From elyraz at mail.com  Fri Jun  5 03:41:11 2015
From: elyraz at mail.com (elyraz at mail.com)
Date: Fri, 5 Jun 2015 00:41:11 -0700 (PDT)
Subject: GLCM with scikit-image
In-Reply-To: <CAEym_HonsLTmb-+t1fezjpd+MP7mMnZyL8O3PcRxo38R3bJWtw@mail.gmail.com>
References: <74a4cdd3-015c-4ca7-ba4f-b5ede4abd49e@googlegroups.com>
 <3b3cba05-3482-488c-b683-1b34156fa704@googlegroups.com> <b0460f03-63cc-4cb5-ac82-690276496904@googlegroups.com>
 <9da24452-ae00-49bf-b3e9-0891121416b2@googlegroups.com> <73f054b0-ba24-4cf7-a5f0-166e090679a9@googlegroups.com>
 <7ddef0ce-064d-450b-b0df-968145517cf7@googlegroups.com>
 <CAEym_HonsLTmb-+t1fezjpd+MP7mMnZyL8O3PcRxo38R3bJWtw@mail.gmail.com>
Message-ID: <bf2dc8f9-5e74-4e5c-b7c8-b0b0bfcd0465@googlegroups.com>

 

I  moved to python 3.4 and scikit_image?0.11.3 amd when I am running a 
script the:

from skimage.util import dtype

dtype.log.disabled = True


I get this error:
Traceback (most recent call last):
  File "C:/Users/ZDesktop/untitled/d.py", line 16, in <module>
    dtype.log.disabled = True
AttributeError: 'module' object has no attribute 'log'

 

If I remove the ?dtype.log.disabled = True?  script line I get this message:

C:\Python34\lib\site-packages\skimage\util\dtype.py:111: UserWarning: 
Possible precision loss when converting from float64 to uint8

  "%s to %s" % (dtypeobj_in, dtypeobj))

 

Therefore, how can I use the dtype and remove the warning message?

 

Thanks a lot
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From helderomar at gmail.com  Fri Jun  5 04:01:02 2015
From: helderomar at gmail.com (=?UTF-8?Q?H=C3=A9lder_Tomas?=)
Date: Fri, 5 Jun 2015 01:01:02 -0700 (PDT)
Subject: problem with io.imread
In-Reply-To: <CAOUdFY45ytQJv4mqcuSGcR0uxRBBxq3zD_=oqR3txBJZSSdk4A@mail.gmail.com>
References: <CAOUdFY45ytQJv4mqcuSGcR0uxRBBxq3zD_=oqR3txBJZSSdk4A@mail.gmail.com>
Message-ID: <c70585b1-5cc7-4052-8087-31617d21d7b6@googlegroups.com>

Hello guys,

I had the same issue and it's due to PIL and the libraries needed to read 
jpeg. It worked fine with png for instance.
Pillow has replaced pil, and we might as well remove pil.

Remove PIL:

*sudo pip uninstall pil*


Install the required libraries:

* sudo apt-get install libtiff4-dev libjpeg8-dev zlib1g-dev 
libfreetype6-dev liblcms2-dev libwebp-dev tcl8.5-dev tk8.5-dev python-tk*


Install/upgrade pillow :

*sudo pip install pillow --upgrade*


And your data.imread should work fine now.

Hope this helps someone!
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From stefanv at berkeley.edu  Fri Jun  5 14:37:22 2015
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Fri, 05 Jun 2015 11:37:22 -0700
Subject: problem with io.imread
In-Reply-To: <c70585b1-5cc7-4052-8087-31617d21d7b6@googlegroups.com>
References: <CAOUdFY45ytQJv4mqcuSGcR0uxRBBxq3zD_=oqR3txBJZSSdk4A@mail.gmail.com> <c70585b1-5cc7-4052-8087-31617d21d7b6@googlegroups.com>
Message-ID: <87h9qmc87x.fsf@berkeley.edu>

Dear H?lder

On 2015-06-05 01:01:02, H?lder Tomas <helderomar at gmail.com> wrote:
> I had the same issue and it's due to PIL and the libraries 
> needed to read  jpeg. It worked fine with png for instance. 
> Pillow has replaced pil, and we might as well remove pil.

Can we catch this problem and then display a workaround to the 
user?  Would you be interested in working on that?

St?fan


From stefanv at berkeley.edu  Fri Jun  5 14:40:58 2015
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Fri, 05 Jun 2015 11:40:58 -0700
Subject: GLCM with scikit-image
In-Reply-To: <e75d8156-525b-4819-9a2f-2fc2d98c861d@googlegroups.com>
References: <74a4cdd3-015c-4ca7-ba4f-b5ede4abd49e@googlegroups.com> <3b3cba05-3482-488c-b683-1b34156fa704@googlegroups.com> <b0460f03-63cc-4cb5-ac82-690276496904@googlegroups.com> <9da24452-ae00-49bf-b3e9-0891121416b2@googlegroups.com> <73f054b0-ba24-4cf7-a5f0-166e090679a9@googlegroups.com> <7ddef0ce-064d-450b-b0df-968145517cf7@googlegroups.com> <CAEym_HonsLTmb-+t1fezjpd+MP7mMnZyL8O3PcRxo38R3bJWtw@mail.gmail.com> <e75d8156-525b-4819-9a2f-2fc2d98c861d@googlegroups.com>
Message-ID: <87eglqc81x.fsf@berkeley.edu>

On 2015-06-05 00:35:54, elyraz at mail.com wrote:
> I  moved to python 3.4 and scikit_image?0.11.3 amnd when I am 
> running a  script the: from skimage.util import dtype 
> dtype.log.disabled = True
>
> I get this error: Traceback (most recent call last): 
>   File "C:/Users/ZDesktop/untitled/d.py", line 16, in <module> 
>     dtype.log.disabled = True 
> AttributeError: 'module' object has no attribute 'log'

The package has changed in the mean time--we no longer use a 
logging mechanism and you can disable the warning using the 
standing Python warnings module.

St?fan


From steven.silvester at gmail.com  Sat Jun  6 11:54:30 2015
From: steven.silvester at gmail.com (Steven Silvester)
Date: Sat, 6 Jun 2015 08:54:30 -0700 (PDT)
Subject: missing kernel or block size in equalize_adapthist
In-Reply-To: <4b57c4b4-1f5f-4cf5-a4e6-3b14e657da2f@googlegroups.com>
References: <4b57c4b4-1f5f-4cf5-a4e6-3b14e657da2f@googlegroups.com>
Message-ID: <ee6a74e3-7cfd-443d-8095-92611d34e672@googlegroups.com>

Hi Kai,

We are having a discussion now about how to fix/improve the adapthist block 
handling:  https://github.com/scikit-image/scikit-image/issues/1541.


