From kpysniak at gmail.com  Fri Nov  8 13:16:54 2013
From: kpysniak at gmail.com (Karol Pysniak)
Date: Fri, 8 Nov 2013 10:16:54 -0800 (PST)
Subject: Contribution to scikit-image, Issue# 167
Message-ID: <d840453f-581f-48e6-a7d7-61bacc8075fd@googlegroups.com>

Hi All,

I am new to scikit-image-dev, but I have been using it for some time and I 
would like to start contributing. Would you recommend any good starting 
issue or a new feature that you think could be worth adding? 

>From what I checked the issue list, the issue# 167 
(https://github.com/scikit-image/scikit-image/issues/167) seems to be still 
opened. Do you know if anyone is working on? If not, would it be possible 
for me to work on this change?

Thanks,
Karol

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From kpysniak at gmail.com  Fri Nov  8 13:19:32 2013
From: kpysniak at gmail.com (Karol Pysniak)
Date: Fri, 8 Nov 2013 10:19:32 -0800 (PST)
Subject: Contribution to scikit-image, Issue# 167
Message-ID: <0ea489ab-e672-48ec-9c0a-c72cfea09bde@googlegroups.com>

Hi All,

I am new to scikit-image-dev, but I have been using it for some time and I 
would like to start contributing. Would you recommend any good starting 
issue or a new feature that you think could be worth adding? 

>From what I checked the issue list, the issue# 167 (
https://github.com/scikit-image/scikit-image/issues/167) seems to be still 
opened. Do you know if anyone is working on? If not, would it be possible 
for me to work on this change?

Thanks,
Karol

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From stefan at sun.ac.za  Sat Nov  9 13:05:19 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sat, 9 Nov 2013 20:05:19 +0200
Subject: Contribution to scikit-image, Issue# 167
In-Reply-To: <0ea489ab-e672-48ec-9c0a-c72cfea09bde@googlegroups.com>
References: <0ea489ab-e672-48ec-9c0a-c72cfea09bde@googlegroups.com>
Message-ID: <CABDkGQkF0c-1gDC0ftFz7M0MoomGHuXVfKU8-D=nMhPyoa-AXw@mail.gmail.com>

Hi Karol

On Fri, Nov 8, 2013 at 8:19 PM, Karol Pysniak <kpysniak at gmail.com> wrote:
> From what I checked the issue list, the issue# 167
> (https://github.com/scikit-image/scikit-image/issues/167) seems to be still
> opened. Do you know if anyone is working on? If not, would it be possible
> for me to work on this change?

No one's working on that, so that's a great place to start.  We also
appreciate help with the TODO list:

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

Furthermore, documentation updates and clean-ups of the gallery are welcome.

Another feature that I'm quite interested in making happen soon: have
examples from the gallery downloadable as IPython notebooks.

Thanks!
St?fan


From stefan at sun.ac.za  Sat Nov  9 13:25:29 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sat, 9 Nov 2013 20:25:29 +0200
Subject: Contribution to scikit-image, Issue# 167
In-Reply-To: <CAKAks=H-p4LgL6aKOrYjQkHXVziY18kXTNNDmBzKW_=n+19xPg@mail.gmail.com>
References: <0ea489ab-e672-48ec-9c0a-c72cfea09bde@googlegroups.com>
 <CABDkGQkF0c-1gDC0ftFz7M0MoomGHuXVfKU8-D=nMhPyoa-AXw@mail.gmail.com> <CAKAks=H-p4LgL6aKOrYjQkHXVziY18kXTNNDmBzKW_=n+19xPg@mail.gmail.com>
Message-ID: <CABDkGQmMexzr+Ya66ASkEHZBoNZ3WFBk13dFgmpNqP9tyQwhWA@mail.gmail.com>

Hi Chintak

On Sat, Nov 9, 2013 at 8:22 PM, Chintak Sheth <chintaksheth at gmail.com> wrote:
>> Another feature that I'm quite interested in making happen soon: have
>> examples from the gallery downloadable as IPython notebooks.
>
> I have an iPython Notebook implementation for the example with Morphology
> functions. plot_morphology.py

Thanks for sharing your notebook--that looks like a good start to a
chapter on morphology!

What I meant earlier is that I'd like the current examples to also be
downloadable as .ipynb files (currently we offer only .py downloads).
So, the generator script should be modified to automatically write out
notebooks that include the inputs and outputs.

St?fan


From stefan at sun.ac.za  Sat Nov  9 13:39:19 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sat, 9 Nov 2013 20:39:19 +0200
Subject: Contribution to scikit-image, Issue# 167
In-Reply-To: <CAKAks=EtwLuw+9S87dvzhbYE6GRYxxXPkkjQfL7vLQw5=gMhQA@mail.gmail.com>
References: <0ea489ab-e672-48ec-9c0a-c72cfea09bde@googlegroups.com>
 <CABDkGQkF0c-1gDC0ftFz7M0MoomGHuXVfKU8-D=nMhPyoa-AXw@mail.gmail.com>
 <CAKAks=H-p4LgL6aKOrYjQkHXVziY18kXTNNDmBzKW_=n+19xPg@mail.gmail.com>
 <CABDkGQmMexzr+Ya66ASkEHZBoNZ3WFBk13dFgmpNqP9tyQwhWA@mail.gmail.com> <CAKAks=EtwLuw+9S87dvzhbYE6GRYxxXPkkjQfL7vLQw5=gMhQA@mail.gmail.com>
Message-ID: <CABDkGQnpWsxGug=KO1Nwz+t_98SGMwy34BEf5puxd3kKwaWQkA@mail.gmail.com>

On Sat, Nov 9, 2013 at 8:27 PM, Chintak Sheth <chintaksheth at gmail.com> wrote:
> Oh, I'd like to take a look into it. Could you point me in the direction?

doc/ext/plot2rst.py


From chintaksheth at gmail.com  Sat Nov  9 13:22:05 2013
From: chintaksheth at gmail.com (Chintak Sheth)
Date: Sat, 9 Nov 2013 23:52:05 +0530
Subject: Contribution to scikit-image, Issue# 167
In-Reply-To: <CABDkGQkF0c-1gDC0ftFz7M0MoomGHuXVfKU8-D=nMhPyoa-AXw@mail.gmail.com>
References: <0ea489ab-e672-48ec-9c0a-c72cfea09bde@googlegroups.com>
	<CABDkGQkF0c-1gDC0ftFz7M0MoomGHuXVfKU8-D=nMhPyoa-AXw@mail.gmail.com>
Message-ID: <CAKAks=H-p4LgL6aKOrYjQkHXVziY18kXTNNDmBzKW_=n+19xPg@mail.gmail.com>

Hi Stefan

> Another feature that I'm quite interested in making happen soon: have
> examples from the gallery downloadable as IPython notebooks.
>

I have an iPython Notebook implementation for the example with Morphology
functions. plot_morphology.py

http://nbviewer.ipython.org/urls/raw.github.com/chintak/scikit-image-examples/master/skimage_morphology.ipynb

May not be up to date but I'll update it in a day or so. Any suggestions on
improving it? And where should I submit a PR for the ipython notebook?

Chintak
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From chintaksheth at gmail.com  Sat Nov  9 13:27:56 2013
From: chintaksheth at gmail.com (Chintak Sheth)
Date: Sat, 9 Nov 2013 23:57:56 +0530
Subject: Contribution to scikit-image, Issue# 167
In-Reply-To: <CABDkGQmMexzr+Ya66ASkEHZBoNZ3WFBk13dFgmpNqP9tyQwhWA@mail.gmail.com>
References: <0ea489ab-e672-48ec-9c0a-c72cfea09bde@googlegroups.com>
	<CABDkGQkF0c-1gDC0ftFz7M0MoomGHuXVfKU8-D=nMhPyoa-AXw@mail.gmail.com>
	<CAKAks=H-p4LgL6aKOrYjQkHXVziY18kXTNNDmBzKW_=n+19xPg@mail.gmail.com>
	<CABDkGQmMexzr+Ya66ASkEHZBoNZ3WFBk13dFgmpNqP9tyQwhWA@mail.gmail.com>
Message-ID: <CAKAks=EtwLuw+9S87dvzhbYE6GRYxxXPkkjQfL7vLQw5=gMhQA@mail.gmail.com>

Oh, I'd like to take a look into it. Could you point me in the direction?

Chintak
On Nov 9, 2013 11:55 PM, "St?fan van der Walt" <stefan at sun.ac.za> wrote:

> Hi Chintak
>
> On Sat, Nov 9, 2013 at 8:22 PM, Chintak Sheth <chintaksheth at gmail.com>
> wrote:
> >> Another feature that I'm quite interested in making happen soon: have
> >> examples from the gallery downloadable as IPython notebooks.
> >
> > I have an iPython Notebook implementation for the example with Morphology
> > functions. plot_morphology.py
>
> Thanks for sharing your notebook--that looks like a good start to a
> chapter on morphology!
>
> What I meant earlier is that I'd like the current examples to also be
> downloadable as .ipynb files (currently we offer only .py downloads).
> So, the generator script should be modified to automatically write out
> notebooks that include the inputs and outputs.
>
> St?fan
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>
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From kmichael.aye at gmail.com  Tue Nov 12 01:40:06 2013
From: kmichael.aye at gmail.com (Michael Aye)
Date: Mon, 11 Nov 2013 22:40:06 -0800 (PST)
Subject: What's 'stable' version currently?
Message-ID: <960f3f18-682f-4b92-aa2e-7935d093e7be@googlegroups.com>

I am asking because the website says 0.9.0, but pip just brought me 0.9.3?
So either 0.9.3 is stable, and the website needs an update, or pip provides 
unstable versions, which would not be in line with what is written on 
skimage's Download page?

Cheers,
Michael


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From stefan at sun.ac.za  Tue Nov 12 04:40:11 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 12 Nov 2013 11:40:11 +0200
Subject: What's 'stable' version currently?
In-Reply-To: <960f3f18-682f-4b92-aa2e-7935d093e7be@googlegroups.com>
References: <960f3f18-682f-4b92-aa2e-7935d093e7be@googlegroups.com>
Message-ID: <CABDkGQmf5b8AjsiHcm0PAo1rv+GGe7VJfSnMWDxixJeM_ezvpg@mail.gmail.com>

Those are all bug fix releases, but yes: the website needs an update. In
fact, why don't we have the website builder just query pipy?
On 12 Nov 2013 14:40, "Michael Aye" <kmichael.aye at gmail.com> wrote:

> I am asking because the website says 0.9.0, but pip just brought me 0.9.3?
> So either 0.9.3 is stable, and the website needs an update, or pip
> provides unstable versions, which would not be in line with what is written
> on skimage's Download page?
>
> Cheers,
> Michael
>
>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>
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From jsch at demuc.de  Tue Nov 12 07:20:03 2013
From: jsch at demuc.de (=?UTF-8?Q?Johannes_Sch=C3=B6nberger?=)
Date: Tue, 12 Nov 2013 13:20:03 +0100
Subject: What's 'stable' version currently?
In-Reply-To: <1183972889.328452.1384258688650.open-xchange@app01>
References: <960f3f18-682f-4b92-aa2e-7935d093e7be@googlegroups.com> <CABDkGQmf5b8AjsiHcm0PAo1rv+GGe7VJfSnMWDxixJeM_ezvpg@mail.gmail.com> <1183972889.328452.1384258688650.open-xchange@app01>
Message-ID: <1500375494.328830.1384258804040.open-xchange@app01.ox.hosteurope.de>

Yes, but only in the documentation section and not on the home page in the sidebar on the top left. 

We should change this to automatically update the version number, because building the docs and uploading it every time is a pain...

