-image/k5K6_vanZVI/unsubscribe.
>> To unsubscribe from this group and all its topics, send an email to
>> scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
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From stefan at sun.ac.za  Wed Dec 10 05:10:40 2014
From: stefan at sun.ac.za (Stefan van der Walt)
Date: Wed, 10 Dec 2014 12:10:40 +0200
Subject: Number of bins in Entropy and Enhance_contrast for uint16
In-Reply-To: <79778062-f708-40ab-bd24-469616fe401b@googlegroups.com>
References: <79778062-f708-40ab-bd24-469616fe401b@googlegroups.com>
Message-ID: <87zjavvmqn.fsf@sun.ac.za>

Hi P?l

On 2014-12-10 12:05:19, P?l Gunnar Ellingsen <paalge at gmail.com> wrote:
> "Bitdepth of 15 may result in bad rank filter performance due to large 
> number of bins".
> I'm wondering if it is possible to reduce the number of bins via an option?
> I've tried to find such a keyword in the documentation and source code, but 
> I haven't been able to find it.

The easiest is to change the image dtype by using, e.g.,

from skimage import img_as_ubyte
image8 = img_as_ubyte(image16)

The algorithm should run much faster on image8 than on image16.

Regards
St?fan


From stefan at sun.ac.za  Wed Dec 10 06:24:24 2014
From: stefan at sun.ac.za (Stefan van der Walt)
Date: Wed, 10 Dec 2014 13:24:24 +0200
Subject: How do you keep documentation so nice?
In-Reply-To: <CAMHV+dAh9WDm+pnXir-BCSi4dumCF26o-d=KUcWTJRYU=9FhiA@mail.gmail.com>
References: <87oarcwhb8.fsf@sun.ac.za> <1418168800486.8d77c162@Nodemailer> <87bnncwekq.fsf@sun.ac.za> <CAMHV+dAh9WDm+pnXir-BCSi4dumCF26o-d=KUcWTJRYU=9FhiA@mail.gmail.com>
Message-ID: <87k31zvjbr.fsf@sun.ac.za>

Hi Adam

On 2014-12-10 02:43:46, Adam Hughes <hughesadam87 at gmail.com> wrote:
> http://hugadams.github.io/scikit-spectra/

That is a very impressive notebook widget shown in the video!  I love
how it interacts with mpl3d.

St?fan


From kmichael.aye at gmail.com  Wed Dec 10 18:14:03 2014
From: kmichael.aye at gmail.com (Michael Aye)
Date: Wed, 10 Dec 2014 15:14:03 -0800 (PST)
Subject: How do you keep documentation so nice?
In-Reply-To: <CAMHV+dA248MbRwq1=xcpOX791ifS=m37MuRgDyJCOn-NtAN=zg@mail.gmail.com>
References: <87oarcwhb8.fsf@sun.ac.za>
 <1418168800486.8d77c162@Nodemailer>
 <87bnncwekq.fsf@sun.ac.za>
 <CAMHV+dAh9WDm+pnXir-BCSi4dumCF26o-d=KUcWTJRYU=9FhiA@mail.gmail.com>
 <87k31zvjbr.fsf@sun.ac.za>
 <CAMHV+dBTXf+q2hER+45gEc_Pe8eqCynUoAbGfcbjA+S=RwPHeQ@mail.gmail.com>
 <CAMHV+dA248MbRwq1=xcpOX791ifS=m37MuRgDyJCOn-NtAN=zg@mail.gmail.com>
Message-ID: <5b7f5a33-ad65-49df-8cad-416a4fa96e36@googlegroups.com>

On 2014-12-10 02:43:46, Adam Hughes <hughes... at gmail.com <javascript:>> 
wrote:

> > http://hugadams.github.io/scikit-spectra/
>>>
>>> That is a very impressive notebook widget shown in the video!  I love
>>> how it interacts with mpl3d.
>>>
>>>
>>> Ditto! Man, can't wait to play with this! Very happy that there's 
finally a package focusing on spectral analysis! It also just comes at the 
right time, just started in my new job working on data from an imaging 
spectrometer for the first time. ;)

Michael
 
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From hughesadam87 at gmail.com  Wed Dec 10 20:01:55 2014
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Wed, 10 Dec 2014 20:01:55 -0500
Subject: How do you keep documentation so nice?
In-Reply-To: <5b7f5a33-ad65-49df-8cad-416a4fa96e36@googlegroups.com>
References: <87oarcwhb8.fsf@sun.ac.za>
	<1418168800486.8d77c162@Nodemailer>
	<87bnncwekq.fsf@sun.ac.za>
	<CAMHV+dAh9WDm+pnXir-BCSi4dumCF26o-d=KUcWTJRYU=9FhiA@mail.gmail.com>
	<87k31zvjbr.fsf@sun.ac.za>
	<CAMHV+dBTXf+q2hER+45gEc_Pe8eqCynUoAbGfcbjA+S=RwPHeQ@mail.gmail.com>
	<CAMHV+dA248MbRwq1=xcpOX791ifS=m37MuRgDyJCOn-NtAN=zg@mail.gmail.com>
	<5b7f5a33-ad65-49df-8cad-416a4fa96e36@googlegroups.com>
Message-ID: <CAMHV+dD=73bo+ZtGTu8-D3X_HCoCi0Ub=bJT-GPtZJdcTmMkYQ@mail.gmail.com>

Thanks Michael.

Be warned, only about 3 people are using the library at the moment, so it's
quite likely that you'll encounter some bugs just by virtue of using a new
dataset that probably will bring to light some considerations that we
overlooked.  In addition, I only support pandas 0.14 right now (0.15 has a
lot of private API changes that directly affect us).  But we did feel like
the library was close enough to ready to share it, and I hope you can try
it out.  If you do want to give it a whirl sometime soon, please feel free
to contact us at skspec at googlegroups.com (or me personally) and we will at
least make sure to help get you up and running.  Let us know what kind of
data you're working on and what type of analysis you're doing.  We've spend
a lot of time putting out datastructures together, but we haven't put a
great deal of thought into the actual spectral utilitiles, workflows and
analysis that we should host, other than correlation spectroscopy and base
things like dynamic baseline fitting.



On Wed, Dec 10, 2014 at 6:14 PM, Michael Aye <kmichael.aye at gmail.com> wrote:

> On 2014-12-10 02:43:46, Adam Hughes <hughes... at gmail.com> wrote:
>
>> > http://hugadams.github.io/scikit-spectra/
>>>>
>>>> That is a very impressive notebook widget shown in the video!  I love
>>>> how it interacts with mpl3d.
>>>>
>>>>
>>>> Ditto! Man, can't wait to play with this! Very happy that there's
> finally a package focusing on spectral analysis! It also just comes at the
> right time, just started in my new job working on data from an imaging
> spectrometer for the first time. ;)
>
> Michael
>
>
> --
> 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/k5K6_vanZVI/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From jni.soma at gmail.com  Wed Dec 10 08:19:49 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Thu, 11 Dec 2014 00:19:49 +1100
Subject: Number of bins in Entropy and Enhance_contrast for uint16
In-Reply-To: <accdecce-678f-4963-9e0b-3b6778986b10@googlegroups.com>
References: <79778062-f708-40ab-bd24-469616fe401b@googlegroups.com>
 <87zjavvmqn.fsf@sun.ac.za> <accdecce-678f-4963-9e0b-3b6778986b10@googlegroups.com>
Message-ID: <CA+JHcKQaWuBgFVVOzj3vvj=Wenf3gwDTMgyJc6mYyrykBbFbJw@mail.gmail.com>

Hi P?l,

Actually, the rank filters are fast up to 12 bits, so if you can (manually)
compress your data to be in 0-2047 in a uint16 array, you might still get
good performance. Hope that helps!

Juan.

On Wed, Dec 10, 2014 at 11:17 PM, P?l Gunnar Ellingsen <paalge at gmail.com>
wrote:

> Hi
>
> Thank you for the quick answer.
> I agree that converting it to uint8 will speed it up by a lot, and I have
> also tried this.
> Though it also removes so much data from my 16 bit grayscale image, that
> the contrast I'm interesting in isn't there anymore.
> This is the reason why I think that changing the binning from 1000 to 100
> or even 50, without changing the data type would be a better choice.
>
> Kind regards
>
> P?l
>
>
>
> On Wednesday, 10 December 2014 11:10:48 UTC+1, Stefan van der Walt wrote:
>>
>> Hi P?l
>>
>> On 2014-12-10 12:05:19, P?l Gunnar Ellingsen <paa... at gmail.com> wrote:
>> > "Bitdepth of 15 may result in bad rank filter performance due to large
>> > number of bins".
>> > I'm wondering if it is possible to reduce the number of bins via an
>> option?
>> > I've tried to find such a keyword in the documentation and source code,
>> but
>> > I haven't been able to find it.
>>
>> The easiest is to change the image dtype by using, e.g.,
>>
>> from skimage import img_as_ubyte
>> image8 = img_as_ubyte(image16)
>>
>> The algorithm should run much faster on image8 than on image16.
>>
>> 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/d/optout.
>
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From jni.soma at gmail.com  Thu Dec 11 06:56:58 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Thu, 11 Dec 2014 03:56:58 -0800 (PST)
Subject: How do you keep documentation so nice?
In-Reply-To: <CAMHV+dD=73bo+ZtGTu8-D3X_HCoCi0Ub=bJT-GPtZJdcTmMkYQ@mail.gmail.com>
References: <CAMHV+dD=73bo+ZtGTu8-D3X_HCoCi0Ub=bJT-GPtZJdcTmMkYQ@mail.gmail.com>
Message-ID: <1418299017813.d4c8c85c@Nodemailer>

Adam, just fyi, we are considering moving away from GoogleGroups... (See a separate discussion on this list). Since you are on the ground floor, you might want to reconsider your choice. I've been using Nabble for my (very low volume!) gala list and it's been really good.