Regards,

Steve

On Monday, May 25, 2015 at 1:49:53 PM UTC-5, Kai Wiechen wrote:
>
>
> <https://lh3.googleusercontent.com/-0jVbtyT6ArM/VWNtiWHECgI/AAAAAAAABOg/AKpRcr4fKHU/s1600/nuclei_equalize_adapthist.jpg>
> Hello,
>
> I am using equalize_adapthist after color deconvolution and some 
> morphological operations to enhance local contrast of nuclei in 
> histological images. There are different results when applying 
> equalize_adapthist when using small patches and larger size whole images 
> (left small patch, right large size whole image). The CLAHE implementation 
> in ImageJ has a 'block size' parameter and the implementation in Pixinsight 
> has a 'Kernel size' parameter to get results depending on the local 
> context. Is it possible to 'simulate' this behaviour with scikit-image?
>
> Best regards,
>
> Kai
>
>
>
>
>
>
>
>
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From stefanv at berkeley.edu  Sun Jun  7 10:34:02 2015
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Sun, 07 Jun 2015 07:34:02 -0700
Subject: Sticker review
Message-ID: <87vbeza8px.fsf@berkeley.edu>

Hi all,

Here is a PR with a potential skimage sticker:

https://github.com/scikit-image/skimage-branding/pull/1

What do you think?

St?fan


From jsch at demuc.de  Sun Jun  7 10:49:44 2015
From: jsch at demuc.de (=?UTF-8?Q?Johannes_Sch=C3=B6nberger?=)
Date: Sun, 7 Jun 2015 07:49:44 -0700
Subject: Sticker review
In-Reply-To: <87vbeza8px.fsf@berkeley.edu>
References: <87vbeza8px.fsf@berkeley.edu>
Message-ID: <CAFTxfLnNYCFPpcbyDOsV2fM3oxs0tRBr2Y1FvJqwD_yX5EKFZw@mail.gmail.com>

Looks nice! How does it look like with a warying white border?

On Sun, Jun 7, 2015 at 7:34 AM, Stefan van der Walt
<stefanv at berkeley.edu> wrote:
> Hi all,
>
> Here is a PR with a potential skimage sticker:
>
> https://github.com/scikit-image/skimage-branding/pull/1
>
> What do you think?
>
> 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.


From msarahan at gmail.com  Sun Jun  7 12:35:32 2015
From: msarahan at gmail.com (Michael Sarahan)
Date: Sun, 07 Jun 2015 16:35:32 +0000
Subject: Sticker review
In-Reply-To: <CAFTxfLnNYCFPpcbyDOsV2fM3oxs0tRBr2Y1FvJqwD_yX5EKFZw@mail.gmail.com>
References: <87vbeza8px.fsf@berkeley.edu> <CAFTxfLnNYCFPpcbyDOsV2fM3oxs0tRBr2Y1FvJqwD_yX5EKFZw@mail.gmail.com>
Message-ID: <CAB9hrOpf2M--x=ppokuY6rSFq2M+n0y5nmew7FHKjy3_GSL4Ow@mail.gmail.com>

Looks great!  I'm excited to put one on my laptop.  My only
comment/question is about the grey space between the k and i.  I think it's
fine as is, but I wonder why you have grey/cutout there, and not in any of
the other large void spaces (like inside the g?)  Disclaimer: I have never
designed a sticker, and don't know best practices.  Among the stickers that
I presently have on my laptop, none have cutouts inside the sticker.

Best,
Michael

On Sun, Jun 7, 2015 at 7:49 AM Johannes Sch?nberger <jsch at demuc.de> wrote:

> Looks nice! How does it look like with a warying white border?
>
> On Sun, Jun 7, 2015 at 7:34 AM, Stefan van der Walt
> <stefanv at berkeley.edu> wrote:
> > Hi all,
> >
> > Here is a PR with a potential skimage sticker:
> >
> > https://github.com/scikit-image/skimage-branding/pull/1
> >
> > What do you think?
> >
> > 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.
>
> --
> 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 stefanv at berkeley.edu  Mon Jun  8 22:22:57 2015
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Mon, 08 Jun 2015 19:22:57 -0700
Subject: Sticker review
In-Reply-To: <CAFTxfLnNYCFPpcbyDOsV2fM3oxs0tRBr2Y1FvJqwD_yX5EKFZw@mail.gmail.com>
References: <87vbeza8px.fsf@berkeley.edu> <CAFTxfLnNYCFPpcbyDOsV2fM3oxs0tRBr2Y1FvJqwD_yX5EKFZw@mail.gmail.com>
Message-ID: <87oakp8vsu.fsf@berkeley.edu>

Hi Johannes

On 2015-06-07 07:49:44, Johannes Sch?nberger <jsch at demuc.de> 
wrote:
> Looks nice! How does it look like with a warying white border?

Varying in which aspect?

St?fan


From stefanv at berkeley.edu  Mon Jun  8 22:26:15 2015
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Mon, 08 Jun 2015 19:26:15 -0700
Subject: Sticker review
In-Reply-To: <CAB9hrOpf2M--x=ppokuY6rSFq2M+n0y5nmew7FHKjy3_GSL4Ow@mail.gmail.com>
References: <87vbeza8px.fsf@berkeley.edu> <CAFTxfLnNYCFPpcbyDOsV2fM3oxs0tRBr2Y1FvJqwD_yX5EKFZw@mail.gmail.com> <CAB9hrOpf2M--x=ppokuY6rSFq2M+n0y5nmew7FHKjy3_GSL4Ow@mail.gmail.com>
Message-ID: <87mw098vnc.fsf@berkeley.edu>

On 2015-06-07 09:35:32, Michael Sarahan <msarahan at gmail.com> 
wrote:
> Looks great!  I'm excited to put one on my laptop.  My only 
> comment/question is about the grey space between the k and i.  I 
> think it's fine as is, but I wonder why you have grey/cutout 
> there, and not in any of the other large void spaces (like 
> inside the g?)  Disclaimer: I have never designed a sticker, and 
> don't know best practices.  Among the stickers that I presently 
> have on my laptop, none have cutouts inside the sticker.

I manually closed the hole inside the g, because someone told me 
it looked weird.  Perhaps it looks even weirder now that it's 
artificially closed?

Here is the original:

https://www.dropbox.com/s/yg4lypzmgjd1aoh/sticker_00.png?dl=0

St?fan


From stefanv at berkeley.edu  Tue Jun  9 01:23:35 2015
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Mon, 08 Jun 2015 22:23:35 -0700
Subject: Sticker review
In-Reply-To: <CA+JHcKRNXWhSDC6JODVk0nm97-Q2fBJAwZEtXP=3DhUEoNspAw@mail.gmail.com>
References: <87vbeza8px.fsf@berkeley.edu> <CAFTxfLnNYCFPpcbyDOsV2fM3oxs0tRBr2Y1FvJqwD_yX5EKFZw@mail.gmail.com> <CAB9hrOpf2M--x=ppokuY6rSFq2M+n0y5nmew7FHKjy3_GSL4Ow@mail.gmail.com> <87mw098vnc.fsf@berkeley.edu> <CAB9hrOrK27z8gSQ3w43wAv5gsWY867t7RVNZ7K4v6=kD8om4hA@mail.gmail.com> <CA+JHcKRNXWhSDC6JODVk0nm97-Q2fBJAwZEtXP=3DhUEoNspAw@mail.gmail.com>
Message-ID: <87a8w98nfs.fsf@berkeley.edu>

Here is the no-holes version:

https://www.dropbox.com/s/yn7p3p1dfs1itc5/sticker_01.png?dl=0

One reason to keep the hole would be to distinguish the two parts: 
scikit vs image.