> Am 12.11.2013 um 12:53 schrieb "Juan Nunez-Iglesias" <jni.soma at gmail.com>:
> 
> I thought we had changed the site version string to read "0.9.x"???
> 
> 
>> On Tue, Nov 12, 2013 at 8:40 PM, St?fan van der Walt <stefan at sun.ac.za> wrote:
>> Those are all bug fix releases, but yes: the website needs an update. In fact, why don't we have the website builder just query pipy?
>> 
>>> On 12 Nov 2013 14:40, "Michael Aye" <kmichael.aye at gmail.com> wrote:
>>> I am asking because the website says 0.9.0, but pip just brought me 0.9.3?
>>> So either 0.9.3 is stable, and the website needs an update, or pip provides unstable versions, which would not be in line with what is written on skimage's Download page?
>>> 
>>> Cheers,
>>> Michael
>>> 
>>> 
>>> -- 
>>> You received this message because you are subscribed to the Google Groups "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
>>> For more options, visit https://groups.google.com/groups/opt_out.
>> 
>> -- 
>> You received this message because you are subscribed to the Google Groups "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/groups/opt_out.
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
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From stefan at sun.ac.za  Tue Nov 12 09:55:58 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 12 Nov 2013 16:55:58 +0200
Subject: What's 'stable' version currently?
In-Reply-To: <1500375494.328830.1384258804040.open-xchange@app01.ox.hosteurope.de>
References: <960f3f18-682f-4b92-aa2e-7935d093e7be@googlegroups.com>
	<CABDkGQmf5b8AjsiHcm0PAo1rv+GGe7VJfSnMWDxixJeM_ezvpg@mail.gmail.com>
	<1183972889.328452.1384258688650.open-xchange@app01>
	<1500375494.328830.1384258804040.open-xchange@app01.ox.hosteurope.de>
Message-ID: <CABDkGQknCQ75PO0KkS2euJFH4CyFcBw23Q=F3ihiEuyZ2F4MWg@mail.gmail.com>

Easiest way to do that is to just grab it from docversions.js.
On 12 Nov 2013 20:20, "Johannes Sch?nberger" <jsch at demuc.de> wrote:

> Yes, but only in the documentation section and not on the home page in the
> sidebar on the top left.
>
> We should change this to automatically update the version number, because
> building the docs and uploading it every time is a pain...
>
> Am 12.11.2013 um 12:53 schrieb "Juan Nunez-Iglesias" <jni.soma at gmail.com>:
>
> I thought we had changed the site version string to read "0.9.x"???
>
>
> On Tue, Nov 12, 2013 at 8:40 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:
>
>> Those are all bug fix releases, but yes: the website needs an update. In
>> fact, why don't we have the website builder just query pipy?
>>  On 12 Nov 2013 14:40, "Michael Aye" <kmichael.aye at gmail.com> wrote:
>>
>>> I am asking because the website says 0.9.0, but pip just brought me
>>> 0.9.3?
>>> So either 0.9.3 is stable, and the website needs an update, or pip
>>> provides unstable versions, which would not be in line with what is written
>>> on skimage's Download page?
>>>
>>> Cheers,
>>> Michael
>>>
>>>
>>>  --
>>> You received this message because you are subscribed to the Google
>>> Groups "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>> For more options, visit https://groups.google.com/groups/opt_out.
>>>
>>  --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
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>
>  --
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From stefan at sun.ac.za  Tue Nov 12 10:31:46 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 12 Nov 2013 17:31:46 +0200
Subject: What's 'stable' version currently?
In-Reply-To: <CABDkGQknCQ75PO0KkS2euJFH4CyFcBw23Q=F3ihiEuyZ2F4MWg@mail.gmail.com>
References: <960f3f18-682f-4b92-aa2e-7935d093e7be@googlegroups.com>
 <CABDkGQmf5b8AjsiHcm0PAo1rv+GGe7VJfSnMWDxixJeM_ezvpg@mail.gmail.com>
 <1183972889.328452.1384258688650.open-xchange@app01> <1500375494.328830.1384258804040.open-xchange@app01.ox.hosteurope.de>
 <CABDkGQknCQ75PO0KkS2euJFH4CyFcBw23Q=F3ihiEuyZ2F4MWg@mail.gmail.com>
Message-ID: <CABDkGQkhwemJdxanSwf5eG3QsZnE3aXJKJSMVpsz7R4jaK2CXA@mail.gmail.com>

Here's a start--this PR grabs it directly from PyPi:

https://github.com/scikit-image/scikit-image-web/pull/13

Some spacing issues etc., so some suggestions on how to tweak welcome.

On Tue, Nov 12, 2013 at 4:55 PM, St?fan van der Walt <stefan at sun.ac.za> wrote:
> Easiest way to do that is to just grab it from docversions.js.
>
> On 12 Nov 2013 20:20, "Johannes Sch?nberger" <jsch at demuc.de> wrote:
>>
>> Yes, but only in the documentation section and not on the home page in the
>> sidebar on the top left.
>>
>> We should change this to automatically update the version number, because
>> building the docs and uploading it every time is a pain...
>>
>> Am 12.11.2013 um 12:53 schrieb "Juan Nunez-Iglesias" <jni.soma at gmail.com>:
>>
>> I thought we had changed the site version string to read "0.9.x"???
>>
>>
>> On Tue, Nov 12, 2013 at 8:40 PM, St?fan van der Walt <stefan at sun.ac.za>
>> wrote:
>>>
>>> Those are all bug fix releases, but yes: the website needs an update. In
>>> fact, why don't we have the website builder just query pipy?
>>>
>>> On 12 Nov 2013 14:40, "Michael Aye" <kmichael.aye at gmail.com> wrote:
>>>>
>>>> I am asking because the website says 0.9.0, but pip just brought me
>>>> 0.9.3?
>>>> So either 0.9.3 is stable, and the website needs an update, or pip
>>>> provides unstable versions, which would not be in line with what is written
>>>> on skimage's Download page?
>>>>
>>>> Cheers,
>>>> Michael
>>>>
>>>>
>>>> --
>>>> You received this message because you are subscribed to the Google
>>>> Groups "scikit-image" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>>> For more options, visit https://groups.google.com/groups/opt_out.
>>>
>>> --
>>> You received this message because you are subscribed to the Google Groups
>>> "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send an
>>> email to scikit-image+unsubscribe at googlegroups.com.
>>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/groups/opt_out.


From jsch at demuc.de  Tue Nov 12 11:37:39 2013
From: jsch at demuc.de (=?windows-1252?Q?Johannes_Sch=F6nberger?=)
Date: Tue, 12 Nov 2013 17:37:39 +0100
Subject: What's 'stable' version currently?
In-Reply-To: <CABDkGQkhwemJdxanSwf5eG3QsZnE3aXJKJSMVpsz7R4jaK2CXA@mail.gmail.com>
References: <960f3f18-682f-4b92-aa2e-7935d093e7be@googlegroups.com> <CABDkGQmf5b8AjsiHcm0PAo1rv+GGe7VJfSnMWDxixJeM_ezvpg@mail.gmail.com> <1183972889.328452.1384258688650.open-xchange@app01> <1500375494.328830.1384258804040.open-xchange@app01.ox.hosteurope.de> <CABDkGQknCQ75PO0KkS2euJFH4CyFcBw23Q=F3ihiEuyZ2F4MWg@mail.gmail.com> <CABDkGQkhwemJdxanSwf5eG3QsZnE3aXJKJSMVpsz7R4jaK2CXA@mail.gmail.com>
Message-ID: <114E0C33-BC10-43C7-AB5B-672846F31289@demuc.de>

Sorry, I didn?t see that you were asking for a review, so I just merged.

See https://github.com/scikit-image/scikit-image-web/pull/14 for a slightly modified layout and automatic release date insertion.

Am 12.11.2013 um 16:31 schrieb St?fan van der Walt <stefan at sun.ac.za>:

> Here's a start--this PR grabs it directly from PyPi:
> 
> https://github.com/scikit-image/scikit-image-web/pull/13
> 
> Some spacing issues etc., so some suggestions on how to tweak welcome.
> 
> On Tue, Nov 12, 2013 at 4:55 PM, St?fan van der Walt <stefan at sun.ac.za> wrote:
>> Easiest way to do that is to just grab it from docversions.js.
>> 
>> On 12 Nov 2013 20:20, "Johannes Sch?nberger" <jsch at demuc.de> wrote:
>>> 
>>> Yes, but only in the documentation section and not on the home page in the
>>> sidebar on the top left.
>>> 
>>> We should change this to automatically update the version number, because
>>> building the docs and uploading it every time is a pain...
>>> 
>>> Am 12.11.2013 um 12:53 schrieb "Juan Nunez-Iglesias" <jni.soma at gmail.com>:
>>> 
>>> I thought we had changed the site version string to read "0.9.x"???
>>> 
>>> 
>>> On Tue, Nov 12, 2013 at 8:40 PM, St?fan van der Walt <stefan at sun.ac.za>
>>> wrote:
>>>> 
>>>> Those are all bug fix releases, but yes: the website needs an update. In
>>>> fact, why don't we have the website builder just query pipy?
>>>> 
>>>> On 12 Nov 2013 14:40, "Michael Aye" <kmichael.aye at gmail.com> wrote:
>>>>> 
>>>>> I am asking because the website says 0.9.0, but pip just brought me
>>>>> 0.9.3?
>>>>> So either 0.9.3 is stable, and the website needs an update, or pip
>>>>> provides unstable versions, which would not be in line with what is written
>>>>> on skimage's Download page?
>>>>> 
>>>>> Cheers,
>>>>> Michael
>>>>> 
>>>>> 
>>>>> --
>>>>> You received this message because you are subscribed to the Google
>>>>> Groups "scikit-image" group.
>>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>>>> For more options, visit https://groups.google.com/groups/opt_out.
>>>> 
>>>> --
>>>> You received this message because you are subscribed to the Google Groups
>>>> "scikit-image" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send an
>>>> email to scikit-image+unsubscribe at googlegroups.com.
>>>> For more options, visit https://groups.google.com/groups/opt_out.
>>> 
>>> 
>>> --
>>> You received this message because you are subscribed to the Google Groups
>>> "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send an
>>> email to scikit-image+unsubscribe at googlegroups.com.
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>>> 
>>> --
>>> You received this message because you are subscribed to the Google Groups
>>> "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send an
>>> email to scikit-image+unsubscribe at googlegroups.com.
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> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
> 



From jni.soma at gmail.com  Tue Nov 12 06:53:00 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Tue, 12 Nov 2013 22:53:00 +1100
Subject: What's 'stable' version currently?
In-Reply-To: <CABDkGQmf5b8AjsiHcm0PAo1rv+GGe7VJfSnMWDxixJeM_ezvpg@mail.gmail.com>
References: <960f3f18-682f-4b92-aa2e-7935d093e7be@googlegroups.com> <CABDkGQmf5b8AjsiHcm0PAo1rv+GGe7VJfSnMWDxixJeM_ezvpg@mail.gmail.com>
Message-ID: <CA+JHcKS2tAhqm_NftqSWWQ+Ntq-N6iWithhxE5_OFy=zr_GurA@mail.gmail.com>

I thought we had changed the site version string to read "0.9.x"???


On Tue, Nov 12, 2013 at 8:40 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> Those are all bug fix releases, but yes: the website needs an update. In
> fact, why don't we have the website builder just query pipy?
>  On 12 Nov 2013 14:40, "Michael Aye" <kmichael.aye at gmail.com> wrote:
>
>> I am asking because the website says 0.9.0, but pip just brought me 0.9.3?
>> So either 0.9.3 is stable, and the website needs an update, or pip
>> provides unstable versions, which would not be in line with what is written
>> on skimage's Download page?
>>
>> Cheers,
>> Michael
>>
>>
>>  --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
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From siggin at gmail.com  Wed Nov 13 06:19:01 2013
From: siggin at gmail.com (Sigmund)
Date: Wed, 13 Nov 2013 03:19:01 -0800 (PST)
Subject: weird behaviour of  skimage.transform.rotate()
Message-ID: <b30e9b17-9e01-4fba-851f-7a9c7671e49f@googlegroups.com>

Moin moin! 