On Thu, Dec 11, 2014 at 12:01 PM, Adam Hughes <hughesadam87 at gmail.com>
wrote:

> Thanks Michael.
> Be warned, only about 3 people are using the library at the moment, so it's
> quite likely that you'll encounter some bugs just by virtue of using a new
> dataset that probably will bring to light some considerations that we
> overlooked.  In addition, I only support pandas 0.14 right now (0.15 has a
> lot of private API changes that directly affect us).  But we did feel like
> the library was close enough to ready to share it, and I hope you can try
> it out.  If you do want to give it a whirl sometime soon, please feel free
> to contact us at skspec at googlegroups.com (or me personally) and we will at
> least make sure to help get you up and running.  Let us know what kind of
> data you're working on and what type of analysis you're doing.  We've spend
> a lot of time putting out datastructures together, but we haven't put a
> great deal of thought into the actual spectral utilitiles, workflows and
> analysis that we should host, other than correlation spectroscopy and base
> things like dynamic baseline fitting.
> On Wed, Dec 10, 2014 at 6:14 PM, Michael Aye <kmichael.aye at gmail.com> wrote:
>> On 2014-12-10 02:43:46, Adam Hughes <hughes... at gmail.com> wrote:
>>
>>> > http://hugadams.github.io/scikit-spectra/
>>>>>
>>>>> That is a very impressive notebook widget shown in the video!  I love
>>>>> how it interacts with mpl3d.
>>>>>
>>>>>
>>>>> Ditto! Man, can't wait to play with this! Very happy that there's
>> finally a package focusing on spectral analysis! It also just comes at the
>> right time, just started in my new job working on data from an imaging
>> spectrometer for the first time. ;)
>>
>> Michael
>>
>>
>> --
>> 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/k5K6_vanZVI/unsubscribe.
>> To unsubscribe from this group and all its topics, send an email to
>> scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
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From hughesadam87 at gmail.com  Thu Dec 11 12:45:27 2014
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Thu, 11 Dec 2014 12:45:27 -0500
Subject: How do you keep documentation so nice?
In-Reply-To: <1418299017813.d4c8c85c@Nodemailer>
References: <CAMHV+dD=73bo+ZtGTu8-D3X_HCoCi0Ub=bJT-GPtZJdcTmMkYQ@mail.gmail.com>
	<1418299017813.d4c8c85c@Nodemailer>
Message-ID: <CAMHV+dD8TPGcWaEc3wEVrshV62Ev2ZGRgzH5FhZUYz2-ANh=0Q@mail.gmail.com>

Thanks, that's great advice.  Also, do you guys pay to host your site?  Can
you recommend a low-cost, or free, static-website hosting vendor?  We are
currently using gh-pages branch on github to host our site, and I really
hate having this secondary branch.  Especially when I need the
documentation to have access to the source code modules or setup.py file
(as it's on a second branch).

On Thu, Dec 11, 2014 at 6:56 AM, Juan Nunez-Iglesias <jni.soma at gmail.com>
wrote:
>
> Adam, just fyi, we are considering moving away from GoogleGroups... (See a
> separate discussion on this list). Since you are on the ground floor, you
> might want to reconsider your choice. I've been using Nabble for my (very
> low volume!) gala list and it's been really good.
>
>
>
>
> On Thu, Dec 11, 2014 at 12:01 PM, Adam Hughes <hughesadam87 at gmail.com>
> wrote:
>
>> Thanks Michael.
>>
>> Be warned, only about 3 people are using the library at the moment, so
>> it's quite likely that you'll encounter some bugs just by virtue of using a
>> new dataset that probably will bring to light some considerations that we
>> overlooked.  In addition, I only support pandas 0.14 right now (0.15 has a
>> lot of private API changes that directly affect us).  But we did feel like
>> the library was close enough to ready to share it, and I hope you can try
>> it out.  If you do want to give it a whirl sometime soon, please feel free
>> to contact us at skspec at googlegroups.com (or me personally) and we will
>> at least make sure to help get you up and running.  Let us know what kind
>> of data you're working on and what type of analysis you're doing.  We've
>> spend a lot of time putting out datastructures together, but we haven't put
>> a great deal of thought into the actual spectral utilitiles, workflows and
>> analysis that we should host, other than correlation spectroscopy and base
>> things like dynamic baseline fitting.
>>
>>
>>
>> On Wed, Dec 10, 2014 at 6:14 PM, Michael Aye <kmichael.aye at gmail.com>
>> wrote:
>>
>>>  On 2014-12-10 02:43:46, Adam Hughes <hughes... at gmail.com> wrote:
>>>
>>>> > http://hugadams.github.io/scikit-spectra/
>>>>>>
>>>>>> That is a very impressive notebook widget shown in the video!  I love
>>>>>> how it interacts with mpl3d.
>>>>>>
>>>>>>
>>>>>> Ditto! Man, can't wait to play with this! Very happy that there's
>>> finally a package focusing on spectral analysis! It also just comes at the
>>> right time, just started in my new job working on data from an imaging
>>> spectrometer for the first time. ;)
>>>
>>> Michael
>>>
>>>
>>> --
>>> 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/k5K6_vanZVI/unsubscribe.
>>> To unsubscribe from this group and all its topics, send an email to
>>> scikit-image+unsubscribe at googlegroups.com.
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>
>>  --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>  --
> 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/k5K6_vanZVI/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From tcaswell at gmail.com  Thu Dec 11 12:57:58 2014
From: tcaswell at gmail.com (Thomas Caswell)
Date: Thu, 11 Dec 2014 17:57:58 +0000
Subject: How do you keep documentation so nice?
References: <CAMHV+dD=73bo+ZtGTu8-D3X_HCoCi0Ub=bJT-GPtZJdcTmMkYQ@mail.gmail.com>
 <1418299017813.d4c8c85c@Nodemailer> <CAMHV+dD8TPGcWaEc3wEVrshV62Ev2ZGRgzH5FhZUYz2-ANh=0Q@mail.gmail.com>
Message-ID: <CAA48SF8a0oa2y4RX-jNHNnsRLu0S0pduNUBUNYruiz5QEuTpmA@mail.gmail.com>

matplotlib uses the organization-level gh-pages to host the documentation
which seems to work pretty well.

On Thu Dec 11 2014 at 12:45:30 PM Adam Hughes <hughesadam87 at gmail.com>
wrote:

> Thanks, that's great advice.  Also, do you guys pay to host your site?
> Can you recommend a low-cost, or free, static-website hosting vendor?  We
> are currently using gh-pages branch on github to host our site, and I
> really hate having this secondary branch.  Especially when I need the
> documentation to have access to the source code modules or setup.py file
> (as it's on a second branch).
>
> On Thu, Dec 11, 2014 at 6:56 AM, Juan Nunez-Iglesias <jni.soma at gmail.com>
> wrote:
>>
>> Adam, just fyi, we are considering moving away from GoogleGroups... (See
>> a separate discussion on this list). Since you are on the ground floor, you
>> might want to reconsider your choice. I've been using Nabble for my (very
>> low volume!) gala list and it's been really good.
>>
>>
>>
>>
>> On Thu, Dec 11, 2014 at 12:01 PM, Adam Hughes <hughesadam87 at gmail.com>
>> wrote:
>>
>>> Thanks Michael.
>>>
>>> Be warned, only about 3 people are using the library at the moment, so
>>> it's quite likely that you'll encounter some bugs just by virtue of using a
>>> new dataset that probably will bring to light some considerations that we
>>> overlooked.  In addition, I only support pandas 0.14 right now (0.15 has a
>>> lot of private API changes that directly affect us).  But we did feel like
>>> the library was close enough to ready to share it, and I hope you can try
>>> it out.  If you do want to give it a whirl sometime soon, please feel free
>>> to contact us at skspec at googlegroups.com (or me personally) and we will
>>> at least make sure to help get you up and running.  Let us know what kind
>>> of data you're working on and what type of analysis you're doing.  We've
>>> spend a lot of time putting out datastructures together, but we haven't put
>>> a great deal of thought into the actual spectral utilitiles, workflows and
>>> analysis that we should host, other than correlation spectroscopy and base
>>> things like dynamic baseline fitting.
>>>
>>>
>>>
>>> On Wed, Dec 10, 2014 at 6:14 PM, Michael Aye <kmichael.aye at gmail.com>
>>> wrote:
>>>
>>>>  On 2014-12-10 02:43:46, Adam Hughes <hughes... at gmail.com> wrote:
>>>>
>>>>> > http://hugadams.github.io/scikit-spectra/
>>>>>>>
>>>>>>> That is a very impressive notebook widget shown in the video!  I love
>>>>>>> how it interacts with mpl3d.
>>>>>>>
>>>>>>>
>>>>>>> Ditto! Man, can't wait to play with this! Very happy that there's
>>>> finally a package focusing on spectral analysis! It also just comes at the
>>>> right time, just started in my new job working on data from an imaging
>>>> spectrometer for the first time. ;)
>>>>
>>>> Michael
>>>>
>>>>
>>>> --
>>>> 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/k5K6_vanZVI/unsubscribe.
>>>> To unsubscribe from this group and all its topics, send an email to
>>>> scikit-image+unsubscribe at googlegroups.com.
>>>> For more options, visit https://groups.google.com/d/optout.
>>>>
>>>
>>>  --
>>> You received this message because you are subscribed to the Google
>>> Groups "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>
>>  --
>> 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/k5K6_vanZVI/unsubscribe.
>> To unsubscribe from this group and all its topics, send an email to
>> scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From h4n5p3ter at gmail.com  Fri Dec 12 04:19:33 2014
From: h4n5p3ter at gmail.com (hans peter)
Date: Fri, 12 Dec 2014 01:19:33 -0800 (PST)
Subject: can not load / use functions from skimage.feature
Message-ID: <6ffbb648-42d3-4042-be68-5a16f3883822@googlegroups.com>

Hi there,
I running Windows 7 (64bit)
with WinPython 2.7* NumPy 1.8.1, SciPy 0.13.3, Matplotlib 1.3.1 guidata 
1.6.1, guiqwt 2.3.2 Cython?0.21.1*
and the skimage from 
http://www.lfd.uci.edu/~gohlke/pythonlibs/#scikits.image ( pre compiled )
Also the python path is correct set ( Path and Pythonpath )

The basic example from the website works fine but after I tryed to import 
*from skimage.feature import blob_dog, blob_log, blob_doh*I got different 
error messages, so I installed and unistalled every thing but nothing works.

My current error message after try to import skimage.featrue 

>>> Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: cannot import name blob_dog

I also had some messages like, could not find .corner and .hough and so on

I have absolutly no clue how to solve this .. 

would be nice if someone could help

thanks
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From stefan at sun.ac.za  Thu Dec 11 19:13:07 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Fri, 12 Dec 2014 02:13:07 +0200
Subject: How do you keep documentation so nice?
In-Reply-To: <CAA48SF8a0oa2y4RX-jNHNnsRLu0S0pduNUBUNYruiz5QEuTpmA@mail.gmail.com>
References: <CAMHV+dD=73bo+ZtGTu8-D3X_HCoCi0Ub=bJT-GPtZJdcTmMkYQ@mail.gmail.com>
	<1418299017813.d4c8c85c@Nodemailer>
	<CAMHV+dD8TPGcWaEc3wEVrshV62Ev2ZGRgzH5FhZUYz2-ANh=0Q@mail.gmail.com>
	<CAA48SF8a0oa2y4RX-jNHNnsRLu0S0pduNUBUNYruiz5QEuTpmA@mail.gmail.com>
Message-ID: <CABDkGQkpczfCgZcfpNNOEGP5N05w-QLADvStgDaYw=Vxg1bG0A@mail.gmail.com>

On Dec 11, 2014 7:58 PM, "Thomas Caswell" <tcaswell at gmail.com> wrote:
>
> matplotlib uses the organization-level gh-pages to host the documentation
which seems to work pretty well.