On 2015-06-08 21:34:50, Juan Nunez-Iglesias <jni.soma at gmail.com> 
wrote:
> @stefanv, I'd favour closing the k-i also.
>
> On Tue, Jun 9, 2015 at 12:51 PM, Michael Sarahan 
> <msarahan at gmail.com> wrote:
>
>> I agree that the open g looks weird. Good work closing 
>> it. Funny how the triangle between the k and i does not look 
>> weird to me. I think it's great as is.
>>
>> On Mon, Jun 8, 2015, 19:26 Stefan van der Walt 
>> <stefanv at berkeley.edu>
>> wrote:
>>
>>> On 2015-06-07 09:35:32, Michael Sarahan <msarahan at gmail.com>
>>> wrote:
>>> > Looks great!  I'm excited to put one on my laptop.  My only 
>>> > comment/question is about the grey space between the k and 
>>> > i.  I think it's fine as is, but I wonder why you have 
>>> > grey/cutout there, and not in any of the other large void 
>>> > spaces (like inside the g?)  Disclaimer: I have never 
>>> > designed a sticker, and don't know best practices.  Among 
>>> > the stickers that I presently have on my laptop, none have 
>>> > cutouts inside the sticker.
>>>
>>> I manually closed the hole inside the g, because someone told 
>>> me it looked weird.  Perhaps it looks even weirder now that 
>>> it's artificially closed?
>>>
>>> Here is the original:
>>>
>>> https://www.dropbox.com/s/yg4lypzmgjd1aoh/sticker_00.png?dl=0
>>>
>>> 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.
>>>
>>  -- 
>> 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 msarahan at gmail.com  Mon Jun  8 22:51:58 2015
From: msarahan at gmail.com (Michael Sarahan)
Date: Tue, 09 Jun 2015 02:51:58 +0000
Subject: Sticker review
In-Reply-To: <87mw098vnc.fsf@berkeley.edu>
References: <87vbeza8px.fsf@berkeley.edu> <CAFTxfLnNYCFPpcbyDOsV2fM3oxs0tRBr2Y1FvJqwD_yX5EKFZw@mail.gmail.com>
 <CAB9hrOpf2M--x=ppokuY6rSFq2M+n0y5nmew7FHKjy3_GSL4Ow@mail.gmail.com> <87mw098vnc.fsf@berkeley.edu>
Message-ID: <CAB9hrOrK27z8gSQ3w43wAv5gsWY867t7RVNZ7K4v6=kD8om4hA@mail.gmail.com>

I agree that the open g looks weird. Good work closing it. Funny how the
triangle between the k and i does not look weird to me. I think it's great
as is.

On Mon, Jun 8, 2015, 19:26 Stefan van der Walt <stefanv at berkeley.edu> wrote:

> On 2015-06-07 09:35:32, Michael Sarahan <msarahan at gmail.com>
> wrote:
> > Looks great!  I'm excited to put one on my laptop.  My only
> > comment/question is about the grey space between the k and i.  I
> > think it's fine as is, but I wonder why you have grey/cutout
> > there, and not in any of the other large void spaces (like
> > inside the g?)  Disclaimer: I have never designed a sticker, and
> > don't know best practices.  Among the stickers that I presently
> > have on my laptop, none have cutouts inside the sticker.
>
> I manually closed the hole inside the g, because someone told me
> it looked weird.  Perhaps it looks even weirder now that it's
> artificially closed?
>
> Here is the original:
>
> https://www.dropbox.com/s/yg4lypzmgjd1aoh/sticker_00.png?dl=0
>
> 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  Tue Jun  9 00:34:50 2015
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Tue, 9 Jun 2015 14:34:50 +1000
Subject: Sticker review
In-Reply-To: <CAB9hrOrK27z8gSQ3w43wAv5gsWY867t7RVNZ7K4v6=kD8om4hA@mail.gmail.com>
References: <87vbeza8px.fsf@berkeley.edu> <CAFTxfLnNYCFPpcbyDOsV2fM3oxs0tRBr2Y1FvJqwD_yX5EKFZw@mail.gmail.com>
 <CAB9hrOpf2M--x=ppokuY6rSFq2M+n0y5nmew7FHKjy3_GSL4Ow@mail.gmail.com>
 <87mw098vnc.fsf@berkeley.edu> <CAB9hrOrK27z8gSQ3w43wAv5gsWY867t7RVNZ7K4v6=kD8om4hA@mail.gmail.com>
Message-ID: <CA+JHcKRNXWhSDC6JODVk0nm97-Q2fBJAwZEtXP=3DhUEoNspAw@mail.gmail.com>

@stefanv, I'd favour closing the k-i also.

On Tue, Jun 9, 2015 at 12:51 PM, Michael Sarahan <msarahan at gmail.com> wrote:

> I agree that the open g looks weird. Good work closing it. Funny how the
> triangle between the k and i does not look weird to me. I think it's great
> as is.
>
> On Mon, Jun 8, 2015, 19:26 Stefan van der Walt <stefanv at berkeley.edu>
> wrote:
>
>> On 2015-06-07 09:35:32, Michael Sarahan <msarahan at gmail.com>
>> wrote:
>> > Looks great!  I'm excited to put one on my laptop.  My only
>> > comment/question is about the grey space between the k and i.  I
>> > think it's fine as is, but I wonder why you have grey/cutout
>> > there, and not in any of the other large void spaces (like
>> > inside the g?)  Disclaimer: I have never designed a sticker, and
>> > don't know best practices.  Among the stickers that I presently
>> > have on my laptop, none have cutouts inside the sticker.
>>
>> I manually closed the hole inside the g, because someone told me
>> it looked weird.  Perhaps it looks even weirder now that it's
>> artificially closed?
>>
>> Here is the original:
>>
>> https://www.dropbox.com/s/yg4lypzmgjd1aoh/sticker_00.png?dl=0
>>
>> 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.
>>
>  --
> 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  Tue Jun  9 19:03:32 2015
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Tue, 9 Jun 2015 16:03:32 -0700 (PDT)
Subject: Sticker review
In-Reply-To: <87a8w98nfs.fsf@berkeley.edu>
References: <87vbeza8px.fsf@berkeley.edu> <CAFTxfLnNYCFPpcbyDOsV2fM3oxs0tRBr2Y1FvJqwD_yX5EKFZw@mail.gmail.com> <CAB9hrOpf2M--x=ppokuY6rSFq2M+n0y5nmew7FHKjy3_GSL4Ow@mail.gmail.com> <87mw098vnc.fsf@berkeley.edu> <CAB9hrOrK27z8gSQ3w43wAv5gsWY867t7RVNZ7K4v6=kD8om4hA@mail.gmail.com> <CA+JHcKRNXWhSDC6JODVk0nm97-Q2fBJAwZEtXP=3DhUEoNspAw@mail.gmail.com>
 <87a8w98nfs.fsf@berkeley.edu>
Message-ID: <c2938251-adfe-4ce6-96d1-e27c7907fee4@googlegroups.com>

I'd vote for no-holes. Everything else aside, complicated stickers with 
cutouts like that usually don't peel off well or reliably if the cutouts 
aren't connected to the surrounding non-sticker region.