(Enthought Canopy Python 2.7.3 | 64-bit | (default, Aug  8 2013, 05:30:12) 
[MSC v.1500 64 bit (AMD64)] on win32)

I noticed that the rotate function is not working correct for me or at 
least not in the way I expect it to function.   
Could someone check this or tell me what I'm doing wrong. 
I would like to rotate a image/array for some degrees. 

import numpy as np
import matplotlib.pyplot as plt
import skimage.transform as sk_trans
im_array = np.ones((30,30))
im_array[12,:]=2
im_array[13,:]=3
im_array[14,:]=4
im_array[15,:]=5
im_array[16,:]=4
im_array[17,:]=3
im_array[18,:]=2
img_rot = sk_trans.rotate(im_array,45)
plt.imshow(im_array,interpolation='none')
plt.show()
plt.imshow(img_rot,interpolation='none')
plt.show()




Thanks
Siggi
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From stefan at sun.ac.za  Wed Nov 13 00:52:15 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 13 Nov 2013 07:52:15 +0200
Subject: What's 'stable' version currently?
In-Reply-To: <114E0C33-BC10-43C7-AB5B-672846F31289@demuc.de>
References: <960f3f18-682f-4b92-aa2e-7935d093e7be@googlegroups.com>
	<CABDkGQmf5b8AjsiHcm0PAo1rv+GGe7VJfSnMWDxixJeM_ezvpg@mail.gmail.com>
	<1183972889.328452.1384258688650.open-xchange@app01>
	<1500375494.328830.1384258804040.open-xchange@app01.ox.hosteurope.de>
	<CABDkGQknCQ75PO0KkS2euJFH4CyFcBw23Q=F3ihiEuyZ2F4MWg@mail.gmail.com>
	<CABDkGQkhwemJdxanSwf5eG3QsZnE3aXJKJSMVpsz7R4jaK2CXA@mail.gmail.com>
	<114E0C33-BC10-43C7-AB5B-672846F31289@demuc.de>
Message-ID: <CABDkGQm2ihTFUup8Sed=cJoBNo=N734Mgpn3djSLEw3PeWfBmQ@mail.gmail.com>

Perfect, thank you.
On 12 Nov 2013 18:37, "Johannes Sch?nberger" <jsch at demuc.de> wrote:

> Sorry, I didn?t see that you were asking for a review, so I just merged.
>
> See https://github.com/scikit-image/scikit-image-web/pull/14 for a
> slightly modified layout and automatic release date insertion.
>
> Am 12.11.2013 um 16:31 schrieb St?fan van der Walt <stefan at sun.ac.za>:
>
> > Here's a start--this PR grabs it directly from PyPi:
> >
> > https://github.com/scikit-image/scikit-image-web/pull/13
> >
> > Some spacing issues etc., so some suggestions on how to tweak welcome.
> >
> > On Tue, Nov 12, 2013 at 4:55 PM, St?fan van der Walt <stefan at sun.ac.za>
> wrote:
> >> Easiest way to do that is to just grab it from docversions.js.
> >>
> >> On 12 Nov 2013 20:20, "Johannes Sch?nberger" <jsch at demuc.de> wrote:
> >>>
> >>> Yes, but only in the documentation section and not on the home page in
> the
> >>> sidebar on the top left.
> >>>
> >>> We should change this to automatically update the version number,
> because
> >>> building the docs and uploading it every time is a pain...
> >>>
> >>> Am 12.11.2013 um 12:53 schrieb "Juan Nunez-Iglesias" <
> jni.soma at gmail.com>:
> >>>
> >>> I thought we had changed the site version string to read "0.9.x"???
> >>>
> >>>
> >>> On Tue, Nov 12, 2013 at 8:40 PM, St?fan van der Walt <stefan at sun.ac.za
> >
> >>> wrote:
> >>>>
> >>>> Those are all bug fix releases, but yes: the website needs an update.
> In
> >>>> fact, why don't we have the website builder just query pipy?
> >>>>
> >>>> On 12 Nov 2013 14:40, "Michael Aye" <kmichael.aye at gmail.com> wrote:
> >>>>>
> >>>>> I am asking because the website says 0.9.0, but pip just brought me
> >>>>> 0.9.3?
> >>>>> So either 0.9.3 is stable, and the website needs an update, or pip
> >>>>> provides unstable versions, which would not be in line with what is
> written
> >>>>> on skimage's Download page?
> >>>>>
> >>>>> Cheers,
> >>>>> Michael
> >>>>>
> >>>>>
> >>>>> --
> >>>>> You received this message because you are subscribed to the Google
> >>>>> Groups "scikit-image" group.
> >>>>> To unsubscribe from this group and stop receiving emails from it,
> send
> >>>>> an email to scikit-image+unsubscribe at googlegroups.com.
> >>>>> For more options, visit https://groups.google.com/groups/opt_out.
> >>>>
> >>>> --
> >>>> You received this message because you are subscribed to the Google
> Groups
> >>>> "scikit-image" group.
> >>>> To unsubscribe from this group and stop receiving emails from it,
> send an
> >>>> email to scikit-image+unsubscribe at googlegroups.com.
> >>>> For more options, visit https://groups.google.com/groups/opt_out.
> >>>
> >>>
> >>> --
> >>> You received this message because you are subscribed to the Google
> Groups
> >>> "scikit-image" group.
> >>> To unsubscribe from this group and stop receiving emails from it, send
> an
> >>> email to scikit-image+unsubscribe at googlegroups.com.
> >>> For more options, visit https://groups.google.com/groups/opt_out.
> >>>
> >>> --
> >>> You received this message because you are subscribed to the Google
> Groups
> >>> "scikit-image" group.
> >>> To unsubscribe from this group and stop receiving emails from it, send
> an
> >>> email to scikit-image+unsubscribe at googlegroups.com.
> >>> For more options, visit https://groups.google.com/groups/opt_out.
> >
> > --
> > You received this message because you are subscribed to the Google
> Groups "scikit-image" group.
> > To unsubscribe from this group and stop receiving emails from it, send
> an email to scikit-image+unsubscribe at googlegroups.com.
> > For more options, visit https://groups.google.com/groups/opt_out.
> >
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
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From jsch at demuc.de  Wed Nov 13 02:21:47 2013
From: jsch at demuc.de (=?windows-1252?Q?Johannes_Sch=F6nberger?=)
Date: Wed, 13 Nov 2013 08:21:47 +0100
Subject: What's 'stable' version currently?
In-Reply-To: <CABDkGQm2ihTFUup8Sed=cJoBNo=N734Mgpn3djSLEw3PeWfBmQ@mail.gmail.com>
References: <960f3f18-682f-4b92-aa2e-7935d093e7be@googlegroups.com> <CABDkGQmf5b8AjsiHcm0PAo1rv+GGe7VJfSnMWDxixJeM_ezvpg@mail.gmail.com> <1183972889.328452.1384258688650.open-xchange@app01> <1500375494.328830.1384258804040.open-xchange@app01.ox.hosteurope.de> <CABDkGQknCQ75PO0KkS2euJFH4CyFcBw23Q=F3ihiEuyZ2F4MWg@mail.gmail.com> <CABDkGQkhwemJdxanSwf5eG3QsZnE3aXJKJSMVpsz7R4jaK2CXA@mail.gmail.com> <114E0C33-BC10-43C7-AB5B-672846F31289@demuc.de> <CABDkGQm2ihTFUup8Sed=cJoBNo=N734Mgpn3djSLEw3PeWfBmQ@mail.gmail.com>
Message-ID: <4450C23A-D68C-4C19-A0BB-5E34F511B004@demuc.de>

Stefan, would you merge and push the update to gh-pages?

Am 13.11.2013 um 06:52 schrieb St?fan van der Walt <stefan at sun.ac.za>:

> Perfect, thank you.
> 
> On 12 Nov 2013 18:37, "Johannes Sch?nberger" <jsch at demuc.de> wrote:
> Sorry, I didn?t see that you were asking for a review, so I just merged.
> 
> See https://github.com/scikit-image/scikit-image-web/pull/14 for a slightly modified layout and automatic release date insertion.
> 
> Am 12.11.2013 um 16:31 schrieb St?fan van der Walt <stefan at sun.ac.za>:
> 
> > Here's a start--this PR grabs it directly from PyPi:
> >
> > https://github.com/scikit-image/scikit-image-web/pull/13
> >
> > Some spacing issues etc., so some suggestions on how to tweak welcome.
> >
> > On Tue, Nov 12, 2013 at 4:55 PM, St?fan van der Walt <stefan at sun.ac.za> wrote:
> >> Easiest way to do that is to just grab it from docversions.js.
> >>
> >> On 12 Nov 2013 20:20, "Johannes Sch?nberger" <jsch at demuc.de> wrote:
> >>>
> >>> Yes, but only in the documentation section and not on the home page in the
> >>> sidebar on the top left.
> >>>
> >>> We should change this to automatically update the version number, because
> >>> building the docs and uploading it every time is a pain...
> >>>
> >>> Am 12.11.2013 um 12:53 schrieb "Juan Nunez-Iglesias" <jni.soma at gmail.com>:
> >>>
> >>> I thought we had changed the site version string to read "0.9.x"???
> >>>
> >>>
> >>> On Tue, Nov 12, 2013 at 8:40 PM, St?fan van der Walt <stefan at sun.ac.za>
> >>> wrote:
> >>>>
> >>>> Those are all bug fix releases, but yes: the website needs an update. In
> >>>> fact, why don't we have the website builder just query pipy?
> >>>>
> >>>> On 12 Nov 2013 14:40, "Michael Aye" <kmichael.aye at gmail.com> wrote:
> >>>>>
> >>>>> I am asking because the website says 0.9.0, but pip just brought me
> >>>>> 0.9.3?
> >>>>> So either 0.9.3 is stable, and the website needs an update, or pip
> >>>>> provides unstable versions, which would not be in line with what is written
> >>>>> on skimage's Download page?
> >>>>>
> >>>>> Cheers,
> >>>>> Michael
> >>>>>
> >>>>>
> >>>>> --
> >>>>> You received this message because you are subscribed to the Google
> >>>>> Groups "scikit-image" group.
> >>>>> To unsubscribe from this group and stop receiving emails from it, send
> >>>>> an email to scikit-image+unsubscribe at googlegroups.com.
> >>>>> For more options, visit https://groups.google.com/groups/opt_out.
> >>>>
> >>>> --
> >>>> You received this message because you are subscribed to the Google Groups
> >>>> "scikit-image" group.
> >>>> To unsubscribe from this group and stop receiving emails from it, send an
> >>>> email to scikit-image+unsubscribe at googlegroups.com.
> >>>> For more options, visit https://groups.google.com/groups/opt_out.
> >>>
> >>>
> >>> --
> >>> You received this message because you are subscribed to the Google Groups
> >>> "scikit-image" group.
> >>> To unsubscribe from this group and stop receiving emails from it, send an
> >>> email to scikit-image+unsubscribe at googlegroups.com.
> >>> For more options, visit https://groups.google.com/groups/opt_out.
> >>>
> >>> --
> >>> You received this message because you are subscribed to the Google Groups
> >>> "scikit-image" group.
> >>> To unsubscribe from this group and stop receiving emails from it, send an
> >>> email to scikit-image+unsubscribe at googlegroups.com.
> >>> For more options, visit https://groups.google.com/groups/opt_out.
> >
> > --
> > You received this message because you are subscribed to the Google Groups "scikit-image" group.
> > To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> > For more options, visit https://groups.google.com/groups/opt_out.
> >
> 
> --
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.



From jsch at demuc.de  Wed Nov 13 06:25:00 2013
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Wed, 13 Nov 2013 12:25:00 +0100
Subject: weird behaviour of  skimage.transform.rotate()
In-Reply-To: <b30e9b17-9e01-4fba-851f-7a9c7671e49f@googlegroups.com>
References: <b30e9b17-9e01-4fba-851f-7a9c7671e49f@googlegroups.com>
Message-ID: <6F720DC5-1B4A-4A92-8FF7-4AF93782444F@demuc.de>

Hi,

it is working as expected. You are just dealing with a dtype issue here.

np.ones((30, 30)) => dtype=double with valid values between [0, 1] as a convention in skimage.

Replace np.ones((30,30)) with im_array = np.ones((30,30), dtype=np.uint8) and your issues should be fixed.

Hope it helps.

Am 13.11.2013 um 12:19 schrieb Sigmund <siggin at gmail.com>:

> Moin moin! 
> 
> (Enthought Canopy Python 2.7.3 | 64-bit | (default, Aug  8 2013, 05:30:12) [MSC v.1500 64 bit (AMD64)] on win32)
> 
> I noticed that the rotate function is not working correct for me or at least not in the way I expect it to function.   
> Could someone check this or tell me what I'm doing wrong. 
> I would like to rotate a image/array for some degrees. 
> 
> import numpy as np
> import matplotlib.pyplot as plt
> import skimage.transform as sk_trans
> im_array = np.ones((30,30))
> im_array[12,:]=2
> im_array[13,:]=3
> im_array[14,:]=4
> im_array[15,:]=5
> im_array[16,:]=4
> im_array[17,:]=3
> im_array[18,:]=2
> img_rot = sk_trans.rotate(im_array,45)
> plt.imshow(im_array,interpolation='none')
> plt.show()
> plt.imshow(img_rot,interpolation='none')
> plt.show()
> 
> 
> 
> 
> Thanks
> Siggi
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.



From siggin at gmail.com  Wed Nov 13 08:38:11 2013
From: siggin at gmail.com (Sigmund Neher)
Date: Wed, 13 Nov 2013 14:38:11 +0100
Subject: weird behaviour of skimage.transform.rotate()
In-Reply-To: <6F720DC5-1B4A-4A92-8FF7-4AF93782444F@demuc.de>
References: <b30e9b17-9e01-4fba-851f-7a9c7671e49f@googlegroups.com>
	<6F720DC5-1B4A-4A92-8FF7-4AF93782444F@demuc.de>
Message-ID: <CALrQn7gK394hBnTXeki8vrFYiybxbDu_um6=fJnGFqH0=+OTFQ@mail.gmail.com>

ahh, ok. And rotate() returns a float.