We do the same thing, in fact.  No go-pages branch needed.

St?fan
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From hughesadam87 at gmail.com  Fri Dec 12 12:46:55 2014
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Fri, 12 Dec 2014 12:46:55 -0500
Subject: How do you keep documentation so nice?
In-Reply-To: <CABDkGQkpczfCgZcfpNNOEGP5N05w-QLADvStgDaYw=Vxg1bG0A@mail.gmail.com>
References: <CAMHV+dD=73bo+ZtGTu8-D3X_HCoCi0Ub=bJT-GPtZJdcTmMkYQ@mail.gmail.com>
	<1418299017813.d4c8c85c@Nodemailer>
	<CAMHV+dD8TPGcWaEc3wEVrshV62Ev2ZGRgzH5FhZUYz2-ANh=0Q@mail.gmail.com>
	<CAA48SF8a0oa2y4RX-jNHNnsRLu0S0pduNUBUNYruiz5QEuTpmA@mail.gmail.com>
	<CABDkGQkpczfCgZcfpNNOEGP5N05w-QLADvStgDaYw=Vxg1bG0A@mail.gmail.com>
Message-ID: <CAMHV+dDkszfoeZMO+9DtTu5FV7Z1iZp3MYKoiKNCp5QD0xmiow@mail.gmail.com>

Wait, so github is hosting scikitimage.org?

To my (outdated) understanding, one had to use a gh-pages branch for github
to find the documentations.  If I were to put the docs in the package
master branch as you've done, how can github find a hook to host the site?

On Thu, Dec 11, 2014 at 7:13 PM, St?fan van der Walt <stefan at sun.ac.za>
wrote:
>
> On Dec 11, 2014 7:58 PM, "Thomas Caswell" <tcaswell at gmail.com> wrote:
> >
> > matplotlib uses the organization-level gh-pages to host the
> documentation which seems to work pretty well.
>
> We do the same thing, in fact.  No go-pages branch needed.
>
> St?fan
>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "scikit-image" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/scikit-image/k5K6_vanZVI/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From steven.silvester at gmail.com  Fri Dec 12 20:37:39 2014
From: steven.silvester at gmail.com (Steven Silvester)
Date: Fri, 12 Dec 2014 17:37:39 -0800 (PST)
Subject: Travis-wheels fix?
In-Reply-To: <1417993256117.cc5d57fd@Nodemailer>
References: <1417993256117.cc5d57fd@Nodemailer>
Message-ID: <70b42ab5-4218-4c7f-93f8-ebb04860dff3@googlegroups.com>

Thanks Oliver, implemented.

On Sunday, December 7, 2014 5:00:58 PM UTC-6, Juan Nunez-Iglesias wrote:
>
>  A bunch of Travis errors are being caused (apparently) by 
> travis-wheels.scikit-image.org not responding. I haven't been following 
> the discussion closely, but my question is, do we need to get rid of it for 
> the Travis build so that we can have a stable build system at the sprint? 
> Or do we perhaps want to add a condition to use regular pip builds if 
> travis-wheels is unavailable?
>
>
>  
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From stefan at sun.ac.za  Fri Dec 12 10:48:59 2014
From: stefan at sun.ac.za (Stefan van der Walt)
Date: Fri, 12 Dec 2014 17:48:59 +0200
Subject: can not load / use functions from skimage.feature
In-Reply-To: <6ffbb648-42d3-4042-be68-5a16f3883822@googlegroups.com>
References: <6ffbb648-42d3-4042-be68-5a16f3883822@googlegroups.com>
Message-ID: <87y4qcuavo.fsf@sun.ac.za>

Hi Hans

On 2014-12-12 11:19:33, hans peter <h4n5p3ter at gmail.com> wrote:
> and the skimage from 
> http://www.lfd.uci.edu/~gohlke/pythonlibs/#scikits.image ( pre compiled )
> Also the python path is correct set ( Path and Pythonpath )
>
> The basic example from the website works fine but after I tryed to import 
> *from skimage.feature import blob_dog, blob_log, blob_doh*I got different 
> error messages, so I installed and unistalled every thing but nothing works.
>
> My current error message after try to import skimage.featrue 

I don't think these features are available in your version yet.  We'll
be releasing 0.11 over the weekend, so you should have access to it
then.

Alternatively, you may download the code and build it yourself (it's not
too hard).

St?fan


From olivier.grisel at ensta.org  Fri Dec 12 13:10:48 2014
From: olivier.grisel at ensta.org (Olivier Grisel)
Date: Fri, 12 Dec 2014 19:10:48 +0100
Subject: Travis-wheels fix?
In-Reply-To: <CAHaFxPzxxDQjyZybja5YMoq4GzWO_GSY9tmOwVYaQE20cidpcg@mail.gmail.com>
References: <1417993256117.cc5d57fd@Nodemailer> <75b9e8e1-9f90-46bf-b54e-8205de75064b@googlegroups.com>
 <CA+JHcKR15W7FPEL6s4-6BrtaUGCe5bf7AQKJ=KjQer77tgCJLw@mail.gmail.com>
 <CAH6Pt5osAD-aZ+_Oxpuvtp=9PGsb4rEjO=3wDd0bQ+xGAofQZQ@mail.gmail.com> <CAHaFxPzxxDQjyZybja5YMoq4GzWO_GSY9tmOwVYaQE20cidpcg@mail.gmail.com>
Message-ID: <CAFvE7K4yXt2TAPkkHmW7XKFx+x2FaB3CEN5j8n1UwWA2Q7NqJA@mail.gmail.com>

Please use `pip install --timeout=60 -f http://wheels.scipy.org
packagename` to increase the default timeout when connecting to the
rackspace container. pip uses a default of 15s which is apparently
sometimes not enough. For scikit-learn the stability of the build has
greatly improved since I switched to 60s timeout.

-- 
Olivier


From jni.soma at gmail.com  Fri Dec 12 06:04:06 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Fri, 12 Dec 2014 22:04:06 +1100
Subject: can not load / use functions from skimage.feature
In-Reply-To: <6ffbb648-42d3-4042-be68-5a16f3883822@googlegroups.com>
References: <6ffbb648-42d3-4042-be68-5a16f3883822@googlegroups.com>
Message-ID: <CA+JHcKQ2x8x5q__vU9FvEnn_8D5BrK3OYY-eDK5ZMt9thQH7Mw@mail.gmail.com>

Hi Hans,

Why does your link point to the old name, scikits.image? (It is now
scikit-image.) You might have an old version. What's the output for

import skimage
skimage.__version__

?

Also, I would recommend the Anaconda Python distribution
<http://continuum.io/downloads>, as it takes away a lot of the pain of
library installs in Python.

On Fri, Dec 12, 2014 at 8:19 PM, hans peter <h4n5p3ter at gmail.com> wrote:
>
> Hi there,
> I running Windows 7 (64bit)
> with WinPython 2.7* NumPy 1.8.1, SciPy 0.13.3, Matplotlib 1.3.1 guidata
> 1.6.1, guiqwt 2.3.2 Cython-0.21.1*
> and the skimage from
> http://www.lfd.uci.edu/~gohlke/pythonlibs/#scikits.image ( pre compiled )
> Also the python path is correct set ( Path and Pythonpath )
>
> The basic example from the website works fine but after I tryed to import
> *from skimage.feature import blob_dog, blob_log, blob_doh*I got different
> error messages, so I installed and unistalled every thing but nothing works.
>
> My current error message after try to import skimage.featrue
>
> >>> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
> ImportError: cannot import name blob_dog
>
> I also had some messages like, could not find .corner and .hough and so on
>
> I have absolutly no clue how to solve this ..
>
> would be nice if someone could help
>
> thanks
>
> --
> 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/d/optout.
>
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From stefan at sun.ac.za  Fri Dec 12 22:55:14 2014
From: stefan at sun.ac.za (Stefan van der Walt)
Date: Sat, 13 Dec 2014 05:55:14 +0200
Subject: How do you keep documentation so nice?
In-Reply-To: <CAMHV+dDkszfoeZMO+9DtTu5FV7Z1iZp3MYKoiKNCp5QD0xmiow@mail.gmail.com>
References: <CAMHV+dD=73bo+ZtGTu8-D3X_HCoCi0Ub=bJT-GPtZJdcTmMkYQ@mail.gmail.com> <1418299017813.d4c8c85c@Nodemailer> <CAMHV+dD8TPGcWaEc3wEVrshV62Ev2ZGRgzH5FhZUYz2-ANh=0Q@mail.gmail.com> <CAA48SF8a0oa2y4RX-jNHNnsRLu0S0pduNUBUNYruiz5QEuTpmA@mail.gmail.com> <CABDkGQkpczfCgZcfpNNOEGP5N05w-QLADvStgDaYw=Vxg1bG0A@mail.gmail.com> <CAMHV+dDkszfoeZMO+9DtTu5FV7Z1iZp3MYKoiKNCp5QD0xmiow@mail.gmail.com>
Message-ID: <87d27otd99.fsf@sun.ac.za>

Hi Adam

On 2014-12-12 19:46:55, Adam Hughes <hughesadam87 at gmail.com> wrote:
> Wait, so github is hosting scikitimage.org?
>
> To my (outdated) understanding, one had to use a gh-pages branch for github
> to find the documentations.  If I were to put the docs in the package
> master branch as you've done, how can github find a hook to host the site?

If you name the repository orgname.github.io, then you can push into the
master branch, IIRC.

Regards
St?fan


From rishabhr123 at gmail.com  Sat Dec 13 10:16:54 2014
From: rishabhr123 at gmail.com (Rishabh Raj)
Date: Sat, 13 Dec 2014 07:16:54 -0800 (PST)
Subject: Generating a painting from a picture
Message-ID: <cabaeb8c-c766-4348-9fef-f5c4f9588c9a@googlegroups.com>

Hey,

I'm working on a project in which the objective is to create a painting 
from a picture taken with a normal camera. This painting could be an oil 
painting or we could try and mimic some specific artist.