On Tuesday, June 9, 2015 at 12:23:39 AM UTC-5, stefanv wrote:
>
> Here is the no-holes version: 
>
> https://www.dropbox.com/s/yn7p3p1dfs1itc5/sticker_01.png?dl=0 
>
> One reason to keep the hole would be to distinguish the two parts: 
> scikit vs image. 
>
> On 2015-06-08 21:34:50, Juan Nunez-Iglesias <jni.soma at gmail.com> 
> wrote: 
> > @stefanv, I'd favour closing the k-i also. 
> > 
> > On Tue, Jun 9, 2015 at 12:51 PM, Michael Sarahan 
> > <msarahan at gmail.com> wrote: 
> > 
> >> I agree that the open g looks weird. Good work closing 
> >> it. Funny how the triangle between the k and i does not look 
> >> weird to me. I think it's great as is. 
> >> 
> >> On Mon, Jun 8, 2015, 19:26 Stefan van der Walt 
> >> <stefanv at berkeley.edu> 
> >> wrote: 
> >> 
> >>> On 2015-06-07 09:35:32, Michael Sarahan <msarahan at gmail.com> 
> >>> wrote: 
> >>> > Looks great!  I'm excited to put one on my laptop.  My only 
> >>> > comment/question is about the grey space between the k and 
> >>> > i.  I think it's fine as is, but I wonder why you have 
> >>> > grey/cutout there, and not in any of the other large void 
> >>> > spaces (like inside the g?)  Disclaimer: I have never 
> >>> > designed a sticker, and don't know best practices.  Among 
> >>> > the stickers that I presently have on my laptop, none have 
> >>> > cutouts inside the sticker. 
> >>> 
> >>> I manually closed the hole inside the g, because someone told 
> >>> me it looked weird.  Perhaps it looks even weirder now that 
> >>> it's artificially closed? 
> >>> 
> >>> Here is the original: 
> >>> 
> >>> https://www.dropbox.com/s/yg4lypzmgjd1aoh/sticker_00.png?dl=0 
> >>> 
> >>> 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. 
> >>> 
> >>  -- 
> >> 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 matthew.m.mccormick at gmail.com  Wed Jun 10 23:53:24 2015
From: matthew.m.mccormick at gmail.com (Matthew McCormick)
Date: Wed, 10 Jun 2015 20:53:24 -0700 (PDT)
Subject: SciPy 2015 Birds-of-a-Feather Submission
Message-ID: <ad2f4da0-bd16-44e0-b968-7d9e0186a7ea@googlegroups.com>

Members of the scikit-image Community,

As one of the co-chairs in charge of organizing the birds-of-a-feather 
sessions at SciPy this year, I wanted to reach out to your community to 
encourage you to submit a BoF proposal. A BoF session is an opportunity to 
open up a discussion on topics related to scikit-image development, future 
or just general questions.  Please let us know if there is anything we can 
help with in terms of organization. More details can be found here:

  http://scipy2015.scipy.org/ehome/115969/259291/?&

Kyle Mandli and Matt McCormick
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From gashjizhou at gmail.com  Fri Jun 12 11:04:46 2015
From: gashjizhou at gmail.com (Ji Zhou)
Date: Fri, 12 Jun 2015 08:04:46 -0700 (PDT)
Subject: problem with measure.label
In-Reply-To: <CAOUdFY7ODU6if+_Xdp_SdJzSgqic4Gc6NgS12NjTi0gRfBEddQ@mail.gmail.com>
References: <CAOUdFY7ODU6if+_Xdp_SdJzSgqic4Gc6NgS12NjTi0gRfBEddQ@mail.gmail.com>
Message-ID: <2ca71be1-114a-4593-bf79-fe60f36f2ce8@googlegroups.com>

Hi,

I have the same issue when using scikit image (Anaconda distribution, which 
is up-to-date) to label some image objects. Error messages are: 

from skimage.measure import label

import numpy as np

?

label(np.zeros(5), connectivity=1)

---------------------------------------------------------------------------TypeError                                 Traceback (most recent call last)<ipython-input-2-df99425b8b1f> in <module>()      2 import numpy as np      3 ----> 4 label(np.zeros(5), connectivity=1)
TypeError: label() got an unexpected keyword argument 'connectivity'



Could you help? 


Ji


On Monday, 4 May 2015 16:46:09 UTC+1, Julien Derr wrote:
>
> Hi everyone, it is me again ...
> I got this error with the label function
> TypeError: label() got an unexpected keyword argument 'connectivity'
>
> but I used it exactly like written in the help : 
>
> cc= label(binary2,connectivity=2)
>
> I thought it was maybe a problem of version, but it is written in my own 
> help when I type ?label, 
> so what could it be ? ideas?
>
> thanks again!
>
> Julien
>
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From stefanv at berkeley.edu  Fri Jun 12 13:20:39 2015
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Fri, 12 Jun 2015 10:20:39 -0700
Subject: problem with measure.label
In-Reply-To: <2ca71be1-114a-4593-bf79-fe60f36f2ce8@googlegroups.com>
References: <CAOUdFY7ODU6if+_Xdp_SdJzSgqic4Gc6NgS12NjTi0gRfBEddQ@mail.gmail.com> <2ca71be1-114a-4593-bf79-fe60f36f2ce8@googlegroups.com>
Message-ID: <87a8w4yhaw.fsf@berkeley.edu>

On 2015-06-12 08:04:46, Ji Zhou <gashjizhou at gmail.com> wrote:
> I have the same issue when using scikit image (Anaconda 
> distribution, which  is up-to-date) to label some image 
> objects. Error messages are:

Can you please verify your version?

import skimage
print(skimage.__version__)

Thanks
St?fan


From silvertrumpet999 at gmail.com  Fri Jun 12 14:33:57 2015
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Fri, 12 Jun 2015 11:33:57 -0700 (PDT)
Subject: problem with measure.label
In-Reply-To: <87a8w4yhaw.fsf@berkeley.edu>
References: <CAOUdFY7ODU6if+_Xdp_SdJzSgqic4Gc6NgS12NjTi0gRfBEddQ@mail.gmail.com> <2ca71be1-114a-4593-bf79-fe60f36f2ce8@googlegroups.com>
 <87a8w4yhaw.fsf@berkeley.edu>
Message-ID: <acfa1e56-d5bd-4e1f-b675-6771f390978d@googlegroups.com>



I cannot reproduce with everything installed fresh via miniconda on Win7.