Thanks for the quick help!


On Wed, Nov 13, 2013 at 12:25 PM, Johannes Sch?nberger <jsch at demuc.de>wrote:

> Hi,
>
> it is working as expected. You are just dealing with a dtype issue here.
>
> np.ones((30, 30)) => dtype=double with valid values between [0, 1] as a
> convention in skimage.
>
> Replace np.ones((30,30)) with im_array = np.ones((30,30), dtype=np.uint8)
> and your issues should be fixed.
>
> Hope it helps.
>
> Am 13.11.2013 um 12:19 schrieb Sigmund <siggin at gmail.com>:
>
> > Moin moin!
> >
> > (Enthought Canopy Python 2.7.3 | 64-bit | (default, Aug  8 2013,
> 05:30:12) [MSC v.1500 64 bit (AMD64)] on win32)
> >
> > I noticed that the rotate function is not working correct for me or at
> least not in the way I expect it to function.
> > Could someone check this or tell me what I'm doing wrong.
> > I would like to rotate a image/array for some degrees.
> >
> > import numpy as np
> > import matplotlib.pyplot as plt
> > import skimage.transform as sk_trans
> > im_array = np.ones((30,30))
> > im_array[12,:]=2
> > im_array[13,:]=3
> > im_array[14,:]=4
> > im_array[15,:]=5
> > im_array[16,:]=4
> > im_array[17,:]=3
> > im_array[18,:]=2
> > img_rot = sk_trans.rotate(im_array,45)
> > plt.imshow(im_array,interpolation='none')
> > plt.show()
> > plt.imshow(img_rot,interpolation='none')
> > plt.show()
> >
> >
> >
> >
> > Thanks
> > Siggi
> >
> > --
> > You received this message because you are subscribed to the Google
> Groups "scikit-image" group.
> > To unsubscribe from this group and stop receiving emails from it, send
> an email to scikit-image+unsubscribe at googlegroups.com.
> > For more options, visit https://groups.google.com/groups/opt_out.
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>
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From bricklemacho at gmail.com  Wed Nov 13 08:19:44 2013
From: bricklemacho at gmail.com (Brickle Macho)
Date: Wed, 13 Nov 2013 21:19:44 +0800
Subject: Surface Curvature from Range Images (or Depth Maps)
Message-ID: <52837C70.20101@gmail.com>

I have implemented mean and gaussian curvature methods in python and 
thought they may be appropriate for inclusion to skimage.  An outline of 
the code is provided below.  It assumes a surface defined as a function 
of two coordinates, e.g. z = Z(x, y).  The curvature calculations are 
from the following two papers

* Kurita, T., & Boulanger, P. (1992). Computation of Surface Curvature 
from Range Images Using Geometrically Intrinsic Weights. In /MVA/ (pp. 
389-392).

* Zhao, C., Zhao, D., & Chen, Y. (1996, August). Simplified Gaussian and 
mean curvatures to range image segmentation. In /Pattern Recognition, 
1996., Proceedings of the 13th International Conference on/ (Vol. 2, pp. 
427-431). IEEE.

If appropriate let me know and I will read the contribution/development 
documentation, make the code more robust and submit formally.

Regards,

Michael.
--


Here is a basic outline of the code (H and K are used as they appear 
common terms used in the literature) :
---------------BEGIN CODE--------------
import numpy as np

Zy, Zx = np.gradient(Z)
Zxy, Zxx = np.gradient(Zx)
Zyy, _ = np.gradient(Zy)

# Mean Curvature - equation (3) from Kurita and Boulanger (1992) paper
# See also Surface in 3D space, http://en.wikipedia.org/wiki/Mean_curvature
H = (1 + (Zx ** 2)) * Zyy + (1 + (Zy ** 2)) * Zxx - 2 * Zx * Zy * Zxy
H = H / ((2 * (1 + (Zx ** 2) + (Zy ** 2))) ** 1.5)

# Gaussian Curvature - equation (4) from Kurita and Boulanger (1992) paper
K = (Zxx * Zyy - (Zxy ** 2)) /  ((1 + (Zx ** 2) + (Zy **2)) ** 2)

# Simplified Mean Curvature - equation (3) from Zhao et.al (1996) paper
H = Zxx + Zyy

#  Simplified Gaussian Curvature - equation (3) from Zhao et.al (1996) 
paper
K = Zxx * Zyy - (Zxy ** 2)
---------------END CODE--------------
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From hughesadam87 at gmail.com  Fri Nov 15 12:02:26 2013
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Fri, 15 Nov 2013 09:02:26 -0800 (PST)
Subject: Advice on improving a analysis on images of nanoparticles
Message-ID: <656876a4-8696-4f8a-b963-8ad42997db68@googlegroups.com>

 

Dear Scikit-Image (SKI) team,


 I have over a hundred scanning electron microscope (SEM) images of gold 
nanoparticles on glass surfaces, and I've generated several scripts in 
ImageJ/Python to batch analyze them.  The analysis is fairly crude, and 
consists mostly of users manually thresholding to make a binary image, 
applying a simple noise filter and performing ImageJ's particle counting 
routine.  Afterwards, my scripts use Python to do plotting, statistics and 
then output .txt, excel and .tex files.   Eventually, I'd like to remove 
the ImageJ portion altogether and refactor the code to use SKI exclusively; 
however, for now, I am mainly interested in improving the results with some 
features of SKI.  


The images are in a .pdf can be downloaded directly here<http://www.4shared.com/office/xX37rOfh/SCIKIT_TEST_Notable.html>. 
(Just a hair too big to attach)

What I'd like to do is to look at a subset of our images and see if SKI can 
enhance the image/remove defects.   I've chosen 10 images to represent 
various cases and attached a summary via googledrive. The images are 
categorized as follows (preliminary questions are in blue):


 *NICE* - Image is about as good as we can get, and shouldn't have many 
artifacts.  Can these be further enhanced?


 *LOWCONTRAST *- Can the contrast in these images be enhanced automatically 
in SKI?  


 *NONCIRC* - Particles appear non-circular due to stigmation offset in 
microscope.  Is it possible to reshape them/make them more circular?


 *WARPED* - Images that have artifacts, or uneven contrast, due to 
aberrations in SEM beam during imaging. * I'm especially interested in 
removing uneven contrast.*


 *WATERSHED* - These images have overlapping AuNPs, and I had hoped that 
SKI's watershedding routines might help disentangle them.  The *watershed 
segmentation guide*<http://scikit-image.org/docs/dev/auto_examples/plot_watershed.html>indicates that there are several ways to approach this problem.


 On the attached PDF, each page shows the original SEM image (converted 
from highres.tiff to png), a binary image, our manually chosen adjustment 
threshold, and two estimates of the particle diameter distribution (don't 
worry about details of this).


 I was really hoping that some SKI experts would examine these images and 
suggest some algorithms or insights to address the aforementioned concerns. 
 *The overall goal is to survey the most common problems in SEM imaging of 
nanoparticles, give examples of each, and demonstrate how SKI can improve 
the particle counting.*


 Thanks for you time, and for making a really nice open-source package.
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From raphael.ackermann at gmail.com  Fri Nov 15 15:00:17 2013
From: raphael.ackermann at gmail.com (Raphael Ackermann)
Date: Fri, 15 Nov 2013 12:00:17 -0800 (PST)
Subject: template matching example with a color image leads to Value Error.
Message-ID: <03cf29fb-729d-4180-8716-7acf956dfd85@googlegroups.com>

Hi

I am trying to do template matching. Running 
http://scikit-image.org/docs/0.9.x/auto_examples/plot_template.html#example-plot-template-py  
works perfectly fine. But when I change image = data.coins() --> image = 
data.lena() to have a non b/w image I get the following error.

Traceback (most recent call last):
  File "/..../template_matching.py", line 11, in <module>
    result = match_template(image, coin)
  File 
"/usr/local/lib/python2.7/dist-packages/scikit_image-0.9.3-py2.7-linux-x86_64.egg/skimage/feature/template.py", 
line 80, in match_template
    result = _template.match_template(image, template)
  File "_template.pyx", line 50, in 
skimage.feature._template.match_template (skimage/feature/_template.c:1967)
ValueError: Buffer has wrong number of dimensions (expected 2, got 3)

Is it not possible to call match_template() with a color image? Or what am 
I doing wrong? I can't find anything in the documentation or the code that 
this should only work for black and white images.

When I replace the scikit-image algorith with one from cv2  
result = match_template(image, coin)     -->  result = 
cv2.matchTemplate(image, coin, cv2.TM_CCOEFF_NORMED)

I can at least continue further in the example and it finds the coordinates 
where the template matches.

Is this a bug? If not the documentation/example should be updated to make 
it clear that this only works for b/w images.

Thanks
Raphael
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From jsch at demuc.de  Sun Nov 17 03:46:34 2013
From: jsch at demuc.de (=?windows-1252?Q?Johannes_Sch=F6nberger?=)
Date: Sun, 17 Nov 2013 09:46:34 +0100
Subject: template matching example with a color image leads to Value Error.
In-Reply-To: <03cf29fb-729d-4180-8716-7acf956dfd85@googlegroups.com>
References: <03cf29fb-729d-4180-8716-7acf956dfd85@googlegroups.com>
Message-ID: <5C933AC0-FF3C-4F55-89A1-69FE7BB8AF20@demuc.de>

Hi

We can consider this as a bug. It must be mentioned in the doc string.

But I don?t see a reason why we shouldn?t support N-D or at least 3- and 4-D (3-D plus channels) images? ?

Am 15.11.2013 um 21:00 schrieb Raphael Ackermann <raphael.ackermann at gmail.com>:

> Hi
> 
> I am trying to do template matching. Running http://scikit-image.org/docs/0.9.x/auto_examples/plot_template.html#example-plot-template-py  works perfectly fine. But when I change image = data.coins() --> image = data.lena() to have a non b/w image I get the following error.
> 
> Traceback (most recent call last):
>   File "/..../template_matching.py", line 11, in <module>
>     result = match_template(image, coin)
>   File "/usr/local/lib/python2.7/dist-packages/scikit_image-0.9.3-py2.7-linux-x86_64.egg/skimage/feature/template.py", line 80, in match_template
>     result = _template.match_template(image, template)
>   File "_template.pyx", line 50, in skimage.feature._template.match_template (skimage/feature/_template.c:1967)
> ValueError: Buffer has wrong number of dimensions (expected 2, got 3)
> 
> Is it not possible to call match_template() with a color image? Or what am I doing wrong? I can't find anything in the documentation or the code that this should only work for black and white images.
> 
> When I replace the scikit-image algorith with one from cv2  
> result = match_template(image, coin)     -->  result = cv2.matchTemplate(image, coin, cv2.TM_CCOEFF_NORMED)
> 
> I can at least continue further in the example and it finds the coordinates where the template matches.
> 
> Is this a bug? If not the documentation/example should be updated to make it clear that this only works for b/w images.
> 
> Thanks
> Raphael
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.



From stefan at sun.ac.za  Sun Nov 17 04:20:52 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 17 Nov 2013 11:20:52 +0200
Subject: template matching example with a color image leads to Value Error.
In-Reply-To: <5C933AC0-FF3C-4F55-89A1-69FE7BB8AF20@demuc.de>
References: <03cf29fb-729d-4180-8716-7acf956dfd85@googlegroups.com> <5C933AC0-FF3C-4F55-89A1-69FE7BB8AF20@demuc.de>
Message-ID: <CABDkGQkqP6HcqX=fWi30XMSLRAVtY_oDXX-Znk69ac3KJFKQkQ@mail.gmail.com>

On Sun, Nov 17, 2013 at 10:46 AM, Johannes Sch?nberger <jsch at demuc.de> wrote:
> We can consider this as a bug. It must be mentioned in the doc string.
>
> But I don?t see a reason why we shouldn?t support N-D or at least 3- and 4-D (3-D plus channels) images? ?

I agree -- let's file a ticket to track this issue.

St?fan


From stefan at sun.ac.za  Sun Nov 17 04:27:12 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 17 Nov 2013 11:27:12 +0200
Subject: Advice on improving a analysis on images of nanoparticles
In-Reply-To: <656876a4-8696-4f8a-b963-8ad42997db68@googlegroups.com>
References: <656876a4-8696-4f8a-b963-8ad42997db68@googlegroups.com>
Message-ID: <CABDkGQ=Syt_z6UEYChpMo3F9GeuKnz9DWJtyfYG1MsWJNXskbw@mail.gmail.com>

Hi Adam

On Fri, Nov 15, 2013 at 7:02 PM, Adam Hughes <hughesadam87 at gmail.com> wrote:
> The images are in a .pdf can be downloaded directly here. (Just a hair too
> big to attach)

This download requires a login--could you please provide us with a
direct link / HTML page showing the images?