I understand this might not be achievable in a very good way by just image 
processing itself but I'm curious about what is achievable with stroke and 
simple pattern recognition for a base result.

Is there support in scikit-image along these lines? Any other inputs are 
welcome.

Best,
Rishabh
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From vighneshbirodkar at gmail.com  Sat Dec 13 11:11:28 2014
From: vighneshbirodkar at gmail.com (Vighnesh Birodkar)
Date: Sat, 13 Dec 2014 08:11:28 -0800 (PST)
Subject: Generating a painting from a picture
In-Reply-To: <20141213152510.GA22675@phare.normalesup.org>
References: <cabaeb8c-c766-4348-9fef-f5c4f9588c9a@googlegroups.com>
 <20141213152510.GA22675@phare.normalesup.org>
Message-ID: <14ef7a1d-b83f-4da9-8eed-d4f27c46791c@googlegroups.com>

Hi

You might want to have a look at this
http://phys.org/news/2012-03-software-automatically-movie-comic.html

Thanks
Vighnesh

On Saturday, December 13, 2014 8:55:11 PM UTC+5:30, Emmanuelle Gouillart 
wrote:
>
> Hi Rishabh, 
>
> I don't think there is a generic enough algorithm that would do this 
> (each artist has her/his own specific style, and a specific algorithm 
> would have to be designed for every style I think). 
>
> Nevertheless, some of the functions in skimage can be used for this 
> purpose. For example, 
> http://scikit-image.org/docs/dev/auto_examples/plot_ncut.html shows how 
> to get a posterized, comics-like image. 
>
> You can also find geometric transformations in skimage.transform, if you 
> want to implement some distortion effect for example. 
> (
> http://scikit-image.org/docs/dev/auto_examples/applications/plot_geometric.html) 
>
>
> Hope you have fun with this project! 
> Emmanuelle 
>
> On Sat, Dec 13, 2014 at 07:16:54AM -0800, Rishabh Raj wrote: 
> > Hey, 
>
> > I'm working on a project in which the objective is to create a painting 
> from a 
> > picture taken with a normal camera. This painting could be an oil 
> painting or 
> > we could try and mimic some specific artist. 
>
> > I understand this might not be achievable in a very good way by just 
> image 
> > processing itself but I'm curious about what is achievable with stroke 
> and 
> > simple pattern recognition for a base result. 
>
> > Is there support in scikit-image along these lines? Any other inputs are 
> > welcome. 
>
> > Best, 
> > Rishabh 
>
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From pratapgr8 at gmail.com  Sat Dec 13 11:20:28 2014
From: pratapgr8 at gmail.com (Pratap Vardhan)
Date: Sat, 13 Dec 2014 08:20:28 -0800 (PST)
Subject: Generating a painting from a picture
In-Reply-To: <cabaeb8c-c766-4348-9fef-f5c4f9588c9a@googlegroups.com>
References: <cabaeb8c-c766-4348-9fef-f5c4f9588c9a@googlegroups.com>
Message-ID: <67cee741-e83b-4cc6-95d9-96b5c8f3fd10@googlegroups.com>

Here's a paper http://cs.brown.edu/~hays/papers/IVBPA_Final.pdf for 
transforming images and videos into painterly animations depicting 
different artistic styles.

Thanks,
Pratap

On Saturday, December 13, 2014 8:46:55 PM UTC+5:30, Rishabh Raj wrote:
>
> Hey,
>
> I'm working on a project in which the objective is to create a painting 
> from a picture taken with a normal camera. This painting could be an oil 
> painting or we could try and mimic some specific artist.
>
> I understand this might not be achievable in a very good way by just image 
> processing itself but I'm curious about what is achievable with stroke and 
> simple pattern recognition for a base result.
>
> Is there support in scikit-image along these lines? Any other inputs are 
> welcome.
>
> Best,
> Rishabh
>
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From stefan at sun.ac.za  Sat Dec 13 07:14:53 2014
From: stefan at sun.ac.za (Stefan van der Walt)
Date: Sat, 13 Dec 2014 14:14:53 +0200
Subject: skimage v0.11 sprint is underway
Message-ID: <87bnn7u4oy.fsf@sun.ac.za>

Hi everyone

A reminder that we are sprinting on scikit-image v0.11 this weekend!

We're working towards this milestone:

https://github.com/scikit-image/scikit-image/milestones/0.11

Follow the events here: https://gitter.im/scikit-image/scikit-image

See you there!
St?fan


From emmanuelle.gouillart at nsup.org  Sat Dec 13 10:25:10 2014
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Sat, 13 Dec 2014 16:25:10 +0100
Subject: Generating a painting from a picture
In-Reply-To: <cabaeb8c-c766-4348-9fef-f5c4f9588c9a@googlegroups.com>
References: <cabaeb8c-c766-4348-9fef-f5c4f9588c9a@googlegroups.com>
Message-ID: <20141213152510.GA22675@phare.normalesup.org>

Hi Rishabh,

I don't think there is a generic enough algorithm that would do this
(each artist has her/his own specific style, and a specific algorithm
would have to be designed for every style I think). 

Nevertheless, some of the functions in skimage can be used for this
purpose. For example,
http://scikit-image.org/docs/dev/auto_examples/plot_ncut.html shows how
to get a posterized, comics-like image. 

You can also find geometric transformations in skimage.transform, if you
want to implement some distortion effect for example.
(http://scikit-image.org/docs/dev/auto_examples/applications/plot_geometric.html)

Hope you have fun with this project!
Emmanuelle 

On Sat, Dec 13, 2014 at 07:16:54AM -0800, Rishabh Raj wrote:
> Hey,

> I'm working on a project in which the objective is to create a painting from a
> picture taken with a normal camera. This painting could be an oil painting or
> we could try and mimic some specific artist.

> I understand this might not be achievable in a very good way by just image
> processing itself but I'm curious about what is achievable with stroke and
> simple pattern recognition for a base result.

> Is there support in scikit-image along these lines? Any other inputs are
> welcome.

> Best,
> Rishabh


From stefan at sun.ac.za  Sat Dec 13 12:52:36 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Sat, 13 Dec 2014 19:52:36 +0200
Subject: can not load / use functions from skimage.feature
In-Reply-To: <CA+JHcKQfzoWsRAXkEm7doKbJJfjjgjKkFGWG4ZHwn-P+QoMYxg@mail.gmail.com>
References: <6ffbb648-42d3-4042-be68-5a16f3883822@googlegroups.com>
 <87y4qcuavo.fsf@sun.ac.za> <CA+JHcKQfzoWsRAXkEm7doKbJJfjjgjKkFGWG4ZHwn-P+QoMYxg@mail.gmail.com>
Message-ID: <CABDkGQmn+Yuoc3i8gYdPnG=cj6tG64MFKY-CdMWCJX=X+uUdLA@mail.gmail.com>

On Sat, Dec 13, 2014 at 3:45 PM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> St?fan, the blob_* functions are supposed to be in 0.10 and up...

Alright, then further investigation is needed.  Hans, can you let us
know your version number?

St?fan


From jni.soma at gmail.com  Sat Dec 13 08:45:41 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Sun, 14 Dec 2014 00:45:41 +1100
Subject: can not load / use functions from skimage.feature
In-Reply-To: <87y4qcuavo.fsf@sun.ac.za>
References: <6ffbb648-42d3-4042-be68-5a16f3883822@googlegroups.com> <87y4qcuavo.fsf@sun.ac.za>
Message-ID: <CA+JHcKQfzoWsRAXkEm7doKbJJfjjgjKkFGWG4ZHwn-P+QoMYxg@mail.gmail.com>

St?fan, the blob_* functions are supposed to be in 0.10 and up...

On Sat, Dec 13, 2014 at 2:48 AM, Stefan van der Walt <stefan at sun.ac.za>
wrote:
>
> Hi Hans
>
> On 2014-12-12 11:19:33, hans peter <h4n5p3ter at gmail.com> wrote:
> > and the skimage from
> > http://www.lfd.uci.edu/~gohlke/pythonlibs/#scikits.image ( pre compiled
> )
> > Also the python path is correct set ( Path and Pythonpath )
> >
> > The basic example from the website works fine but after I tryed to import
> > *from skimage.feature import blob_dog, blob_log, blob_doh*I got different
> > error messages, so I installed and unistalled every thing but nothing
> works.
> >
> > My current error message after try to import skimage.featrue
>
> I don't think these features are available in your version yet.  We'll
> be releasing 0.11 over the weekend, so you should have access to it
> then.
>
> Alternatively, you may download the code and build it yourself (it's not
> too hard).
>
> 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/d/optout.
>
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From pratapgr8 at gmail.com  Sun Dec 14 11:48:11 2014
From: pratapgr8 at gmail.com (Pratap Vardhan)
Date: Sun, 14 Dec 2014 08:48:11 -0800 (PST)
Subject: substitute for imsubtract
Message-ID: <32eb02a1-c82e-4382-b044-9fd335c80c75@googlegroups.com>

if

a = np.array([ [255,10,75], [44, 225, 100]], dtype=np.uint8)
b = np.array([ [50, 50, 50],[50, 50, 50] ], dtype=np.uint8)

can (a.astype(int) - b.astype(int)).clip(0, 255) be good substitute for 
imsubtract function? If so or not so, is there a need to have this kind of 
function in skimage library?
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From silvertrumpet999 at gmail.com  Sun Dec 14 19:28:04 2014
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Sun, 14 Dec 2014 16:28:04 -0800 (PST)
Subject: substitute for imsubtract
In-Reply-To: <32eb02a1-c82e-4382-b044-9fd335c80c75@googlegroups.com>
References: <32eb02a1-c82e-4382-b044-9fd335c80c75@googlegroups.com>
Message-ID: <ff29d235-1385-439e-97ca-6d46eaf53269@googlegroups.com>



Yes, as far as I?m aware the one-liner you wrote duplicates it. You?ve 
handled the main issue, namely, wraparound in an unsigned dtype. Still a 
one-liner. 

MatLAB holds the user?s hands to a ridiculous degree. We?ve elected not to 
duplicate the trivial functionality of this as well as a few of the other 
im_____ functions.