>>> from skimage.measure import label>>> import numpy as np>>> label(np.zeros(5), connectivity=1)
array([0, 0, 0, 0, 0], dtype=int64)

On Friday, June 12, 2015 at 12:20:43 PM UTC-5, stefanv wrote:

On 2015-06-12 08:04:46, Ji Zhou <gashjizhou at gmail.com> wrote: 
> > I have the same issue when using scikit image (Anaconda 
> > distribution, which  is up-to-date) to label some image 
> > objects. Error messages are: 
>
> Can you please verify your version? 
>
> import skimage 
> print(skimage.__version__) 
>
> Thanks 
> St?fan 
>
?
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From gashjizhou at gmail.com  Sat Jun 13 09:50:03 2015
From: gashjizhou at gmail.com (Ji Zhou)
Date: Sat, 13 Jun 2015 06:50:03 -0700 (PDT)
Subject: problem with measure.label
In-Reply-To: <CA+JHcKQR5y_2AzHuCxZ7n53kQZJPJ_jVexTg8uJogOojvwmumQ@mail.gmail.com>
References: <CAOUdFY7ODU6if+_Xdp_SdJzSgqic4Gc6NgS12NjTi0gRfBEddQ@mail.gmail.com>
 <2ca71be1-114a-4593-bf79-fe60f36f2ce8@googlegroups.com> <87a8w4yhaw.fsf@berkeley.edu>
 <acfa1e56-d5bd-4e1f-b675-6771f390978d@googlegroups.com>
 <CA+JHcKQR5y_2AzHuCxZ7n53kQZJPJ_jVexTg8uJogOojvwmumQ@mail.gmail.com>
Message-ID: <6858e0a2-786b-46e2-81d9-56198f864dc1@googlegroups.com>

Dear all, 

Many thanks for the prompt response! I checked the version of scikit image, 
which suggests that it is 0.10.1. 

However, after I used conda install scikit-image=0.11.3

I still cannot update the version of iPython notebook. Could you please 
give me a hand? 

Cheers,
Ji


On Saturday, 13 June 2015 02:28:35 UTC+1, Juan Nunez-Iglesias wrote:
>
> This looks like a version problem. Connectivity was added in 0.11.
>
> On Sat, Jun 13, 2015 at 4:33 AM, Josh Warner <silvertr... at gmail.com 
> <javascript:>> wrote:
>
>> I cannot reproduce with everything installed fresh via miniconda on Win7.
>>
>> >>> from skimage.measure import label>>> import numpy as np>>> label(np.zeros(5), connectivity=1)
>> array([0, 0, 0, 0, 0], dtype=int64)
>>
>> On Friday, June 12, 2015 at 12:20:43 PM UTC-5, stefanv wrote:
>>
>> On 2015-06-12 08:04:46, Ji Zhou <gashj... at gmail.com <javascript:>> 
>>> wrote: 
>>> > I have the same issue when using scikit image (Anaconda 
>>> > distribution, which  is up-to-date) to label some image 
>>> > objects. Error messages are: 
>>>
>>> Can you please verify your version? 
>>>
>>> import skimage 
>>> print(skimage.__version__) 
>>>
>>> Thanks 
>>> St?fan 
>>>
>> ?
>>
>> -- 
>> You received this message because you are subscribed to the Google Groups 
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an 
>> email to scikit-image... at googlegroups.com <javascript:>.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>
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From stefanv at berkeley.edu  Sat Jun 13 11:33:36 2015
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Sat, 13 Jun 2015 08:33:36 -0700
Subject: problem with measure.label
In-Reply-To: <6858e0a2-786b-46e2-81d9-56198f864dc1@googlegroups.com>
References: <CAOUdFY7ODU6if+_Xdp_SdJzSgqic4Gc6NgS12NjTi0gRfBEddQ@mail.gmail.com> <2ca71be1-114a-4593-bf79-fe60f36f2ce8@googlegroups.com> <87a8w4yhaw.fsf@berkeley.edu> <acfa1e56-d5bd-4e1f-b675-6771f390978d@googlegroups.com> <CA+JHcKQR5y_2AzHuCxZ7n53kQZJPJ_jVexTg8uJogOojvwmumQ@mail.gmail.com> <6858e0a2-786b-46e2-81d9-56198f864dc1@googlegroups.com>
Message-ID: <87twubwrlb.fsf@berkeley.edu>

On 2015-06-13 06:50:03, Ji Zhou <gashjizhou at gmail.com> wrote:
> I still cannot update the version of iPython notebook. Could you 
> please give me a hand?

What do you mean by this?  Do you mean that you cannot access the 
latest version of skimage?  You'll have to restart your notebook 
kernel.

St?fan


From jni.soma at gmail.com  Fri Jun 12 21:28:14 2015
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Sat, 13 Jun 2015 11:28:14 +1000
Subject: problem with measure.label
In-Reply-To: <acfa1e56-d5bd-4e1f-b675-6771f390978d@googlegroups.com>
References: <CAOUdFY7ODU6if+_Xdp_SdJzSgqic4Gc6NgS12NjTi0gRfBEddQ@mail.gmail.com>
 <2ca71be1-114a-4593-bf79-fe60f36f2ce8@googlegroups.com> <87a8w4yhaw.fsf@berkeley.edu>
 <acfa1e56-d5bd-4e1f-b675-6771f390978d@googlegroups.com>
Message-ID: <CA+JHcKQR5y_2AzHuCxZ7n53kQZJPJ_jVexTg8uJogOojvwmumQ@mail.gmail.com>

This looks like a version problem. Connectivity was added in 0.11.