> LOWCONTRAST - Can the contrast in these images be enhanced automatically in
> SKI?

We have several histogram equalization algorithms, including Contrast
Limited Histogram Equalization, which should do the trick.

> NONCIRC - Particles appear non-circular due to stigmation offset in
> microscope.  Is it possible to reshape them/make them more circular?

It depends on what you mean by "make them more circular".  We have
geometric transformation utilities in `skimage.transform`.

> WARPED - Images that have artifacts, or uneven contrast, due to aberrations
> in SEM beam during imaging.  I'm especially interested in removing uneven
> contrast.

Localized contrast equalization in the `skimage.filter.rank` module might help.

> WATERSHED - These images have overlapping AuNPs, and I had hoped that SKI's
> watershedding routines might help disentangle them.  The watershed
> segmentation guide indicates that there are several ways to approach this
> problem.

See Juan's post here:
https://groups.google.com/d/msg/scikit-image/4z-hPiFFDj8/2gIDMxfGrU4J

Regards
St?fan


From raphael.ackermann at gmail.com  Sun Nov 17 09:55:01 2013
From: raphael.ackermann at gmail.com (Raphael Ackermann)
Date: Sun, 17 Nov 2013 15:55:01 +0100
Subject: template matching example with a color image leads to Value Error.
In-Reply-To: <CABDkGQkqP6HcqX=fWi30XMSLRAVtY_oDXX-Znk69ac3KJFKQkQ@mail.gmail.com>
References: <03cf29fb-729d-4180-8716-7acf956dfd85@googlegroups.com>
 <5C933AC0-FF3C-4F55-89A1-69FE7BB8AF20@demuc.de> <CABDkGQkqP6HcqX=fWi30XMSLRAVtY_oDXX-Znk69ac3KJFKQkQ@mail.gmail.com>
Message-ID: <CA+Ot0qK=Pwoj=t+i_MWYNBy2sLKM5sBcEApmHytANdeJPJN6Ug@mail.gmail.com>

On Sun, Nov 17, 2013 at 10:20 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> On Sun, Nov 17, 2013 at 10:46 AM, Johannes Sch?nberger <jsch at demuc.de>
> wrote:
> > We can consider this as a bug. It must be mentioned in the doc string.
> >
> > But I don?t see a reason why we shouldn?t support N-D or at least 3- and
> 4-D (3-D plus channels) images? ?
>
> I agree -- let's file a ticket to track this issue.
>
>
Done: https://github.com/scikit-image/scikit-image/issues/818
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From pierre.villeneuve at gmail.com  Sun Nov 17 23:57:56 2013
From: pierre.villeneuve at gmail.com (Pierre Villeneuve)
Date: Sun, 17 Nov 2013 20:57:56 -0800 (PST)
Subject: Kakadu JP2000 reader
In-Reply-To: <b0ab6704-f2c2-48c9-9fde-d904f198c59c@googlegroups.com>
References: <b0ab6704-f2c2-48c9-9fde-d904f198c59c@googlegroups.com>
Message-ID: <234fcb19-bb64-430a-bb72-1bce3f577035@googlegroups.com>

What about the OpenJPEG library: http://www.openjpeg.org.  Could that be an alternative?

From jdunn4000 at gmail.com  Mon Nov 18 05:13:40 2013
From: jdunn4000 at gmail.com (Jeremy Dunne)
Date: Mon, 18 Nov 2013 02:13:40 -0800 (PST)
Subject: SLIC Module in SciKit
Message-ID: <0e7255fd-3f39-42e7-846d-fd24117b40c5@googlegroups.com>



Morning All,

 

I have been trying to port my linux python code to a windows x32 
environment and am very close however I just can?t seem to find a way of 
Python 2.7 recognising the SLIC Module that is within sci-image. Having 
used Chris Gohlke?s Windows Extensions everything works up until my code 
looks to import SLIC from SciKit. 

 

Error : No module SLIC 

 

Anyone else had this issue or solved this problem ? 

 

Cheers 

 

Jeremy. 
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From stuart at mumford.me.uk  Mon Nov 18 02:10:10 2013
From: stuart at mumford.me.uk (Stuart Mumford)
Date: Mon, 18 Nov 2013 07:10:10 +0000
Subject: Kakadu JP2000 reader
In-Reply-To: <CABDkGQmStLPefrPYtqdndSNZkwtxvk-K1C5PFTqCzQfsxBZsmw@mail.gmail.com>
References: <b0ab6704-f2c2-48c9-9fde-d904f198c59c@googlegroups.com>
	<CABDkGQmStLPefrPYtqdndSNZkwtxvk-K1C5PFTqCzQfsxBZsmw@mail.gmail.com>
Message-ID: <CAJ3G1Jq9oYFoXausBnXxt_j_vdsfQezgP8RLt2DQ4C0Yz+3HAw@mail.gmail.com>

You might want to checkout the glymur project.

https://github.com/quintusdias/glymur

Stuart
On 18 Nov 2013 06:57, "St?fan van der Walt" <stefan at sun.ac.za> wrote:

> Dear Michael
>
> On Tue, Oct 29, 2013 at 12:59 AM, Michael Aye <kmichael.aye at gmail.com>
> wrote:
> > I was wondering if it would be possible to implement the Kakadu JP2000
> > reader into scikit-image? I believe but am not sure that the reader only
> > could be used without licensing fees? At least it's worth investigating
> > because that reader is really the most powerful JP2000 reader out there
> and
> > the only one that can deal with the large HiRISE images of the MRO
> > spacecraft.
>
> Does FreeImage then fail on these images?  Do you have an example
> image for us to test on?
>
> Thanks
> St?fan
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>
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From jdunn4000 at gmail.com  Mon Nov 18 10:34:42 2013
From: jdunn4000 at gmail.com (Jeremy Dunne)
Date: Mon, 18 Nov 2013 07:34:42 -0800 (PST)
Subject: SLIC Module in SciKit
In-Reply-To: <CA+JHcKS9wAavND_1pAiZrCmQb6Pz7U_Xi5FC9A2ks+ts4L8Fmg@mail.gmail.com>
References: <0e7255fd-3f39-42e7-846d-fd24117b40c5@googlegroups.com>
 <CA+JHcKS9wAavND_1pAiZrCmQb6Pz7U_Xi5FC9A2ks+ts4L8Fmg@mail.gmail.com>
Message-ID: <dd2be0e5-2146-427d-817b-606d5fd99ff3@googlegroups.com>

Hi Juan,

Nope that's not the issue. Although I checked to make sure. From the code 
it is called as below

import slic as slic

This is the only module it bulks at, all the others are fine. There are a 
lot but they all seem to be fine.

#!/usr/bin/python

import os
import numpy as np
from scipy import ndimage as ndi
from skimage.segmentation.boundaries import find_boundaries
import scipy.ndimage.measurements as msr
import slic as slic
import skimage.color as skic
from sklearn import svm
from sklearn.preprocessing import StandardScaler
from sklearn.cross_validation import StratifiedKFold
from sklearn.grid_search import GridSearchCV
import scipy.ndimage.morphology as morph
from  skimage.filter import threshold_otsu
from sklearn import decomposition
from scipy.ndimage import convolve
import gabor as gb
import ogr_gdal as og
import matplotlib.pyplot as plt
from params import *

Cheers. 

Jeremy. 



On Monday, 18 November 2013 13:08:33 UTC, Juan Nunez-Iglesias wrote:
>
> Hi Jeremy,
>
> is this just an issue of case? ie "slic" vs "SLIC"? The correct import 
> line should be:
>
> from skimage.segmentation import slic
>
> I hope this helps!
>
> Juan. 
>
> On Monday, November 18, 2013, Jeremy Dunne wrote:
>
>> Morning All,
>>
>>  
>>
>> I have been trying to port my linux python code to a windows x32 
>> environment and am very close however I just can?t seem to find a way of 
>> Python 2.7 recognising the SLIC Module that is within sci-image. Having 
>> used Chris Gohlke?s Windows Extensions everything works up until my code 
>> looks to import SLIC from SciKit. 
>>
>>  
>>
>> Error : No module SLIC 
>>
>>  
>>
>> Anyone else had this issue or solved this problem ? 
>>
>>  
>>
>> Cheers 
>>
>>  
>>
>> Jeremy. 
>>
>> -- 
>> You received this message because you are subscribed to the Google Groups 
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an 
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>
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From jdunn4000 at gmail.com  Mon Nov 18 11:09:31 2013
From: jdunn4000 at gmail.com (Jeremy Dunne)
Date: Mon, 18 Nov 2013 08:09:31 -0800 (PST)
Subject: SLIC Module in SciKit
In-Reply-To: <CABDkGQ=+JtJUpTN5JD-SPtWaxunTyfL3cOkaUeB0ZAsnMUBW=Q@mail.gmail.com>
References: <0e7255fd-3f39-42e7-846d-fd24117b40c5@googlegroups.com>
 <CA+JHcKS9wAavND_1pAiZrCmQb6Pz7U_Xi5FC9A2ks+ts4L8Fmg@mail.gmail.com> <dd2be0e5-2146-427d-817b-606d5fd99ff3@googlegroups.com>
 <CABDkGQ=+JtJUpTN5JD-SPtWaxunTyfL3cOkaUeB0ZAsnMUBW=Q@mail.gmail.com>
Message-ID: <45105a74-57ee-4e37-a42a-d050120f24e1@googlegroups.com>

Hi Stefan,

This is everything that I am importing, does order matter ? 

#!/usr/bin/python
import os
import numpy as np
from scipy import ndimage as ndi
from skimage.segmentation.boundaries import find_boundaries
import scipy.ndimage.measurements as msr
import slic as slic
import skimage.color as skic
from sklearn import svm
from sklearn.preprocessing import StandardScaler
from sklearn.cross_validation import StratifiedKFold
from sklearn.grid_search import GridSearchCV
import scipy.ndimage.morphology as morph
from  skimage.filter import threshold_otsu
from sklearn import decomposition
from scipy.ndimage import convolve
import gabor as gb
import ogr_gdal as og
import matplotlib.pyplot as plt
from params import *

Alot but the only issue is slic, if I comment it out code run until it 
needs slic. Is it supported in skimage ? 

Error

Traceback (most recent call last):
  File 
"C:\Users\jeremydunn\Desktop\GroundSure\Algorithm\Wales_Drew\Tadas\Algorithm\run3.py", 
line 2, in <module>
    from algorithm import *
  File 
"C:\Users\jeremydunn\Desktop\GroundSure\Algorithm\Wales_Drew\Tadas\Algorithm\algorithm.py", 
line 7, in <module>
    import slic as slic
ImportError: No module named slic

Cheers. 

Jeremy. 

On Monday, 18 November 2013 15:51:34 UTC, Stefan van der Walt wrote:
>
> On Mon, Nov 18, 2013 at 5:34 PM, Jeremy Dunne <jdun... at gmail.com<javascript:>> 
> wrote: 
> > Nope that's not the issue. Although I checked to make sure. From the 
> code it 
> > is called as below 
> > 
> > import slic as slic 
>
> You cannot import slic by itself, you need to import 
> ``skimage.segmentation.slic``, or just import segmentation and use 
> ``segmentation.slic``. 
>
> St?fan 
>
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From jdunn4000 at gmail.com  Mon Nov 18 11:27:37 2013
From: jdunn4000 at gmail.com (Jeremy Dunne)
Date: Mon, 18 Nov 2013 08:27:37 -0800 (PST)
Subject: SLIC Module in SciKit
In-Reply-To: <CABDkGQkXWrohcOzjKD-nBp7oDanEJ57ysFmxcZ7ZPJhoUdezQA@mail.gmail.com>
References: <0e7255fd-3f39-42e7-846d-fd24117b40c5@googlegroups.com>
 <CA+JHcKS9wAavND_1pAiZrCmQb6Pz7U_Xi5FC9A2ks+ts4L8Fmg@mail.gmail.com>
 <dd2be0e5-2146-427d-817b-606d5fd99ff3@googlegroups.com> <CABDkGQ=+JtJUpTN5JD-SPtWaxunTyfL3cOkaUeB0ZAsnMUBW=Q@mail.gmail.com>
 <45105a74-57ee-4e37-a42a-d050120f24e1@googlegroups.com>
 <CABDkGQkXWrohcOzjKD-nBp7oDanEJ57ysFmxcZ7ZPJhoUdezQA@mail.gmail.com>
Message-ID: <3ccd65cb-b44f-4560-b1a8-06b4a3f316fd@googlegroups.com>

Hi Stefan,

Ok I have tried this a couple of ways but still the same error.....