@JDWarner

On Sunday, December 14, 2014 10:48:11 AM UTC-6, Pratap Vardhan wrote:

if
>
> a = np.array([ [255,10,75], [44, 225, 100]], dtype=np.uint8)
> b = np.array([ [50, 50, 50],[50, 50, 50] ], dtype=np.uint8)
>
> can (a.astype(int) - b.astype(int)).clip(0, 255) be good substitute for 
> imsubtract function? If so or not so, is there a need to have this kind of 
> function in skimage library?
>
?
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From silvertrumpet999 at gmail.com  Sun Dec 14 19:37:14 2014
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Sun, 14 Dec 2014 16:37:14 -0800 (PST)
Subject: can not load / use functions from skimage.feature
In-Reply-To: <CABDkGQmn+Yuoc3i8gYdPnG=cj6tG64MFKY-CdMWCJX=X+uUdLA@mail.gmail.com>
References: <6ffbb648-42d3-4042-be68-5a16f3883822@googlegroups.com>
 <87y4qcuavo.fsf@sun.ac.za> <CA+JHcKQfzoWsRAXkEm7doKbJJfjjgjKkFGWG4ZHwn-P+QoMYxg@mail.gmail.com>
 <CABDkGQmn+Yuoc3i8gYdPnG=cj6tG64MFKY-CdMWCJX=X+uUdLA@mail.gmail.com>
Message-ID: <feff3974-3ea2-42ab-880f-ca3325515b87@googlegroups.com>



AFAIK the name switch which removed the plural and added the dash happened 
in the transition from 0.7.x to 0.8. That?s a long time ago; around my 
first PR! It?s a long time in advance of the addition of the blob_* 
functions.

I think it?s possible Chris Gohlke maintained installers separately for the 
old name until recently. If so, you probably have version 0.7ish.

To let us know your version number, open a Python shell and run

>>> import skimage>>> print skimage.__version__

(In any event, switching to the Anaconda distribution would almost 
certainly fix this and allow painless updates to the entire ecosystem? 
without even requiring elevated privileges!)

Josh

On Saturday, December 13, 2014 11:52:58 AM UTC-6, Stefan van der Walt wrote:

On Sat, Dec 13, 2014 at 3:45 PM, Juan Nunez-Iglesias wrote: 
> > St?fan, the blob_* functions are supposed to be in 0.10 and up... 
>
> Alright, then further investigation is needed.  Hans, can you let us 
> know your version number? 
>
> St?fan 
>
?
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From rishabhr123 at gmail.com  Mon Dec 15 03:22:11 2014
From: rishabhr123 at gmail.com (Rishabh Raj)
Date: Mon, 15 Dec 2014 00:22:11 -0800 (PST)
Subject: Generating a painting from a picture
In-Reply-To: <20141213152510.GA22675@phare.normalesup.org>
References: <cabaeb8c-c766-4348-9fef-f5c4f9588c9a@googlegroups.com>
 <20141213152510.GA22675@phare.normalesup.org>
Message-ID: <2421618c-4dae-4df5-b0c9-0aa0316c2435@googlegroups.com>

I read a few publications on the subject. Processing an image per pixel to 
generate a few effects seems to be straightforward.

But most of the literature is based on modelling brush strokes in paintings 
which are modeled as cubic B spline curves [1]. Do we have support for 
generating curves while processing an image?

[1] http://www.mrl.nyu.edu/publications/hertzmann-thesis/hertzmann-thesis-72dpi.pdf 
- Section 3. Fast and Loose Painterly Image Processing

On Saturday, December 13, 2014 8:55:11 PM UTC+5:30, Emmanuelle Gouillart 
wrote:
>
> Hi Rishabh, 
>
> I don't think there is a generic enough algorithm that would do this 
> (each artist has her/his own specific style, and a specific algorithm 
> would have to be designed for every style I think). 
>
> Nevertheless, some of the functions in skimage can be used for this 
> purpose. For example, 
> http://scikit-image.org/docs/dev/auto_examples/plot_ncut.html shows how 
> to get a posterized, comics-like image. 
>
> You can also find geometric transformations in skimage.transform, if you 
> want to implement some distortion effect for example. 
> (
> http://scikit-image.org/docs/dev/auto_examples/applications/plot_geometric.html) 
>
>
> Hope you have fun with this project! 
> Emmanuelle 
>
> On Sat, Dec 13, 2014 at 07:16:54AM -0800, Rishabh Raj wrote: 
> > Hey, 
>
> > I'm working on a project in which the objective is to create a painting 
> from a 
> > picture taken with a normal camera. This painting could be an oil 
> painting or 
> > we could try and mimic some specific artist. 
>
> > I understand this might not be achievable in a very good way by just 
> image 
> > processing itself but I'm curious about what is achievable with stroke 
> and 
> > simple pattern recognition for a base result. 
>
> > Is there support in scikit-image along these lines? Any other inputs are 
> > welcome. 
>
> > Best, 
> > Rishabh 
>
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From jni.soma at gmail.com  Mon Dec 15 17:19:51 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Mon, 15 Dec 2014 14:19:51 -0800 (PST)
Subject: peak detectors
In-Reply-To: <20141215220654.GA15640@phare.normalesup.org>
References: <20141215220654.GA15640@phare.normalesup.org>
Message-ID: <1418681990969.f7649315@Nodemailer>

Hi Emma!




This one is a bit slow (based on morphological reconstruction) but works well:





https://github.com/janelia-flyem/gala/blob/master/gala/morpho.py#L122




Juan.

On Tue, Dec 16, 2014 at 9:06 AM, Emmanuelle Gouillart
<emmanuelle.gouillart at nsup.org> wrote:

> 	Hi list,
> 	just a quick survey: which algorithms are you using for peak
> detection (detection of local maxima in a grayscale image), and which
> ones are you most satisfied of? We were wondering about the existence of
> good peak detectors during the scikit-image sprint, following
> difficulties with existing ones such as our feature.peak_local_max (see
> for example the discussion in
> https://github.com/scikit-image/scikit-image/pull/1248).
> 	Cheers,
> 	Emma
> -- 
> 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/d/optout.
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From silvertrumpet999 at gmail.com  Mon Dec 15 19:56:29 2014
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Mon, 15 Dec 2014 16:56:29 -0800 (PST)
Subject: Generating a painting from a picture
In-Reply-To: <2421618c-4dae-4df5-b0c9-0aa0316c2435@googlegroups.com>
References: <cabaeb8c-c766-4348-9fef-f5c4f9588c9a@googlegroups.com>
 <20141213152510.GA22675@phare.normalesup.org>
 <2421618c-4dae-4df5-b0c9-0aa0316c2435@googlegroups.com>
Message-ID: <40deeb7b-5c51-4aab-9b0c-6b7b8394657c@googlegroups.com>

SciPy has some good B-spline (and many other interpolation) routines. We 
haven't re-implemented these, because we depend on SciPy. Feel free to 
mix-and-match these routines with scikit-image functions.

Check out the `scipy.signal` module for 1d, or `scipy.interpolate` for 
multi-dimensional:
http://docs.scipy.org/doc/scipy-0.14.0/reference/interpolate.html
http://docs.scipy.org/doc/scipy-0.14.0/reference/signal.html

Looks interesting!
Josh

On Monday, December 15, 2014 2:22:12 AM UTC-6, Rishabh Raj wrote:
>
> I read a few publications on the subject. Processing an image per pixel to 
> generate a few effects seems to be straightforward.
>
> But most of the literature is based on modelling brush strokes in 
> paintings which are modeled as cubic B spline curves [1]. Do we have 
> support for generating curves while processing an image?
>
> [1] 
> http://www.mrl.nyu.edu/publications/hertzmann-thesis/hertzmann-thesis-72dpi.pdf 
> - Section 3. Fast and Loose Painterly Image Processing
>
> On Saturday, December 13, 2014 8:55:11 PM UTC+5:30, Emmanuelle Gouillart 
> wrote:
>>
>> Hi Rishabh, 
>>
>> I don't think there is a generic enough algorithm that would do this 
>> (each artist has her/his own specific style, and a specific algorithm 
>> would have to be designed for every style I think). 
>>
>> Nevertheless, some of the functions in skimage can be used for this 
>> purpose. For example, 
>> http://scikit-image.org/docs/dev/auto_examples/plot_ncut.html shows how 
>> to get a posterized, comics-like image. 
>>
>> You can also find geometric transformations in skimage.transform, if you 
>> want to implement some distortion effect for example. 
>> (
>> http://scikit-image.org/docs/dev/auto_examples/applications/plot_geometric.html) 
>>
>>
>> Hope you have fun with this project! 
>> Emmanuelle 
>>
>> On Sat, Dec 13, 2014 at 07:16:54AM -0800, Rishabh Raj wrote: 
>> > Hey, 
>>
>> > I'm working on a project in which the objective is to create a painting 
>> from a 
>> > picture taken with a normal camera. This painting could be an oil 
>> painting or 
>> > we could try and mimic some specific artist. 
>>
>> > I understand this might not be achievable in a very good way by just 
>> image 
>> > processing itself but I'm curious about what is achievable with stroke 
>> and 
>> > simple pattern recognition for a base result. 
>>
>> > Is there support in scikit-image along these lines? Any other inputs 
>> are 
>> > welcome. 
>>
>> > Best, 
>> > Rishabh 
>>
>
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From emmanuelle.gouillart at nsup.org  Mon Dec 15 17:06:54 2014
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Mon, 15 Dec 2014 23:06:54 +0100
Subject: peak detectors
Message-ID: <20141215220654.GA15640@phare.normalesup.org>

	Hi list,

	just a quick survey: which algorithms are you using for peak
detection (detection of local maxima in a grayscale image), and which
ones are you most satisfied of? We were wondering about the existence of
good peak detectors during the scikit-image sprint, following
difficulties with existing ones such as our feature.peak_local_max (see
for example the discussion in
https://github.com/scikit-image/scikit-image/pull/1248).

	Cheers,
	Emma



From pratapgr8 at gmail.com  Tue Dec 16 06:35:25 2014
From: pratapgr8 at gmail.com (Pratap Vardhan)
Date: Tue, 16 Dec 2014 03:35:25 -0800 (PST)
Subject: Pattern and object recognition with COSFIRE
In-Reply-To: <87zjan6dee.fsf@sun.ac.za>
References: <54900E26.3020607@gmail.com>
 <87zjan6dee.fsf@sun.ac.za>
Message-ID: <6fd44996-fbf4-4151-8bdd-e9e9e0aef928@googlegroups.com>

Here's the original PAMI 
paper http://www.computer.org/csdl/trans/tp/2013/02/ttp2013020490.pdf

George Azzopardi and Nicolai Petkov, "Trainable COSFIRE filters for 
keypoint detection and pattern recognition", IEEE Transactions on Pattern 
Analysis and Machine Intelligence, vol. 35(2), pp. 490-503, 2013.