On Sat, Jun 13, 2015 at 4:33 AM, Josh Warner <silvertrumpet999 at gmail.com>
wrote:

> I cannot reproduce with everything installed fresh via miniconda on Win7.
>
> >>> from skimage.measure import label>>> import numpy as np>>> label(np.zeros(5), connectivity=1)
> array([0, 0, 0, 0, 0], dtype=int64)
>
> On Friday, June 12, 2015 at 12:20:43 PM UTC-5, stefanv wrote:
>
> On 2015-06-12 08:04:46, Ji Zhou <gashjizhou at gmail.com> wrote:
>> > I have the same issue when using scikit image (Anaconda
>> > distribution, which  is up-to-date) to label some image
>> > objects. Error messages are:
>>
>> Can you please verify your version?
>>
>> import skimage
>> print(skimage.__version__)
>>
>> Thanks
>> St?fan
>>
> ?
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From silvertrumpet999 at gmail.com  Sat Jun 13 19:57:07 2015
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Sat, 13 Jun 2015 16:57:07 -0700 (PDT)
Subject: problem with measure.label
In-Reply-To: <CAAFycyqXfbZwt-uc=B9RT71wzFJkjiVMnHfjcJOhZcLkVDiJ0Q@mail.gmail.com>
References: <CAOUdFY7ODU6if+_Xdp_SdJzSgqic4Gc6NgS12NjTi0gRfBEddQ@mail.gmail.com>
 <2ca71be1-114a-4593-bf79-fe60f36f2ce8@googlegroups.com>
 <87a8w4yhaw.fsf@berkeley.edu>
 <acfa1e56-d5bd-4e1f-b675-6771f390978d@googlegroups.com>
 <CA+JHcKQR5y_2AzHuCxZ7n53kQZJPJ_jVexTg8uJogOojvwmumQ@mail.gmail.com>
 <6858e0a2-786b-46e2-81d9-56198f864dc1@googlegroups.com>
 <87twubwrlb.fsf@berkeley.edu>
 <CAAFycyqXfbZwt-uc=B9RT71wzFJkjiVMnHfjcJOhZcLkVDiJ0Q@mail.gmail.com>
Message-ID: <1a3b0082-112c-4414-b64e-beace1efebd9@googlegroups.com>

This sounds like you may have conflicting Python installations. `conda` 
updating scikit-image successfully means you should have version 11.3 
_somewhere_, but your PATH may still be preferentially finding a different 
Python/IPython different from the one your `conda` points to.

Investigate this with `which python` to see what the system is doing when 
you ask for Python.

Further instructions would probably best be obtained through the conda 
mailing list. 


On Saturday, June 13, 2015 at 3:37:56 PM UTC-5, Ji Zhou wrote:
>
> I use conda to update scikit image package on mac. However after undating 
> and restarting the kernel, the scikit image was still 0.10.1 on mac.
>
> Interestingly, on my Windows machine, the same procedure has successfully 
> update scikit image. 
>
> One thing I shall point out is that I tried to uninstall anaconda on my 
> mac and was failed. 
>
> Ji
> On 13 Jun 2015 16:33, "Stefan van der Walt" <stefanv at berkeley.edu> wrote:
>
>> On 2015-06-13 06:50:03, Ji Zhou <gashjizhou at gmail.com> wrote:
>>
>>> I still cannot update the version of iPython notebook. Could you please 
>>> give me a hand?
>>>
>>
>> What do you mean by this?  Do you mean that you cannot access the latest 
>> version of skimage?  You'll have to restart your notebook kernel.
>>
>> 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/-YegZib4VK8/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 gashjizhou at gmail.com  Sat Jun 13 16:37:54 2015
From: gashjizhou at gmail.com (Ji Zhou)
Date: Sat, 13 Jun 2015 21:37:54 +0100
Subject: problem with measure.label
In-Reply-To: <87twubwrlb.fsf@berkeley.edu>
References: <CAOUdFY7ODU6if+_Xdp_SdJzSgqic4Gc6NgS12NjTi0gRfBEddQ@mail.gmail.com>
	<2ca71be1-114a-4593-bf79-fe60f36f2ce8@googlegroups.com>
	<87a8w4yhaw.fsf@berkeley.edu>
	<acfa1e56-d5bd-4e1f-b675-6771f390978d@googlegroups.com>
	<CA+JHcKQR5y_2AzHuCxZ7n53kQZJPJ_jVexTg8uJogOojvwmumQ@mail.gmail.com>
	<6858e0a2-786b-46e2-81d9-56198f864dc1@googlegroups.com>
	<87twubwrlb.fsf@berkeley.edu>
Message-ID: <CAAFycyqXfbZwt-uc=B9RT71wzFJkjiVMnHfjcJOhZcLkVDiJ0Q@mail.gmail.com>

I use conda to update scikit image package on mac. However after undating
and restarting the kernel, the scikit image was still 0.10.1 on mac.

Interestingly, on my Windows machine, the same procedure has successfully
update scikit image.

One thing I shall point out is that I tried to uninstall anaconda on my mac
and was failed.

Ji
On 13 Jun 2015 16:33, "Stefan van der Walt" <stefanv at berkeley.edu> wrote:

> On 2015-06-13 06:50:03, Ji Zhou <gashjizhou at gmail.com> wrote:
>
>> I still cannot update the version of iPython notebook. Could you please
>> give me a hand?
>>
>
> What do you mean by this?  Do you mean that you cannot access the latest
> version of skimage?  You'll have to restart your notebook kernel.
>
> 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/-YegZib4VK8/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 aprier90 at gmail.com  Tue Jun 16 11:25:46 2015
From: aprier90 at gmail.com (Anders Prier Lindvig)
Date: Tue, 16 Jun 2015 08:25:46 -0700 (PDT)
Subject: Major and Minor axis length
Message-ID: <b87bb53a-850c-42fb-a192-ce0d68e95fbd@googlegroups.com>

I have been using the scikit-image library for a segmentation task in my 
master thesis. More specifically I have used the regionprops function for 
calculation of major and minor axis length of objects. I was wondering why 
exactly, the eigenvalues are multiplied by 4, before returning the axis 
length? I realize that you multiply by 2 to get the full length, and I 
think you multiply by 2 again because of the standard deviation, but I am 
unsure about this.

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From jsch at demuc.de  Tue Jun 16 23:59:46 2015
From: jsch at demuc.de (=?UTF-8?Q?Johannes_Sch=C3=B6nberger?=)
Date: Tue, 16 Jun 2015 20:59:46 -0700
Subject: Major and Minor axis length
In-Reply-To: <b87bb53a-850c-42fb-a192-ce0d68e95fbd@googlegroups.com>
References: <b87bb53a-850c-42fb-a192-ce0d68e95fbd@googlegroups.com>
Message-ID: <CAFTxfLkjKu0h_c+M2Yps_WJ9sS7HA=0BVXdUGFHHRoC4jTVRNg@mail.gmail.com>

Hi Anders,

there is different formulations for axis lengths and eccentricity in
literature. At the moment, I cannot recall which formulation I used when I
implemented the functions. In the end, it does not matter what scaling
factor you use, as long as it is consistent. A quick Google search reveals
this page:
https://books.google.com/books?id=4gBUz_IkkSsC&lpg=PA230&ots=mAAFbCrng_&pg=PA231#v=onepage&q&f=false
which seems to confirm my implementation.

Following the references, you should be able to figure out more about that.

Hope that helps.