Error 1

Traceback (most recent call last):
  File 
"C:\Users\jeremydunn\Desktop\GroundSure\Algorithm\Wales_Drew\Tadas\Algorithm\run3.py", 
line 2, in <module>
    from algorithm import *
  File 
"C:\Users\jeremydunn\Desktop\GroundSure\Algorithm\Wales_Drew\Tadas\Algorithm\algorithm.py", 
line 7, in <module>
    from skimage.segmentation.slic import slic
ImportError: No module named slic


Error 2

Traceback (most recent call last):
  File 
"C:\Users\jeremydunn\Desktop\GroundSure\Algorithm\Wales_Drew\Tadas\Algorithm\run3.py", 
line 2, in <module>
    from algorithm import *
  File 
"C:\Users\jeremydunn\Desktop\GroundSure\Algorithm\Wales_Drew\Tadas\Algorithm\algorithm.py", 
line 7, in <module>
    from skimage.morphology import slic
ImportError: cannot import name slic

Am I missing something basic here ? Probably. 

Cheers. 

Jeremy. 


On Monday, 18 November 2013 16:15:28 UTC, Stefan van der Walt wrote:
>
> On Mon, Nov 18, 2013 at 6:09 PM, Jeremy Dunne <jdun... at gmail.com<javascript:>> 
> wrote: 
> > This is everything that I am importing, does order matter ? 
>
> No, but there is no such stand-alone module as "slic".  You have to 
> import it as follows: 
>
> from skimage.morphology import slic 
>
> St?fan 
>
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From jdunn4000 at gmail.com  Mon Nov 18 11:49:26 2013
From: jdunn4000 at gmail.com (Jeremy Dunne)
Date: Mon, 18 Nov 2013 08:49:26 -0800 (PST)
Subject: SLIC Module in SciKit
In-Reply-To: <CABDkGQ=Ay6uF41PgjGL87i_TTEgtt5FO0nVusDcG_f+s0nqQEA@mail.gmail.com>
References: <0e7255fd-3f39-42e7-846d-fd24117b40c5@googlegroups.com>
 <CA+JHcKS9wAavND_1pAiZrCmQb6Pz7U_Xi5FC9A2ks+ts4L8Fmg@mail.gmail.com>
 <dd2be0e5-2146-427d-817b-606d5fd99ff3@googlegroups.com> <CABDkGQ=+JtJUpTN5JD-SPtWaxunTyfL3cOkaUeB0ZAsnMUBW=Q@mail.gmail.com>
 <45105a74-57ee-4e37-a42a-d050120f24e1@googlegroups.com> <CABDkGQkXWrohcOzjKD-nBp7oDanEJ57ysFmxcZ7ZPJhoUdezQA@mail.gmail.com>
 <CABDkGQ=Ay6uF41PgjGL87i_TTEgtt5FO0nVusDcG_f+s0nqQEA@mail.gmail.com>
Message-ID: <2524ae2f-7c8e-4401-be24-6bdcec5dbd46@googlegroups.com>

Stefan,

Well that seems to have solved it...thank you very much....atleast I have a 
new error .....

resizing rgb and nir images
RGB image name 
\Users\jeremydunn\Desktop\GroundSure\Algorithm\Wales_Drew\Tadas\Area2\Imagery\gm0F6F0.jpg

Traceback (most recent call last):
  File 
"C:\Users\jeremydunn\Desktop\GroundSure\Algorithm\Wales_Drew\Tadas\Algorithm\run3.py", 
line 79, in <module>
    training_1 = TrainImage(trainingrgb, trainingnir, object_size, 
size_to_filter, jappos = trainingpos, japneg = trainingneg)
  File 
"C:\Users\jeremydunn\Desktop\GroundSure\Algorithm\Wales_Drew\Tadas\Algorithm\algorithm.py", 
line 51, in __init__
    self.pixres,self.gt,self.prj) = 
og.initialize(filename,nirfile,jappos,japneg)
  File 
"C:\Users\jeremydunn\Desktop\GroundSure\Algorithm\Wales_Drew\Tadas\Algorithm\ogr_gdal.py", 
line 171, in initialize
    proc = 
subprocess.Popen(['gdal_translate','-of','JPEG','-projwin',str(extents[0]),str(extents[1]),str(extents[2]),str(extents[3]),filename,'tmp_rgb.jpg'])
  File "C:\Python27\ArcGIS10.2\lib\subprocess.py", line 679, in __init__
    errread, errwrite)
  File "C:\Python27\ArcGIS10.2\lib\subprocess.py", line 896, in 
_execute_child
    startupinfo)
WindowsError: [Error 2] The system cannot find the file specified

Thank you for the help, 

Cheers. 

Jeremy. 



On Monday, 18 November 2013 16:28:40 UTC, Stefan van der Walt wrote:
>
> On Mon, Nov 18, 2013 at 6:15 PM, St?fan van der Walt <ste... at sun.ac.za<javascript:>> 
> wrote: 
> > from skimage.morphology import slic 
>
> Sorry, where is my mind: 
>
> from skimage.segmentation import slic 
>
> St?fan 
>
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From jdunn4000 at gmail.com  Mon Nov 18 11:54:21 2013
From: jdunn4000 at gmail.com (Jeremy Dunne)
Date: Mon, 18 Nov 2013 08:54:21 -0800 (PST)
Subject: SLIC Module in SciKit
In-Reply-To: <CABDkGQ=aZC6u4FwscqHLj8B5ro9Um6JkLEeAkxTvH2uoGA0wEQ@mail.gmail.com>
References: <0e7255fd-3f39-42e7-846d-fd24117b40c5@googlegroups.com>
 <CA+JHcKS9wAavND_1pAiZrCmQb6Pz7U_Xi5FC9A2ks+ts4L8Fmg@mail.gmail.com>
 <dd2be0e5-2146-427d-817b-606d5fd99ff3@googlegroups.com> <CABDkGQ=+JtJUpTN5JD-SPtWaxunTyfL3cOkaUeB0ZAsnMUBW=Q@mail.gmail.com>
 <45105a74-57ee-4e37-a42a-d050120f24e1@googlegroups.com> <CABDkGQkXWrohcOzjKD-nBp7oDanEJ57ysFmxcZ7ZPJhoUdezQA@mail.gmail.com>
 <CABDkGQ=Ay6uF41PgjGL87i_TTEgtt5FO0nVusDcG_f+s0nqQEA@mail.gmail.com> <2524ae2f-7c8e-4401-be24-6bdcec5dbd46@googlegroups.com>
 <CABDkGQ=aZC6u4FwscqHLj8B5ro9Um6JkLEeAkxTvH2uoGA0wEQ@mail.gmail.com>
Message-ID: <9ad89702-dea9-4c87-9e7f-2dc7c7def1e0@googlegroups.com>

Yep I'd say so. 

Cheers Stefan

Regards. 

Jeremy. 

On Monday, 18 November 2013 16:50:49 UTC, Stefan van der Walt wrote:
>
> On Mon, Nov 18, 2013 at 6:49 PM, Jeremy Dunne <jdun... at gmail.com<javascript:>> 
> wrote: 
> > Well that seems to have solved it...thank you very much....atleast I 
> have a 
> > new error ..... 
>
> Great!  The new error seems unrelated to skimage. 
>
> St?fan 
>
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From stefan at sun.ac.za  Mon Nov 18 01:57:37 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 18 Nov 2013 08:57:37 +0200
Subject: Kakadu JP2000 reader
In-Reply-To: <b0ab6704-f2c2-48c9-9fde-d904f198c59c@googlegroups.com>
References: <b0ab6704-f2c2-48c9-9fde-d904f198c59c@googlegroups.com>
Message-ID: <CABDkGQmStLPefrPYtqdndSNZkwtxvk-K1C5PFTqCzQfsxBZsmw@mail.gmail.com>

Dear Michael

On Tue, Oct 29, 2013 at 12:59 AM, Michael Aye <kmichael.aye at gmail.com> wrote:
> I was wondering if it would be possible to implement the Kakadu JP2000
> reader into scikit-image? I believe but am not sure that the reader only
> could be used without licensing fees? At least it's worth investigating
> because that reader is really the most powerful JP2000 reader out there and
> the only one that can deal with the large HiRISE images of the MRO
> spacecraft.

Does FreeImage then fail on these images?  Do you have an example
image for us to test on?

Thanks
St?fan


From stefan at sun.ac.za  Mon Nov 18 02:13:54 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 18 Nov 2013 09:13:54 +0200
Subject: scikit-image paper
In-Reply-To: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com>
Message-ID: <CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com>

On Mon, Nov 18, 2013 at 3:23 AM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> * This and Johannes's email sparked a discussion about possible homes for
> it. Current suggestions:
>    - F1000 Research

I'm a bit concerned by what I read here:

http://scholarlykitchen.sspnet.org/2013/01/15/pubmed-and-f1000-research-unclear-standards-applied-unevenly/

>    - JMLR MLOSS [sklearn published here]

Impact factor is about 3.4, which at least gives some indication that
its content is valued.

>    - Journal on Image and Video Processing (jivp.eurasipjournals.com)

And about 0.5 for this one.

Let's stick to using wrapped lines, otherwise editing using our normal
configurations becomes painful.

St?fan


From stefan at sun.ac.za  Mon Nov 18 03:59:22 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 18 Nov 2013 10:59:22 +0200
Subject: scikit-image paper
In-Reply-To: <CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com>
 <CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com> <CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com>
Message-ID: <CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com>

On Mon, Nov 18, 2013 at 10:47 AM, Juan Nunez-Iglesias
<jni.soma at gmail.com> wrote:
> If we are going to worry about JIF, PLOS ONE has 3.7, and does accept papers
> from all disciplines. (You will also find a Scholarly Kitchen post about how
> a JIF of 3.7 is a sign that PLOS and open access are doomed.)

Thanks, I won't take Scholarly Kitchen too seriously then.  I know
that impact factors are a lousy way (by itself) to determine where to
publish, but that's a whole other kettle of fish.

> Currently my two top candidates then are JMLR MLOSS and PLOS ONE. (The
> latter does charge $1300 US per article.)

Open access fees should not pose too much of a problem:

http://library.sun.ac.za/English/services/oa/Pages/su-oafund.aspx

Let's get started on some content!

I think we would do well to emphasize the following in the paper:

- Pythonic API
- Building block for reproducible research, use in academic world (we
need a list of publications of work that used skimage)
- Educational aspects (skimage.novice)
- Google Summer of Code contributions
- Use in industry (do we have examples here?)
- ... other ideas?

St?fan


From jsch at demuc.de  Mon Nov 18 05:54:13 2013
From: jsch at demuc.de (=?windows-1252?Q?Johannes_Sch=F6nberger?=)
Date: Mon, 18 Nov 2013 11:54:13 +0100
Subject: scikit-image paper
In-Reply-To: <CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com> <CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com> <CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com> <CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com>
Message-ID: <07C5CA12-B383-4EC4-AA6D-42D94E69F162@demuc.de>

> Currently my two top candidates then are JMLR MLOSS and PLOS ONE.

+1

> Let's get started on some content!

+1, but I must mention that I might be short of time over the coming weeks as I am about to move to another continent, so unfortunately I have a ton of other things to do :-)

> I think we would do well to emphasize the following in the paper:
> 
> - Pythonic API
> - Building block for reproducible research, use in academic world (we
> need a list of publications of work that used skimage)
> - Educational aspects (skimage.novice)
> - Google Summer of Code contributions
> - Use in industry (do we have examples here?)
> - ... other ideas?

 - Extensive documentation (although the docs need some more ?love? for 0.10)
 - Easy to use API for prototyping and testing algorithms (probably covered by "Pythonic API?)

I have mainly used skimage for prototyping, but did not directly mention it in a publication.

Johannes



From hughesadam87 at gmail.com  Mon Nov 18 15:03:11 2013
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Mon, 18 Nov 2013 12:03:11 -0800 (PST)
Subject: scikit-image paper
In-Reply-To: <CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com>
 <CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com> <CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com>
 <CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com>
Message-ID: <b1cb53b7-793c-438a-ab37-76575209cc89@googlegroups.com>

On Monday, November 18, 2013 3:59:22 AM UTC-5, Stefan van der Walt wrote:

> On Mon, Nov 18, 2013 at 10:47 AM, Juan Nunez-Iglesias 
> <jni.... at gmail.com <javascript:>> wrote: 
> > If we are going to worry about JIF, PLOS ONE has 3.7, and does accept 
> papers 
> > from all disciplines. (You will also find a Scholarly Kitchen post about 
> how 
> > a JIF of 3.7 is a sign that PLOS and open access are doomed.) 
>
> Thanks, I won't take Scholarly Kitchen too seriously then.  I know 
> that impact factors are a lousy way (by itself) to determine where to 
> publish, but that's a whole other kettle of fish. 
>
> > Currently my two top candidates then are JMLR MLOSS and PLOS ONE. (The 
> > latter does charge $1300 US per article.) 
>
> Open access fees should not pose too much of a problem: 
>
> http://library.sun.ac.za/English/services/oa/Pages/su-oafund.aspx 
>
> Let's get started on some content! 
>
> I think we would do well to emphasize the following in the paper: 
>
> - Pythonic API 
> - Building block for reproducible research, use in academic world (we 
> need a list of publications of work that used skimage) 
> - Educational aspects (skimage.novice) 
> - Google Summer of Code contributions 
> - Use in industry (do we have examples here?) 
>

It may be non-disclosable, but I know that Enthought may have some 
industrial examples.
 