Thanks,
Pratap

On Tuesday, December 16, 2014 4:59:53 PM UTC+5:30, Stefan van der Walt 
wrote:
>
> Hi Almar 
>
> On 2014-12-16 12:49:10, Almar Klein <almar... at gmail.com <javascript:>> 
> wrote: 
> > The filter is inspired by how the brain processes visual information, 
> > and according to the author the algorithm is actually quite simple. The 
> > algorithm was the topic of his PhD and he's going to continue working on 
> > it in his new job. 
>
> COSFIRE sounds fascinating!  Do you think the author would be interested 
> in getting involved? 
>
> > Some links: 
> > 
> > - PhD thesis: http://www.cs.rug.nl/~george/phd-thesis/ 
> > - Matlab code: nl.mathworks.com/matlabcentral/fileexchange/37395 
> > - Paper in MIA: 
> > 
> http://www.medicalimageanalysisjournal.com/article/S1361-8415%2814%2900136-4/abstract 
>
> This is the B-COSFIRE paper--do you know where the original paper is 
> published? 
>
> St?fan 
>
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From pratapgr8 at gmail.com  Tue Dec 16 06:57:15 2014
From: pratapgr8 at gmail.com (Pratap Vardhan)
Date: Tue, 16 Dec 2014 03:57:15 -0800 (PST)
Subject: Pattern and object recognition with COSFIRE
In-Reply-To: <CABDkGQ=NyQKXbhg_-mPYiMpLjoxkxt6VNYHJKo4pvyOyWXNbGA@mail.gmail.com>
References: <54900E26.3020607@gmail.com> <87zjan6dee.fsf@sun.ac.za> <6fd44996-fbf4-4151-8bdd-e9e9e0aef928@googlegroups.com>
 <CABDkGQ=NyQKXbhg_-mPYiMpLjoxkxt6VNYHJKo4pvyOyWXNbGA@mail.gmail.com>
Message-ID: <78dcd628-2008-441b-a478-ff4e2eff39cd@googlegroups.com>

I found few copies of the paper hosted by universities. I haven't checked 
if these are the actual pre-prints - However, by the citation it looks like 
it.

http://iwi.eldoc.ub.rug.nl/FILES/root/2013/IEEETPAMIAzzopardi/2013IEEETPAMIAzzopardi.pdf
http://bmia.bmt.tue.nl/Education/Courses/FEV/course/pdf/pami2013cosfire.pdf

Pratap


On Tuesday, December 16, 2014 5:17:19 PM UTC+5:30, Stefan van der Walt 
wrote:
>
> On Tue, Dec 16, 2014 at 1:35 PM, Pratap Vardhan <prat... at gmail.com 
> <javascript:>> wrote: 
> > Here's the original PAMI paper 
> > http://www.computer.org/csdl/trans/tp/2013/02/ttp2013020490.pdf 
>
> Unfortunately, that paper is behind a pay-wall.  Perhaps we can 
> request a pre-print from the author. 
>
> St?fan 
>
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From guillaume at mitotic-machine.org  Tue Dec 16 03:23:33 2014
From: guillaume at mitotic-machine.org (Guillaume Gay)
Date: Tue, 16 Dec 2014 09:23:33 +0100
Subject: peak detectors
In-Reply-To: <1418681990969.f7649315@Nodemailer>
References: <20141215220654.GA15640@phare.normalesup.org> <1418681990969.f7649315@Nodemailer>
Message-ID: <548FEC05.1050906@mitotic-machine.org>

Hi Emma,

We implemented this some time ago:

https://github.com/bnoi/scikit-tracker/blob/master/sktracker/detection/peak_detector.py

It depends slightly on the rest of the module, but it shouldn't be too 
hard to extract only the detection module.

It's based on this paper:
http://www.nature.com/nmeth/journal/v5/n8/full/nmeth.1233.html


Best,

Guillaume


Le 15/12/2014 23:19, Juan Nunez-Iglesias a ?crit :
> Hi Emma!
>
> This one is a bit slow (based on morphological reconstruction) but 
> works well:
>
> https://github.com/janelia-flyem/gala/blob/master/gala/morpho.py#L122
>
> Juan.
>
>
>
>
> On Tue, Dec 16, 2014 at 9:06 AM, Emmanuelle Gouillart 
> <emmanuelle.gouillart at nsup.org <mailto:emmanuelle.gouillart at nsup.org>> 
> wrote:
>
>     Hi list,
>
>     just a quick survey: which algorithms are you using for peak
>     detection (detection of local maxima in a grayscale image), and which
>     ones are you most satisfied of? We were wondering about the
>     existence of
>     good peak detectors during the scikit-image sprint, following
>     difficulties with existing ones such as our feature.peak_local_max
>     (see
>     for example the discussion in
>     https://github.com/scikit-image/scikit-image/pull/1248).
>
>     Cheers,
>     Emma
>
>     -- 
>     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/d/optout.
>
>
> -- 
> You received this message because you are subscribed to the Google 
> Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send 
> an email to scikit-image+unsubscribe at googlegroups.com 
> <mailto:scikit-image+unsubscribe at googlegroups.com>.
> For more options, visit https://groups.google.com/d/optout.

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From almar.klein at gmail.com  Tue Dec 16 05:49:10 2014
From: almar.klein at gmail.com (Almar Klein)
Date: Tue, 16 Dec 2014 11:49:10 +0100
Subject: Pattern and object recognition with COSFIRE
Message-ID: <54900E26.3020607@gmail.com>

Hi all,

Just wanted to mention an algorithm which I was very impressed by and 
which might be an awesome addition to scikit-image. The algorithm is 
called COSFIRE (Combination of Shifted Filter Responses).

I saw a talk by Geore Azzopardi, who presented the use of the algorithm 
for object and patter recognition. I was very impressed with the quality 
of segmentation of the shown examples, but also with the wide variety of 
image data (e.g. retina images, traffic signs, hand-written characters, 
and more).

The filter is inspired by how the brain processes visual information, 
and according to the author the algorithm is actually quite simple. The 
algorithm was the topic of his PhD and he's going to continue working on 
it in his new job.

The code (in Matlab) is available, so it might be worth a shot to try 
and port it to Python.

Some links:

- PhD thesis: http://www.cs.rug.nl/~george/phd-thesis/
- Matlab code: nl.mathworks.com/matlabcentral/fileexchange/37395
- Paper in MIA: 
http://www.medicalimageanalysisjournal.com/article/S1361-8415%2814%2900136-4/abstract

- Almar



From stefan at sun.ac.za  Tue Dec 16 06:29:45 2014
From: stefan at sun.ac.za (Stefan van der Walt)
Date: Tue, 16 Dec 2014 13:29:45 +0200
Subject: Pattern and object recognition with COSFIRE
In-Reply-To: <54900E26.3020607@gmail.com>
References: <54900E26.3020607@gmail.com>
Message-ID: <87zjan6dee.fsf@sun.ac.za>

Hi Almar

On 2014-12-16 12:49:10, Almar Klein <almar.klein at gmail.com> wrote:
> The filter is inspired by how the brain processes visual information, 
> and according to the author the algorithm is actually quite simple. The 
> algorithm was the topic of his PhD and he's going to continue working on 
> it in his new job.

COSFIRE sounds fascinating!  Do you think the author would be interested
in getting involved?

> Some links:
>
> - PhD thesis: http://www.cs.rug.nl/~george/phd-thesis/
> - Matlab code: nl.mathworks.com/matlabcentral/fileexchange/37395
> - Paper in MIA: 
> http://www.medicalimageanalysisjournal.com/article/S1361-8415%2814%2900136-4/abstract

This is the B-COSFIRE paper--do you know where the original paper is
published?

St?fan


From stefan at sun.ac.za  Tue Dec 16 06:46:58 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Tue, 16 Dec 2014 13:46:58 +0200
Subject: Pattern and object recognition with COSFIRE
In-Reply-To: <6fd44996-fbf4-4151-8bdd-e9e9e0aef928@googlegroups.com>
References: <54900E26.3020607@gmail.com> <87zjan6dee.fsf@sun.ac.za> <6fd44996-fbf4-4151-8bdd-e9e9e0aef928@googlegroups.com>
Message-ID: <CABDkGQ=NyQKXbhg_-mPYiMpLjoxkxt6VNYHJKo4pvyOyWXNbGA@mail.gmail.com>

On Tue, Dec 16, 2014 at 1:35 PM, Pratap Vardhan <pratapgr8 at gmail.com> wrote:
> Here's the original PAMI paper
> http://www.computer.org/csdl/trans/tp/2013/02/ttp2013020490.pdf

Unfortunately, that paper is behind a pay-wall.  Perhaps we can
request a pre-print from the author.

St?fan


From fboulogne at sciunto.org  Tue Dec 16 14:39:49 2014
From: fboulogne at sciunto.org (=?UTF-8?B?RnJhbsOnb2lzIEJvdWxvZ25l?=)
Date: Tue, 16 Dec 2014 14:39:49 -0500
Subject: peak detectors
In-Reply-To: <20141215220654.GA15640@phare.normalesup.org>
References: <20141215220654.GA15640@phare.normalesup.org>
Message-ID: <54908A85.7050007@sciunto.org>

Hi Emma,
> 	just a quick survey: which algorithms are you using for peak
> detection (detection of local maxima in a grayscale image), and which
> ones are you most satisfied of? We were wondering about the existence of
> good peak detectors during the scikit-image sprint, following
> difficulties with existing ones such as our feature.peak_local_max (see
> for example the discussion in
> https://github.com/scikit-image/scikit-image/pull/1248).
>
>

Something I had in mind at some point is a peak detection based on
wavelets, but I did not find the time to finish that.
In my notes, I have this repository
https://github.com/johnmgregoire/PyWaveletPeakID which contains a code
working with pywavelet and a link to the paper. They got nice results on
a very noisy signal. Might not be universal, but useful for sure.

As you may know, I worked a bit with Ralf (Ralf did more than I) to
clean up pywavelet (mainly documentation, coding style, API). Ralf has a
clone on his github page. Pywavelet is not maintained anymore by its
original author. The next step is to integrate the code to scipy but we
need to find somebody who wants to play with C-python bindings. (The
last Gsoc project on that was not accepted). Definitely something that
would be useful to scikit-image and probably many other users.