Best, Johannes

On Tue, Jun 16, 2015 at 8:25 AM, Anders Prier Lindvig <aprier90 at gmail.com>
wrote:

> I have been using the scikit-image library for a segmentation task in my
> master thesis. More specifically I have used the regionprops function for
> calculation of major and minor axis length of objects. I was wondering why
> exactly, the eigenvalues are multiplied by 4, before returning the axis
> length? I realize that you multiply by 2 to get the full length, and I
> think you multiply by 2 again because of the standard deviation, but I am
> unsure about this.
>
>  --
> 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 gashjizhou at gmail.com  Wed Jun 17 17:29:02 2015
From: gashjizhou at gmail.com (Ji Zhou)
Date: Wed, 17 Jun 2015 14:29:02 -0700 (PDT)
Subject: problem with measure.label
In-Reply-To: <CAOUdFY7ODU6if+_Xdp_SdJzSgqic4Gc6NgS12NjTi0gRfBEddQ@mail.gmail.com>
References: <CAOUdFY7ODU6if+_Xdp_SdJzSgqic4Gc6NgS12NjTi0gRfBEddQ@mail.gmail.com>
Message-ID: <00c6fc40-12f4-4693-a255-4b4ab44b65a8@googlegroups.com>

Dear all, thanks for the help! I eventually figure out the issue is iPython 
Notebook is referring to a different skimage library, which was included in 
the Canopy distribution... 

import os
path = os.path.dirname(skimage.__file__)

/Users/zhouj/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/skimage


So after uninstalling the Canopy distribution, it is working okay now :-) 


Cheers,

Ji


On Monday, 4 May 2015 16:46:09 UTC+1, Julien Derr wrote:
>
> Hi everyone, it is me again ...
> I got this error with the label function
> TypeError: label() got an unexpected keyword argument 'connectivity'
>
> but I used it exactly like written in the help : 
>
> cc= label(binary2,connectivity=2)
>
> I thought it was maybe a problem of version, but it is written in my own 
> help when I type ?label, 
> so what could it be ? ideas?
>
> thanks again!
>
> Julien
>
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From nadavh.horesh at gmail.com  Fri Jun 19 13:16:43 2015
From: nadavh.horesh at gmail.com (Nadav Horesh)
Date: Fri, 19 Jun 2015 10:16:43 -0700 (PDT)
Subject: (Histogram?) plugin behaviour change?
Message-ID: <aa3e554b-2e69-472e-89d8-a70353799593@googlegroups.com>

Maybe there is a plugin behaviour change, since the color_histogram.py does 
not function as it used to, I suspect that for some reason the 
RectangleTool is attached to the image rather to the histogram window. I'd 
to have instructions how to fix it, since I've build a modification to 
ColorHistogram that it would be nice to fix.

  Thanks

    Nadav
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From fboulogne at sciunto.org  Fri Jun 19 13:10:32 2015
From: fboulogne at sciunto.org (=?windows-1252?Q?Fran=E7ois_Boulogne?=)
Date: Fri, 19 Jun 2015 13:10:32 -0400
Subject: Fwd: Your PeerJ article has been selected as one of our top bioinformatics
 papers
In-Reply-To: <31e101d0aab2$84153f70$8c3fbe50$@peerj.com>
References: <31e101d0aab2$84153f70$8c3fbe50$@peerj.com>
Message-ID: <55844D08.9050603@sciunto.org>

Dear all,

The paper has been selected for the Top Bioinformatics Papers - June
2015. See the email of the editor below.

Best.
Fr.


-------- Message transf?r? --------
Sujet : 	Your PeerJ article has been selected as one of our top
bioinformatics papers
Date : 	Fri, 19 Jun 2015 10:07:32 -0700
De : 	Peter Binfield <pete at peerj.com>
Pour : 	boulogne at princeton.edu



Dear Fran?ois,

 

On behalf of the PeerJ Team, I am writing to let you know that your
PeerJ article (?/scikit-image: image processing in Python/? at
https://peerj.com/articles/453/) has been named as one of our ?top?
bioinformatics articles and is listed in our ?Top Bioinformatics Papers
- June 2015? Collection.

 

More information about this Collection is at:
https://peerj.com/blog/post/115284878050/ and the Collection itself is
at: https://peerj.com/collections/18-bioinf-062015/

 

Congratulations on this selection! We hope you consider PeerJ for your
future publications.

 

Yours

 

Pete Binfield

 

. . .

 

Peter Binfield, PhD

Co-Founder and Publisher, PeerJ

 

Email: pete at PeerJ.com <mailto:pete at peerj.com>

Web: PeerJ.com <https://peerj.com/>

Twitter: @p_binfield <https://twitter.com/p_binfield>& @ThePeerJ
<https://twitter.com/ThePeerJ>

Blog: blog.PeerJ.com <http://blog.peerj.com/> 

 

Check out our new journal in Computer Science
<https://peerj.com/computer-science/>





From steven.silvester at gmail.com  Sat Jun 20 07:54:17 2015
From: steven.silvester at gmail.com (Steven Silvester)
Date: Sat, 20 Jun 2015 04:54:17 -0700 (PDT)
Subject: (Histogram?) plugin behaviour change?
In-Reply-To: <aa3e554b-2e69-472e-89d8-a70353799593@googlegroups.com>
References: <aa3e554b-2e69-472e-89d8-a70353799593@googlegroups.com>
Message-ID: <24fefb1b-23a2-4950-8551-25a2ea0d21c6@googlegroups.com>

Hi Nadav,

Thanks for spotting that!  This was indeed a regression, now 
addressed: https://github.com/scikit-image/scikit-image/pull/1565.


Regards,

Steve

On Friday, June 19, 2015 at 12:16:43 PM UTC-5, Nadav Horesh wrote:
>
> Maybe there is a plugin behaviour change, since the color_histogram.py 
> does not function as it used to, I suspect that for some reason the 
> RectangleTool is attached to the image rather to the histogram window. I'd 
> to have instructions how to fix it, since I've build a modification to 
> ColorHistogram that it would be nice to fix.
>
>   Thanks
>
>     Nadav
>
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From kevin.keraudren at googlemail.com  Sun Jun 21 14:58:32 2015
From: kevin.keraudren at googlemail.com (Kevin Keraudren)
Date: Sun, 21 Jun 2015 19:58:32 +0100
Subject: Enquiring about companies that rely on scikit-image
Message-ID: <CADe6jSo=m60bVawymkd6K6EBb6j14YP6ihJ713qyMkQmLPecvw@mail.gmail.com>

Hi,

I just came back from PyData London, which was a great experience. I
thought I would see a bit more image processing outside of an academic
context, but Lyst is the only one I noticed.

I was surprised by the success of scikit-learn outside of academia [1], and
I was wondering if people on the mailing list were aware of companies that
would similarly rely on scikit-image?