> - ... other ideas? 
>
> St?fan 
>
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From jni.soma at gmail.com  Sun Nov 17 20:23:33 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Mon, 18 Nov 2013 12:23:33 +1100
Subject: scikit-image paper
Message-ID: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com>

Hi All,

I'm moving the discussion of the paper to the mailing list, as requested by
Stefan. Here's a summary of the points so far:

* Josh brought up a Computational Science and Discovery special issue as
not only a possible venue for the paper but a general renewed call to
action about this paper.

* I vetoed the CSD special issue, despite having no formal power of veto
=P, and suggested we opt instead for a fully open access journal, such as
F1000Research.

* This and Johannes's email sparked a discussion about possible homes for
it. Current suggestions:
   - F1000 Research
   - JMLR MLOSS [sklearn published here]
   - Journal of Open Research Software [mahotas published here]
   - Image Processing On Line (ipol.im)
   - Journal on Image and Video Processing (jivp.eurasipjournals.com)

* Stefan suggested as the author list, "currently active core
contributors", but would certainly add more authors that have "made a
substantial contribution to the package." I feel the same way and I imagine
other current core devs would not object to this either. (?)

* There is a markdown template PR here:
https://github.com/scikit-image/scikit-image-paper/pull/2
Johannes gave a +1 to merging that, and I give another, so that makes +2,
I'll merge following this email. =)
(I have a question about this point: for managing LaTeX papers on git, I
have usually stuck to the convention of "1 sentence: 1 line". Do we want
this for this paper, or wrap at 72 characters, or something else?)

I think that's everything, though I'm sure the discussion will continue!

Stefan asked me to elaborate on my suggestion of F1000. I must admit I
don't know much about the other journals on the list, and would need to
look into them. Things that I *expect* from our eventual home are:
 - open access.
 - CC or similar licensing that allows text mining applications.
Further niceties offered by F1000Res:
 - papers published immediately as preprint.
 - open peer review
 - once two reviewers have signed off on the paper, it is considered "peer
reviewed". Reviewers can request modifications, and full paper and revision
history is maintained.
 - peer reviewed articles are indexed by PubMed.

Essentially, the review model is quite similar to the GitHub PR process,
which sounds great to me. PeerJ offers a similar (identical?) model, but is
currently not LaTeX friendly, which pretty much rules it out for this.

Juan.
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From stefan at sun.ac.za  Mon Nov 18 10:51:34 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 18 Nov 2013 17:51:34 +0200
Subject: SLIC Module in SciKit
In-Reply-To: <dd2be0e5-2146-427d-817b-606d5fd99ff3@googlegroups.com>
References: <0e7255fd-3f39-42e7-846d-fd24117b40c5@googlegroups.com>
 <CA+JHcKS9wAavND_1pAiZrCmQb6Pz7U_Xi5FC9A2ks+ts4L8Fmg@mail.gmail.com> <dd2be0e5-2146-427d-817b-606d5fd99ff3@googlegroups.com>
Message-ID: <CABDkGQ=+JtJUpTN5JD-SPtWaxunTyfL3cOkaUeB0ZAsnMUBW=Q@mail.gmail.com>

On Mon, Nov 18, 2013 at 5:34 PM, Jeremy Dunne <jdunn4000 at gmail.com> wrote:
> Nope that's not the issue. Although I checked to make sure. From the code it
> is called as below
>
> import slic as slic

You cannot import slic by itself, you need to import
``skimage.segmentation.slic``, or just import segmentation and use
``segmentation.slic``.

St?fan


From stefan at sun.ac.za  Mon Nov 18 11:15:28 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 18 Nov 2013 18:15:28 +0200
Subject: SLIC Module in SciKit
In-Reply-To: <45105a74-57ee-4e37-a42a-d050120f24e1@googlegroups.com>
References: <0e7255fd-3f39-42e7-846d-fd24117b40c5@googlegroups.com>
 <CA+JHcKS9wAavND_1pAiZrCmQb6Pz7U_Xi5FC9A2ks+ts4L8Fmg@mail.gmail.com>
 <dd2be0e5-2146-427d-817b-606d5fd99ff3@googlegroups.com> <CABDkGQ=+JtJUpTN5JD-SPtWaxunTyfL3cOkaUeB0ZAsnMUBW=Q@mail.gmail.com>
 <45105a74-57ee-4e37-a42a-d050120f24e1@googlegroups.com>
Message-ID: <CABDkGQkXWrohcOzjKD-nBp7oDanEJ57ysFmxcZ7ZPJhoUdezQA@mail.gmail.com>

On Mon, Nov 18, 2013 at 6:09 PM, Jeremy Dunne <jdunn4000 at gmail.com> wrote:
> This is everything that I am importing, does order matter ?

No, but there is no such stand-alone module as "slic".  You have to
import it as follows:

from skimage.morphology import slic

St?fan


From stefan at sun.ac.za  Mon Nov 18 11:28:40 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 18 Nov 2013 18:28:40 +0200
Subject: SLIC Module in SciKit
In-Reply-To: <CABDkGQkXWrohcOzjKD-nBp7oDanEJ57ysFmxcZ7ZPJhoUdezQA@mail.gmail.com>
References: <0e7255fd-3f39-42e7-846d-fd24117b40c5@googlegroups.com>
 <CA+JHcKS9wAavND_1pAiZrCmQb6Pz7U_Xi5FC9A2ks+ts4L8Fmg@mail.gmail.com>
 <dd2be0e5-2146-427d-817b-606d5fd99ff3@googlegroups.com> <CABDkGQ=+JtJUpTN5JD-SPtWaxunTyfL3cOkaUeB0ZAsnMUBW=Q@mail.gmail.com>
 <45105a74-57ee-4e37-a42a-d050120f24e1@googlegroups.com> <CABDkGQkXWrohcOzjKD-nBp7oDanEJ57ysFmxcZ7ZPJhoUdezQA@mail.gmail.com>
Message-ID: <CABDkGQ=Ay6uF41PgjGL87i_TTEgtt5FO0nVusDcG_f+s0nqQEA@mail.gmail.com>

On Mon, Nov 18, 2013 at 6:15 PM, St?fan van der Walt <stefan at sun.ac.za> wrote:
> from skimage.morphology import slic

Sorry, where is my mind:

from skimage.segmentation import slic

St?fan


From marianne.corvellec at ens-lyon.org  Mon Nov 18 21:50:48 2013
From: marianne.corvellec at ens-lyon.org (Marianne Corvellec)
Date: Mon, 18 Nov 2013 18:50:48 -0800 (PST)
Subject: scikit-image paper
In-Reply-To: <CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com>
 <CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com> <CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com>
 <CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com>
Message-ID: <bf9ff28b-cb0a-4f18-9184-34679c31dbe8@googlegroups.com>

Hello all,

What an exciting project!

On Monday, November 18, 2013 3:59:22 AM UTC-5, Stefan van der Walt wrote:
>
> Let's get started on some content! 
>
> I think we would do well to emphasize the following in the paper: 
>
> - Pythonic API 
> - Building block for reproducible research, use in academic world (we 
> need a list of publications of work that used skimage) 
> - Educational aspects (skimage.novice) 
> - Google Summer of Code contributions 
> - Use in industry (do we have examples here?) 
> - ... other ideas?
>

I believe it would be fitting to cite Dharhas Pothina's recent work.
St?fan (and possibly others) know more about it than I do, but it could be 
considered both academic and industrial.

I believe Tony S Yu would have lots to share as well. :)

Marianne
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From stefan at sun.ac.za  Mon Nov 18 11:50:49 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 18 Nov 2013 18:50:49 +0200
Subject: SLIC Module in SciKit
In-Reply-To: <2524ae2f-7c8e-4401-be24-6bdcec5dbd46@googlegroups.com>
References: <0e7255fd-3f39-42e7-846d-fd24117b40c5@googlegroups.com>
 <CA+JHcKS9wAavND_1pAiZrCmQb6Pz7U_Xi5FC9A2ks+ts4L8Fmg@mail.gmail.com>
 <dd2be0e5-2146-427d-817b-606d5fd99ff3@googlegroups.com> <CABDkGQ=+JtJUpTN5JD-SPtWaxunTyfL3cOkaUeB0ZAsnMUBW=Q@mail.gmail.com>
 <45105a74-57ee-4e37-a42a-d050120f24e1@googlegroups.com> <CABDkGQkXWrohcOzjKD-nBp7oDanEJ57ysFmxcZ7ZPJhoUdezQA@mail.gmail.com>
 <CABDkGQ=Ay6uF41PgjGL87i_TTEgtt5FO0nVusDcG_f+s0nqQEA@mail.gmail.com> <2524ae2f-7c8e-4401-be24-6bdcec5dbd46@googlegroups.com>
Message-ID: <CABDkGQ=aZC6u4FwscqHLj8B5ro9Um6JkLEeAkxTvH2uoGA0wEQ@mail.gmail.com>

On Mon, Nov 18, 2013 at 6:49 PM, Jeremy Dunne <jdunn4000 at gmail.com> wrote:
> Well that seems to have solved it...thank you very much....atleast I have a
> new error .....

Great!  The new error seems unrelated to skimage.

St?fan


From jni.soma at gmail.com  Mon Nov 18 03:47:25 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Mon, 18 Nov 2013 19:47:25 +1100
Subject: scikit-image paper
In-Reply-To: <CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com>
 <CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com>
Message-ID: <CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com>

Hey St?fan,

On Mon, Nov 18, 2013 at 6:13 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> >    - F1000 Research
>
> I'm a bit concerned by what I read here:
>
> http://scholarlykitchen.sspnet.org/2013/01/15/pubmed-and-f1000-research-unclear-standards-applied-unevenly/


Scholarly Kitchen have it in for open access in general and seem to think
there is nothing wrong with the business-as-usual model of scientific
publishing. I imagine that this is not true of the present list of authors,
but am happy to be corrected. Just have a quick browse of their past posts
and try to find something positive about OA.

You can just read a few of Fernando Perez's blog posts, particularly the
recent one about the Sloan/Moore data science initiative, to find out what
I think of business-as-usual science and publishing.

Quick rebuttals of the post's two main points:
"unclear standards applied unevenly" "cynical and confusing m?lange of
incomplete editorial practices"
Yeah, welcome to peer review. This is true of all journals ? the fact that
it's not open doesn't mean it's not there.
"Yet, these rejected articles continue to be published on the F1000
Research site."
It's called a preprint. arXiv papers don't get taken down when they don't
pass peer review (ditto for closed github PRs). Why should these? They are
clearly marked as Rejected. F1000 Research is an experiment in openness in
publishing and I think it's a worthwhile one.

Having said these things, it's definitely a risk publishing there. (My
impression though is that scikit-image as a library speaks for itself and
the choice of journal is a choice of what model we want to support, rather
than which journal will be more prestigious.) *But, *more importantly, it
seems that F1000 Research is indeed slanted towards the biological
sciences; I was under the impression that it was a catchall journal. So, it
might not be the best fit.

[rant over] =)

>    - JMLR MLOSS [sklearn published here]
>
> Impact factor is about 3.4, which at least gives some indication that
> its content is valued.
>

If we are going to worry about JIF, PLOS ONE has 3.7, and *does* accept
papers from all disciplines. (You will also find a Scholarly Kitchen post
about how a JIF of 3.7 is a sign that PLOS and open access are doomed.)

Currently my two top candidates then are JMLR MLOSS and PLOS ONE. (The
latter does charge $1300 US per article.)

Let's stick to using wrapped lines, otherwise editing using our normal
> configurations becomes painful.
>

Agreed.