Best,

-- 
Fran?ois Boulogne.
http://www.sciunto.org
GPG: 32D5F22F




From stefan at sun.ac.za  Tue Dec 16 09:22:24 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Tue, 16 Dec 2014 16:22:24 +0200
Subject: Pattern and object recognition with COSFIRE
In-Reply-To: <78dcd628-2008-441b-a478-ff4e2eff39cd@googlegroups.com>
References: <54900E26.3020607@gmail.com> <87zjan6dee.fsf@sun.ac.za>
 <6fd44996-fbf4-4151-8bdd-e9e9e0aef928@googlegroups.com> <CABDkGQ=NyQKXbhg_-mPYiMpLjoxkxt6VNYHJKo4pvyOyWXNbGA@mail.gmail.com>
 <78dcd628-2008-441b-a478-ff4e2eff39cd@googlegroups.com>
Message-ID: <CABDkGQmE2sOxKe04Un0SGBh4sBMoFCxKv3i5goA_ujSTVi5+0A@mail.gmail.com>

On Tue, Dec 16, 2014 at 1:57 PM, Pratap Vardhan <pratapgr8 at gmail.com> wrote:
> I found few copies of the paper hosted by universities. I haven't checked if
> these are the actual pre-prints - However, by the citation it looks like it.

Thanks!  I've added it to the list:

https://github.com/scikit-image/scikit-image/wiki/Requested-features

St?fan


From ralf.gommers at gmail.com  Tue Dec 16 16:36:32 2014
From: ralf.gommers at gmail.com (Ralf Gommers)
Date: Tue, 16 Dec 2014 22:36:32 +0100
Subject: peak detectors
In-Reply-To: <54908A85.7050007@sciunto.org>
References: <20141215220654.GA15640@phare.normalesup.org>
	<54908A85.7050007@sciunto.org>
Message-ID: <CABL7CQjOcpxJuD6YgWXn+3pnX5nqj_R5tbZsB7jQcQwcbjj2Fw@mail.gmail.com>

On Tue, Dec 16, 2014 at 8:39 PM, Fran?ois Boulogne <fboulogne at sciunto.org>
wrote:
>
> Hi Emma,
> >       just a quick survey: which algorithms are you using for peak
> > detection (detection of local maxima in a grayscale image), and which
> > ones are you most satisfied of? We were wondering about the existence of
> > good peak detectors during the scikit-image sprint, following
> > difficulties with existing ones such as our feature.peak_local_max (see
> > for example the discussion in
> > https://github.com/scikit-image/scikit-image/pull/1248).
> >
> >
>
> Something I had in mind at some point is a peak detection based on
> wavelets, but I did not find the time to finish that.
> In my notes, I have this repository
> https://github.com/johnmgregoire/PyWaveletPeakID which contains a code
> working with pywavelet and a link to the paper. They got nice results on
> a very noisy signal. Might not be universal, but useful for sure.
>
> As you may know, I worked a bit with Ralf (Ralf did more than I) to
> clean up pywavelet (mainly documentation, coding style, API). Ralf has a
> clone on his github page. Pywavelet is not maintained anymore by its
> original author. The next step is to integrate the code to scipy but we
> need to find somebody who wants to play with C-python bindings. (The
> last Gsoc project on that was not accepted). Definitely something that
> would be useful to scikit-image and probably many other users.
>

It's still on the todo list, but I kind of ran out of steam. After
https://github.com/rgommers/pywt/pull/55 goes in, it's pretty close to
being ready. The final issues to solve are all API-related (we only get one
chance to get those right). Those API issues wouldn't be a problem for
shipping a private copy in scikit-image though, so if you're comfortable
doing that then I'd say go for it.

Cheers,
Ralf
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From geazzo at gmail.com  Wed Dec 17 05:48:26 2014
From: geazzo at gmail.com (George Azzopardi)
Date: Wed, 17 Dec 2014 02:48:26 -0800 (PST)
Subject: Pattern and object recognition with COSFIRE
In-Reply-To: <CABDkGQmE2sOxKe04Un0SGBh4sBMoFCxKv3i5goA_ujSTVi5+0A@mail.gmail.com>
References: <54900E26.3020607@gmail.com> <87zjan6dee.fsf@sun.ac.za>
 <6fd44996-fbf4-4151-8bdd-e9e9e0aef928@googlegroups.com> <CABDkGQ=NyQKXbhg_-mPYiMpLjoxkxt6VNYHJKo4pvyOyWXNbGA@mail.gmail.com>
 <78dcd628-2008-441b-a478-ff4e2eff39cd@googlegroups.com>
 <CABDkGQmE2sOxKe04Un0SGBh4sBMoFCxKv3i5goA_ujSTVi5+0A@mail.gmail.com>
Message-ID: <717836ab-0fc4-49f0-8bfb-d25b7fd5acc5@googlegroups.com>

Dear all, 

I am pleased to see interest in the COSFIRE approach that I started during 
my PhD studies.

The COSFIRE approach is a trainable pattern recognition approach which can 
be applied to several applications, including feature detection, object 
recognition and localization, image classification, contour detection and 
vessel segmentation. The selectively for a pattern of interest is 
automatically configured in a training process. The method involves several 
computations that are independent of each other, and thus it can be easily 
implemented using parallel programming (e.g. on a GPU). The original paper 
(http://www.cs.rug.nl/~george/articles/PAMI2013.pdf) combines information 
about the contours of the concerned pattern. We now have another paper 
which is currently being reviewed for CVPR2015 where we show that by adding 
colour information COSFIRE filters become even more robust.

Please feel free to send me other ideas on how this work can be developed 
further.

I would be very happy and available to work with an undergraduate or a 
postgraduate student (or any other person) to have this parallel 
implementation in Python. I see that you already added it to the 
Requested-features page. You can also add my contact details (geazzo at gmail) 
there for the interested readers.

All my papers can be freely downloaded from my 
website: http://www.cs.rug.nl/~george/research-activities/

regards,
George

On Tuesday, 16 December 2014 15:22:45 UTC+1, Stefan van der Walt wrote:
>
> On Tue, Dec 16, 2014 at 1:57 PM, Pratap Vardhan <prat... at gmail.com 
> <javascript:>> wrote: 
> > I found few copies of the paper hosted by universities. I haven't 
> checked if 
> > these are the actual pre-prints - However, by the citation it looks like 
> it. 
>
> Thanks!  I've added it to the list: 
>
> https://github.com/scikit-image/scikit-image/wiki/Requested-features 
>
> St?fan 
>
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From salvatorescaramuzzino at gmail.com  Wed Dec 17 05:50:59 2014
From: salvatorescaramuzzino at gmail.com (Salvatore Scaramuzzino)
Date: Wed, 17 Dec 2014 02:50:59 -0800 (PST)
Subject: User Interaction with RectangleTool
Message-ID: <a29684d7-1477-4ee5-aa50-c323ae2e4611@googlegroups.com>

Hi to all

I'm new in scikit-image, and i develop algorithms for medical applications.

Sometimes is very very useful to have user interaction, in particular 
Region of Interest (ROI) selection over an image. I found in skimage the 
RectangleTool and i'm trying to write a simple ROI selector in order to use 
the rectangle coords in successive computations.

unfortunately i can't be able to handle mouse events: for example if i've:

#import
import skimage as sk
from skimage import data
import matplotlib.pyplot as plt
from skimage.viewer.canvastools import RectangleTool
import numpy as np
from skimage.draw import polygon
from skimage.draw import line

im = data.lena()
f, ax = plt.subplots()
plt.imshow(im)

def cable(img):
    
   # is here usable "extents?"


rect_tool = RectangleTool(ax,on_enter=cable(im))





i simply want to see "extents" which is the attribute that store coords for 
user-selected rectangle according to
http://scikit-image.org/docs/dev/api/skimage.viewer.canvastools.html?highlight=rectangle#skimage.viewer.canvastools.RectangleTool

i hope this is clear and if it's possible i think is useful to embed this 
example in docs.

thanks in advance
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From google at terre-adelie.org  Wed Dec 17 01:46:27 2014
From: google at terre-adelie.org (=?ISO-8859-1?Q?J=E9r=F4me?= Kieffer)
Date: Wed, 17 Dec 2014 07:46:27 +0100
Subject: peak detectors
In-Reply-To: <20141215220654.GA15640@phare.normalesup.org>
References: <20141215220654.GA15640@phare.normalesup.org>
Message-ID: <20141217074627.05e3b981861ac09677935b37@terre-adelie.org>

Hi,

I had a trainee implementing a peak-picking based on difference of gaussian ...
it is available on https://github.com/kif/pyFAI/blob/master/pyFAI-src/blob_detection.py
but it turned out to be quite sensitive to noise.

Cheers,
-- 
J?r?me Kieffer <google at terre-adelie.org>


From steven.silvester at gmail.com  Thu Dec 18 21:40:08 2014
From: steven.silvester at gmail.com (Steven Silvester)
Date: Thu, 18 Dec 2014 18:40:08 -0800 (PST)
Subject: User Interaction with RectangleTool
In-Reply-To: <a29684d7-1477-4ee5-aa50-c323ae2e4611@googlegroups.com>
References: <a29684d7-1477-4ee5-aa50-c323ae2e4611@googlegroups.com>
Message-ID: <a74fe7ee-649d-48b2-afbb-388e39573d9d@googlegroups.com>



Hi Salvatore,

on_enter is expecting a function object, but you?ve passed the *result* of 
a function call. Here?s what it should look like:

def cable(extents):
   print(extents)

rect_tool = RectangleTool(ax,on_enter=cable)

Once you get it working, we?d love for you to submit a Pull Request with an 
example in the docstring for RectangleTool.

Regards,

Steve 
?
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From stefan at sun.ac.za  Thu Dec 18 19:09:54 2014
From: stefan at sun.ac.za (Stefan van der Walt)
Date: Fri, 19 Dec 2014 02:09:54 +0200
Subject: Pattern and object recognition with COSFIRE
In-Reply-To: <717836ab-0fc4-49f0-8bfb-d25b7fd5acc5@googlegroups.com>
References: <54900E26.3020607@gmail.com> <87zjan6dee.fsf@sun.ac.za> <6fd44996-fbf4-4151-8bdd-e9e9e0aef928@googlegroups.com> <CABDkGQ=NyQKXbhg_-mPYiMpLjoxkxt6VNYHJKo4pvyOyWXNbGA@mail.gmail.com> <78dcd628-2008-441b-a478-ff4e2eff39cd@googlegroups.com> <CABDkGQmE2sOxKe04Un0SGBh4sBMoFCxKv3i5goA_ujSTVi5+0A@mail.gmail.com> <717836ab-0fc4-49f0-8bfb-d25b7fd5acc5@googlegroups.com>
Message-ID: <87oar05wkt.fsf@sun.ac.za>

Hi George

On 2014-12-17 12:48:26, George Azzopardi <geazzo at gmail.com> wrote:
> I would be very happy and available to work with an undergraduate or a 
> postgraduate student (or any other person) to have this parallel 
> implementation in Python. I see that you already added it to the 
> Requested-features page. You can also add my contact details (geazzo at gmail) 
> there for the interested readers.