Kind Regards,

Kevin


[1] http://scikit-learn.org/stable/testimonials/testimonials.html
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From nadavh.horesh at gmail.com  Mon Jun 22 01:55:48 2015
From: nadavh.horesh at gmail.com (Nadav Horesh)
Date: Sun, 21 Jun 2015 22:55:48 -0700 (PDT)
Subject: (Histogram?) plugin behaviour change?
In-Reply-To: <24fefb1b-23a2-4950-8551-25a2ea0d21c6@googlegroups.com>
References: <aa3e554b-2e69-472e-89d8-a70353799593@googlegroups.com>
 <24fefb1b-23a2-4950-8551-25a2ea0d21c6@googlegroups.com>
Message-ID: <9f77a14e-9f42-44cf-ab00-b862a1b97898@googlegroups.com>

Thank you. I'll follow.

  Nadav

?????? ??? ???, 20 ????? 2015 ???? 14:54:17 UTC+3, ??? Steven Silvester:
>
> Hi Nadav,
>
> Thanks for spotting that!  This was indeed a regression, now addressed: 
> https://github.com/scikit-image/scikit-image/pull/1565.
>
>
> Regards,
>
> Steve
>
> On Friday, June 19, 2015 at 12:16:43 PM UTC-5, Nadav Horesh wrote:
>>
>> Maybe there is a plugin behaviour change, since the color_histogram.py 
>> does not function as it used to, I suspect that for some reason the 
>> RectangleTool is attached to the image rather to the histogram window. I'd 
>> to have instructions how to fix it, since I've build a modification to 
>> ColorHistogram that it would be nice to fix.
>>
>>   Thanks
>>
>>     Nadav
>>
>
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From manandey1 at gmail.com  Wed Jun 24 20:46:13 2015
From: manandey1 at gmail.com (Manan Dey)
Date: Wed, 24 Jun 2015 17:46:13 -0700 (PDT)
Subject: HOG feature extraction
Message-ID: <3c7d6333-7dcf-4b11-8cbd-6ba2c0ab3953@googlegroups.com>

Hi

I want to extract HOG features from Handwritten Arabic Line Images. When I 
run the test_hog.py file from the scimage library from scikit. It runs 
without any errors but it doesnt print any features as output. Can anyone 
please help me how to print the features. The link to the program is 
https://code.google.com/p/pythonxy/source/browse/src/python/scikits.image/PLATLIB/skimage/feature/tests/test_hog.py?repo=xy-27&r=13342d4c8c84fdc4dd3201bbde6201d8ba5b0683

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From silvertrumpet999 at gmail.com  Thu Jun 25 19:12:39 2015
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Thu, 25 Jun 2015 16:12:39 -0700 (PDT)
Subject: HOG feature extraction
In-Reply-To: <3c7d6333-7dcf-4b11-8cbd-6ba2c0ab3953@googlegroups.com>
References: <3c7d6333-7dcf-4b11-8cbd-6ba2c0ab3953@googlegroups.com>
Message-ID: <69edff80-495f-499b-bd81-e71f7e48270d@googlegroups.com>

Hi Manan,

First, that is a very old version of the package. Farther up the tree 
`version.py` states it's version 0.6.1 - we are currently shipping version 
0.11.3. I hope Python(X,Y) isn't still shipping 0.6.1. Before anything 
else, upgrade your scikit-image installation if needed.

Second, the test files is designed to test the package, not as direct 
examples of usage. They can be helpful to understand how files work, but 
realize they are unit tests. We run all files matching `test_*.py` in the 
repo using nosetests in our continuous integration builds. We don't want 
output from these; they are designed to pass if everything is well. So the 
fact that you don't get any output is working as intended, and reassuring. 
That means HOG is operating on your system.

The documentation for HOG is located 
here: http://scikit-image.org/docs/stable/api/skimage.feature.html#hog

I hope that helps set you on your way,

Josh

On Wednesday, June 24, 2015 at 8:15:48 PM UTC-5, Manan Dey wrote:
>
> Hi
>
> I want to extract HOG features from Handwritten Arabic Line Images. When I 
> run the test_hog.py file from the scimage library from scikit. It runs 
> without any errors but it doesnt print any features as output. Can anyone 
> please help me how to print the features. The link to the program is 
> https://code.google.com/p/pythonxy/source/browse/src/python/scikits.image/PLATLIB/skimage/feature/tests/test_hog.py?repo=xy-27&r=13342d4c8c84fdc4dd3201bbde6201d8ba5b0683
>
>
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From geazzo at gmail.com  Fri Jun 26 14:32:33 2015
From: geazzo at gmail.com (George Azzopardi)
Date: Fri, 26 Jun 2015 11:32:33 -0700 (PDT)
Subject: Pattern and object recognition with COSFIRE
In-Reply-To: <87oar05wkt.fsf@sun.ac.za>
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>
 <87oar05wkt.fsf@sun.ac.za>
Message-ID: <6ec5edfd-f0ff-4727-926e-09b02f4b51a7@googlegroups.com>

Hi Stefan,

I'm seeing this message rather late. If I'm in still in time, I would be 
interested to co-mentor a student ...

Let me know. You may also contact me directly on email: 
geazzo<at>gmail<dot>com

George

On Friday, 19 December 2014 01:10:00 UTC+1, Stefan van der Walt wrote:
>
> Hi George 
>
> On 2014-12-17 12:48:26, George Azzopardi <gea... at gmail.com <javascript:>> 
> 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 
>
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From ug201313015 at iitj.ac.in  Fri Jun 26 16:55:38 2015
From: ug201313015 at iitj.ac.in (Joshi ACHYUT SANJAY)
Date: Fri, 26 Jun 2015 13:55:38 -0700 (PDT)
Subject: New to scikit-image Contribution
Message-ID: <79225f5a-8651-45d5-9a53-d4dc662f897d@googlegroups.com>

Hello,

I am Achyut Joshi. I am new to the open source development and scikit-image 
intrigued me. Where and how can I start working?


Thanks
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From vighneshbirodkar at gmail.com  Mon Jun 29 05:27:23 2015
From: vighneshbirodkar at gmail.com (Vighnesh Birodkar)
Date: Mon, 29 Jun 2015 02:27:23 -0700 (PDT)
Subject: New to scikit-image Contribution
In-Reply-To: <79225f5a-8651-45d5-9a53-d4dc662f897d@googlegroups.com>
References: <79225f5a-8651-45d5-9a53-d4dc662f897d@googlegroups.com>
Message-ID: <cac7ba73-7a97-4c56-af54-f154bb6c3171@googlegroups.com>

Hello Achyut

Head over to the Issues List[1] to see if you can fix something. The 
wiki[2] also has a list of some features that we want. 

You will need to clone the repo, make a branch, and raise a pull request to 
contribute.

[1]:https://github.com/scikit-image/scikit-image/issues
[2]:https://github.com/scikit-image/scikit-image/wiki/Requested-features

Thanks
Vighnesh

On Saturday, June 27, 2015 at 11:00:28 AM UTC+5:30, Joshi ACHYUT SANJAY 
wrote:
>
> Hello,
>
> I am Achyut Joshi. I am new to the open source development and 
> scikit-image intrigued me. Where and how can I start working?
>
>
> Thanks
>
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