Thank you for getting in touch!  If you are interested in co-mentoring a
student, we can consider applying for a Google Summer of Code
sponsorship to develop the color version of COSFIRE.

> All my papers can be freely downloaded from my 
> website: http://www.cs.rug.nl/~george/research-activities/

Thank you for this--I've updated the wiki page accordingly.

St?fan


From hughesadam87 at gmail.com  Sun Dec 21 17:37:42 2014
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Sun, 21 Dec 2014 14:37:42 -0800 (PST)
Subject: How do you keep documentation so nice?
In-Reply-To: <CAA48SF8a0oa2y4RX-jNHNnsRLu0S0pduNUBUNYruiz5QEuTpmA@mail.gmail.com>
References: <CAMHV+dD=73bo+ZtGTu8-D3X_HCoCi0Ub=bJT-GPtZJdcTmMkYQ@mail.gmail.com>
 <1418299017813.d4c8c85c@Nodemailer> <CAMHV+dD8TPGcWaEc3wEVrshV62Ev2ZGRgzH5FhZUYz2-ANh=0Q@mail.gmail.com>
 <CAA48SF8a0oa2y4RX-jNHNnsRLu0S0pduNUBUNYruiz5QEuTpmA@mail.gmail.com>
Message-ID: <fe938f58-2391-4b42-9db9-2ad1d8b51dc7@googlegroups.com>

Hey Thomas,

Sorry for late reply.  Can you expand on this a little bit?  Benjamin Root 
said to ask you about how the docs work.  Essentially, how do you host them 
on the master branch under the docs folder and still have them hosted at 
matplotlib.org?  Instead of hosting them on gh-pages and having them show 
up as github.com/matplotlib?   I'm having the hardest time finding info on 
this.

On Thursday, December 11, 2014 12:58:00 PM UTC-5, Thomas Caswell wrote:
>
> matplotlib uses the organization-level gh-pages to host the documentation 
> which seems to work pretty well.
>
> On Thu Dec 11 2014 at 12:45:30 PM Adam Hughes <hughes... at gmail.com 
> <javascript:>> wrote:
>
>> Thanks, that's great advice.  Also, do you guys pay to host your site?  
>> Can you recommend a low-cost, or free, static-website hosting vendor?  We 
>> are currently using gh-pages branch on github to host our site, and I 
>> really hate having this secondary branch.  Especially when I need the 
>> documentation to have access to the source code modules or setup.py file 
>> (as it's on a second branch).
>>
>> On Thu, Dec 11, 2014 at 6:56 AM, Juan Nunez-Iglesias <jni.... at gmail.com 
>> <javascript:>> wrote:
>>>
>>> Adam, just fyi, we are considering moving away from GoogleGroups... (See 
>>> a separate discussion on this list). Since you are on the ground floor, you 
>>> might want to reconsider your choice. I've been using Nabble for my (very 
>>> low volume!) gala list and it's been really good.
>>>
>>>
>>>
>>>
>>> On Thu, Dec 11, 2014 at 12:01 PM, Adam Hughes <hughes... at gmail.com 
>>> <javascript:>> wrote:
>>>
>>>> Thanks Michael.
>>>>
>>>> Be warned, only about 3 people are using the library at the moment, so 
>>>> it's quite likely that you'll encounter some bugs just by virtue of using a 
>>>> new dataset that probably will bring to light some considerations that we 
>>>> overlooked.  In addition, I only support pandas 0.14 right now (0.15 has a 
>>>> lot of private API changes that directly affect us).  But we did feel like 
>>>> the library was close enough to ready to share it, and I hope you can try 
>>>> it out.  If you do want to give it a whirl sometime soon, please feel free 
>>>> to contact us at sks... at googlegroups.com <javascript:> (or me 
>>>> personally) and we will at least make sure to help get you up and running.  
>>>> Let us know what kind of data you're working on and what type of analysis 
>>>> you're doing.  We've spend a lot of time putting out datastructures 
>>>> together, but we haven't put a great deal of thought into the actual 
>>>> spectral utilitiles, workflows and analysis that we should host, other than 
>>>> correlation spectroscopy and base things like dynamic baseline fitting.
>>>>
>>>>
>>>>  
>>>> On Wed, Dec 10, 2014 at 6:14 PM, Michael Aye <kmicha... at gmail.com 
>>>> <javascript:>> wrote:
>>>>
>>>>>  On 2014-12-10 02:43:46, Adam Hughes <hughes... at gmail.com> wrote:
>>>>>
>>>>>> > http://hugadams.github.io/scikit-spectra/
>>>>>>>>
>>>>>>>> That is a very impressive notebook widget shown in the video!  I 
>>>>>>>> love
>>>>>>>> how it interacts with mpl3d.
>>>>>>>>
>>>>>>>>
>>>>>>>> Ditto! Man, can't wait to play with this! Very happy that there's 
>>>>> finally a package focusing on spectral analysis! It also just comes at the 
>>>>> right time, just started in my new job working on data from an imaging 
>>>>> spectrometer for the first time. ;)
>>>>>
>>>>> Michael
>>>>>  
>>>>>   
>>>>> -- 
>>>>> 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/k5K6_vanZVI/unsubscribe
>>>>> .
>>>>> To unsubscribe from this group and all its topics, send an email to 
>>>>> scikit-image... at googlegroups.com <javascript:>.
>>>>> For more options, visit https://groups.google.com/d/optout.
>>>>>
>>>>  
>>>>  -- 
>>>> You received this message because you are subscribed to the Google 
>>>> Groups "scikit-image" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send 
>>>> an email to scikit-image... at googlegroups.com <javascript:>.
>>>> For more options, visit https://groups.google.com/d/optout.
>>>>
>>>
>>>  -- 
>>> 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/k5K6_vanZVI/unsubscribe.
>>> To unsubscribe from this group and all its topics, send an email to 
>>> scikit-image... at googlegroups.com <javascript:>.
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>  -- 
>> You received this message because you are subscribed to the Google Groups 
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an 
>> email to scikit-image... at googlegroups.com <javascript:>.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
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From stefan at sun.ac.za  Sun Dec 28 04:14:49 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Sun, 28 Dec 2014 11:14:49 +0200
Subject: Fwd: [Numpy-discussion] numpy dev-version-string change
In-Reply-To: <CABL7CQiMwWLD+mYPqUgHGSn2SS+Cgs0HRQqnHy07j4RSBSsh-Q@mail.gmail.com>
References: <CABL7CQiMwWLD+mYPqUgHGSn2SS+Cgs0HRQqnHy07j4RSBSsh-Q@mail.gmail.com>
Message-ID: <CABDkGQ=o3qdBuidm4dwSBv=7CxsYFk2__LBnSCXvR835CpyFeQ@mail.gmail.com>

---------- Forwarded message ----------
From: "Ralf Gommers" <ralf.gommers at gmail.com>
Date: Dec 28, 2014 10:43 AM
Subject: [Numpy-discussion] numpy dev-version-string change
To: "Discussion of Numerical Python" <numpy-discussion at scipy.org>
Cc:

Hi all,

This is a heads up that the numpy version string for development versions
is changing from x.y.z.dev-githash to x.y.z.dev+githash (note the +). This
is due to PEP 440 [1], which specifies local (i.e. non-released) versions
have to use a "+". Pip 6.0, released a few days ago, enforces this so we
noticed immediately that without this version string change pip sorted the
latest dev wheel build from master below any released version.

Change in numpy at [2]; identical change in scipy at [3]. Note that this is
unlikely but not impossible to break custom version string parsers (like
[4]).

Cheers,
Ralf

[1] https://www.python.org/dev/peps/pep-0440/
[2] https://github.com/numpy/numpy/pull/5387
[3] https://github.com/scipy/scipy/pull/4307
[4] https://github.com/scipy/scipy/blob/master/scipy/lib/_version.py

_______________________________________________
NumPy-Discussion mailing list
NumPy-Discussion at scipy.org
http://mail.scipy.org/mailman/listinfo/numpy-discussion
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From maqianlie at gmail.com  Tue Dec 30 10:59:06 2014
From: maqianlie at gmail.com (Ma ChienLi)
Date: Tue, 30 Dec 2014 07:59:06 -0800 (PST)
Subject: Hi, I would like to offer my help in the next GSoC
Message-ID: <bea20f89-bc11-45e0-ac34-a6749662f1c9@googlegroups.com>

Hi, everybody~

I am Ma Chienli, an undergraduate from China, majoring in electronic and 
information engineering.
I have beed using python for scientific computation for a year and now I am 
learning cython.
I would like to offer my for your next (possible) GSoC project of writting 
the scipy.ndimage in cython :)
So, at first, from where should I start?

Cheers
Ma

P.S. I just created another thread which did not show up. If this thread 
conflicts with it, please delete one of them .
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From jni.soma at gmail.com  Tue Dec 30 17:27:27 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Tue, 30 Dec 2014 14:27:27 -0800 (PST)
Subject: Hi, I would like to offer my help in the next GSoC
In-Reply-To: <bea20f89-bc11-45e0-ac34-a6749662f1c9@googlegroups.com>
References: <bea20f89-bc11-45e0-ac34-a6749662f1c9@googlegroups.com>
Message-ID: <1419978447394.2a278b2a@Nodemailer>

Hi Ma,




The best way to get started is to contribute! Have a look at our contribution guidelines [1], and then look at the project's issues list [2] and see where you can make a difference! The more practice you get making good, clean pull requests on GitHub, the better your chances.




Cheers back!




Juan.




[1] https://github.com/scikit-image/scikit-image/blob/master/CONTRIBUTING.txt

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




PS: Sorry you didn't get a quick response on Gitter ? it's a busy time of year! But that is the right place to chat about development questions. Give it a try when you have quick questions, and come back to this list if you don't get a quick response.

On Wed, Dec 31, 2014 at 7:44 AM, Ma ChienLi <maqianlie at gmail.com> wrote:

> Hi, everybody~
> I am Ma Chienli, an undergraduate from China, majoring in electronic and 
> information engineering.
> I have beed using python for scientific computation for a year and now I am 
> learning cython.
> I would like to offer my for your next (possible) GSoC project of writting 
> the scipy.ndimage in cython :)
> So, at first, from where should I start?
> Cheers
> Ma
> P.S. I just created another thread which did not show up. If this thread 
> conflicts with it, please delete one of them .
> -- 
> 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/d/optout.
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