Juan.
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From tsyu80 at gmail.com  Mon Nov 18 23:49:40 2013
From: tsyu80 at gmail.com (Tony Yu)
Date: Mon, 18 Nov 2013 22:49:40 -0600
Subject: scikit-image paper
In-Reply-To: <bf9ff28b-cb0a-4f18-9184-34679c31dbe8@googlegroups.com>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com>
 <CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com>
 <CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com>
 <CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com> <bf9ff28b-cb0a-4f18-9184-34679c31dbe8@googlegroups.com>
Message-ID: <CAEym_Hpj8X2E9aw-Z37Am_2hJouci0eY4zUi=cP1b13bjmg5JA@mail.gmail.com>

On Mon, Nov 18, 2013 at 8:50 PM, Marianne Corvellec <
marianne.corvellec at ens-lyon.org> wrote:

> Hello all,
>
> What an exciting project!
>
>
> On Monday, November 18, 2013 3:59:22 AM UTC-5, Stefan van der Walt wrote:
>
>> Let's get started on some content!
>>
>> I think we would do well to emphasize the following in the paper:
>>
>> - Pythonic API
>> - Building block for reproducible research, use in academic world (we
>> need a list of publications of work that used skimage)
>> - Educational aspects (skimage.novice)
>> - Google Summer of Code contributions
>> - Use in industry (do we have examples here?)
>> - ... other ideas?
>>
>
> I believe it would be fitting to cite Dharhas Pothina's recent work.
> St?fan (and possibly others) know more about it than I do, but it could be
> considered both academic and industrial.
>
> I believe Tony S Yu would have lots to share as well. :)
>

Thanks for pinging me.

Unfortunately, the current project I'm working on isn't public (at least
when I last checked). There's another enthought project that is public:
I'll ask around to see if it's OK to make a direct reference to the project.

-T
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From jni.soma at gmail.com  Mon Nov 18 08:08:33 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Tue, 19 Nov 2013 00:08:33 +1100
Subject: SLIC Module in SciKit
In-Reply-To: <0e7255fd-3f39-42e7-846d-fd24117b40c5@googlegroups.com>
References: <0e7255fd-3f39-42e7-846d-fd24117b40c5@googlegroups.com>
Message-ID: <CA+JHcKS9wAavND_1pAiZrCmQb6Pz7U_Xi5FC9A2ks+ts4L8Fmg@mail.gmail.com>

Hi Jeremy,

is this just an issue of case? ie "slic" vs "SLIC"? The correct import line
should be:

from skimage.segmentation import slic

I hope this helps!

Juan.

On Monday, November 18, 2013, Jeremy Dunne wrote:

> Morning All,
>
>
>
> I have been trying to port my linux python code to a windows x32
> environment and am very close however I just can?t seem to find a way of
> Python 2.7 recognising the SLIC Module that is within sci-image. Having
> used Chris Gohlke?s Windows Extensions everything works up until my code
> looks to import SLIC from SciKit.
>
>
>
> Error : No module SLIC
>
>
>
> Anyone else had this issue or solved this problem ?
>
>
>
> Cheers
>
>
>
> Jeremy.
>
> --
> 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 <javascript:_e({},
> 'cvml', 'scikit-image%2Bunsubscribe at googlegroups.com');>.
> For more options, visit https://groups.google.com/groups/opt_out.
>
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From hughesadam87 at gmail.com  Tue Nov 19 15:44:41 2013
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Tue, 19 Nov 2013 12:44:41 -0800 (PST)
Subject: Advice on improving a analysis on images of nanoparticles
In-Reply-To: <CABDkGQ=Syt_z6UEYChpMo3F9GeuKnz9DWJtyfYG1MsWJNXskbw@mail.gmail.com>
References: <656876a4-8696-4f8a-b963-8ad42997db68@googlegroups.com>
 <CABDkGQ=Syt_z6UEYChpMo3F9GeuKnz9DWJtyfYG1MsWJNXskbw@mail.gmail.com>
Message-ID: <f45c0b91-fd22-460c-b961-0bf05d7537bb@googlegroups.com>

Thanks for the help Stefan.  Here is a direct link that anyone can view:  

http://www.scribd.com/doc/185189653/Scikit-Test-Notable

To download without an account, I am not familiar with any hosting 
solution, but if you guys have any recommendations I'd love to hear them.

Thank you for you help, I will test out the methods you suggested

On Sunday, November 17, 2013 4:27:12 AM UTC-5, Stefan van der Walt wrote:
>
> Hi Adam 
>
> On Fri, Nov 15, 2013 at 7:02 PM, Adam Hughes <hughes... at gmail.com<javascript:>> 
> wrote: 
> > The images are in a .pdf can be downloaded directly here. (Just a hair 
> too 
> > big to attach) 
>
> This download requires a login--could you please provide us with a 
> direct link / HTML page showing the images? 
>
> > LOWCONTRAST - Can the contrast in these images be enhanced automatically 
> in 
> > SKI? 
>
> We have several histogram equalization algorithms, including Contrast 
> Limited Histogram Equalization, which should do the trick. 
>
> > NONCIRC - Particles appear non-circular due to stigmation offset in 
> > microscope.  Is it possible to reshape them/make them more circular? 
>
> It depends on what you mean by "make them more circular".  We have 
> geometric transformation utilities in `skimage.transform`. 
>
> > WARPED - Images that have artifacts, or uneven contrast, due to 
> aberrations 
> > in SEM beam during imaging.  I'm especially interested in removing 
> uneven 
> > contrast. 
>
> Localized contrast equalization in the `skimage.filter.rank` module might 
> help. 
>
> > WATERSHED - These images have overlapping AuNPs, and I had hoped that 
> SKI's 
> > watershedding routines might help disentangle them.  The watershed 
> > segmentation guide indicates that there are several ways to approach 
> this 
> > problem. 
>
> See Juan's post here: 
> https://groups.google.com/d/msg/scikit-image/4z-hPiFFDj8/2gIDMxfGrU4J 
>
> Regards 
> St?fan 
>
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From stefan at sun.ac.za  Tue Nov 19 10:37:15 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 19 Nov 2013 17:37:15 +0200
Subject: Surface Curvature from Range Images (or Depth Maps)
In-Reply-To: <52837C70.20101@gmail.com>
References: <52837C70.20101@gmail.com>
Message-ID: <CABDkGQmYcWtH6UyCAvwvTW4a-_hUH6C4Mez1UFD8bSB26z292Q@mail.gmail.com>

Dear Michael

On Wed, Nov 13, 2013 at 3:19 PM, Brickle Macho <bricklemacho at gmail.com> wrote:
> I have implemented mean and gaussian curvature methods in python and thought
> they may be appropriate for inclusion to skimage.  An outline of the code is
> provided below.  It assumes a surface defined as a function of two
> coordinates, e.g. z = Z(x, y).  The curvature calculations are from the
> following two papers

Thank you for your post, and sorry for not responding earlier: I was
hoping someone more knowledgeable would jump in.  Since I am not that
person, would you mind explaining to me the gist of this work, and
what it aims to do, perhaps with some example images?

Thanks!
St?fan


From evelzw at gmail.com  Tue Nov 19 23:45:19 2013
From: evelzw at gmail.com (Evelyn Liu)
Date: Tue, 19 Nov 2013 20:45:19 -0800 (PST)
Subject: Advice on improving a analysis on images of nanoparticles
In-Reply-To: <CA+JHcKRE4Rr1QxqfhQy36W-BBfX0OVt4o+yxO8MF1ygQiob0vw@mail.gmail.com>
References: <656876a4-8696-4f8a-b963-8ad42997db68@googlegroups.com>
 <CABDkGQ=Syt_z6UEYChpMo3F9GeuKnz9DWJtyfYG1MsWJNXskbw@mail.gmail.com> <f45c0b91-fd22-460c-b961-0bf05d7537bb@googlegroups.com>
 <CA+JHcKRE4Rr1QxqfhQy36W-BBfX0OVt4o+yxO8MF1ygQiob0vw@mail.gmail.com>
Message-ID: <9964284d-a6e4-439f-b32b-ef6f07d13992@googlegroups.com>

Hi Juan,

On Tuesday, November 19, 2013 9:39:47 PM UTC-5, Juan Nunez-Iglesias wrote:
>
> Is the goal only to count particles? In that case, I think a local 
> thresholding (threshold_adaptive) would work on all these images. Then, 
> just do a labelling (scipy.ndimage.label) and draw a histogram of particle 
> sizes. You'll get a sharp peak around the true particle size, with bigger 
> peaks for clumps
>

I'd like to use scikit to plot the size distribution histogram of particles 
in an image, which is similar with Adam's. I tried 
scipy.ndimage.measurements.label(image), which I thought would give an 
array about particle sizes. However, the output array is with all 1, 
obviously nothing about size. I must get something wrong...So which 
function should i call for the size distribution? Thanks Juan!


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From stefan at sun.ac.za  Wed Nov 20 01:13:57 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 20 Nov 2013 08:13:57 +0200
Subject: Advice on improving a analysis on images of nanoparticles
In-Reply-To: <CA+JHcKSh3F_d4Ugzmn7VhEpXr-hdrkWfTEYYvq=wFX-TX8UTcA@mail.gmail.com>
References: <656876a4-8696-4f8a-b963-8ad42997db68@googlegroups.com>
	<CABDkGQ=Syt_z6UEYChpMo3F9GeuKnz9DWJtyfYG1MsWJNXskbw@mail.gmail.com>
	<f45c0b91-fd22-460c-b961-0bf05d7537bb@googlegroups.com>
	<CA+JHcKRE4Rr1QxqfhQy36W-BBfX0OVt4o+yxO8MF1ygQiob0vw@mail.gmail.com>
	<9964284d-a6e4-439f-b32b-ef6f07d13992@googlegroups.com>
	<CA+JHcKSh3F_d4Ugzmn7VhEpXr-hdrkWfTEYYvq=wFX-TX8UTcA@mail.gmail.com>
Message-ID: <CABDkGQmzMar1SCBaEvnWCiL8tqN0T=sMsrLEg3-fK3JmYBOwQA@mail.gmail.com>

On 20 Nov 2013 07:33, "Juan Nunez-Iglesias" <jni.soma at gmail.com> wrote:
>
> I'm guessing you are applying label() directly to your image, which is
not the right way to use it.

Looks like isolating objects is a common problem. Time for another gallery
example? We already have the coins, but perhaps something more realistic
with some biological data.

St?fan
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From guillaume at mitotic-machine.org  Wed Nov 20 02:32:44 2013
From: guillaume at mitotic-machine.org (Guillaume Gay)
Date: Wed, 20 Nov 2013 08:32:44 +0100
Subject: Advice on improving a analysis on images of nanoparticles
In-Reply-To: <CABDkGQmzMar1SCBaEvnWCiL8tqN0T=sMsrLEg3-fK3JmYBOwQA@mail.gmail.com>
References: <656876a4-8696-4f8a-b963-8ad42997db68@googlegroups.com>	<CABDkGQ=Syt_z6UEYChpMo3F9GeuKnz9DWJtyfYG1MsWJNXskbw@mail.gmail.com>	<f45c0b91-fd22-460c-b961-0bf05d7537bb@googlegroups.com>	<CA+JHcKRE4Rr1QxqfhQy36W-BBfX0OVt4o+yxO8MF1ygQiob0vw@mail.gmail.com>	<9964284d-a6e4-439f-b32b-ef6f07d13992@googlegroups.com>	<CA+JHcKSh3F_d4Ugzmn7VhEpXr-hdrkWfTEYYvq=wFX-TX8UTcA@mail.gmail.com> <CABDkGQmzMar1SCBaEvnWCiL8tqN0T=sMsrLEg3-fK3JmYBOwQA@mail.gmail.com>
Message-ID: <528C659C.4070708@mitotic-machine.org>

Hi all,

I'm currently working with cell nuclei segmentation (in 3D) with 
fluorescence imagery. I'm know using quite a pannel of sckimage routines 
to segment those out (local contrast enhancement, threshold otsu, 
etc.)?. Would you be interested if I turned that into an example (maybe 
something that could be chunked in several pieces?).

Best,

Guillaume

On 20/11/2013 07:13, St?fan van der Walt wrote:
>
> On 20 Nov 2013 07:33, "Juan Nunez-Iglesias" <jni.soma at gmail.com 
> <mailto:jni.soma at gmail.com>> wrote:
> >
> > I'm guessing you are applying label() directly to your image, which 
> is not the right way to use it.
>
> Looks like isolating objects is a common problem. Time for another 
> gallery example? We already have the coins, but perhaps something more 
> realistic with some biological data.
>
> St?fan
>
> -- 
> You received this message because you are subscribed to the Google 
> Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send 
> an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.

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From fboulogne at sciunto.org  Wed Nov 20 08:53:55 2013
From: fboulogne at sciunto.org (=?ISO-8859-1?Q?Fran=E7ois_Boulogne?=)
Date: Wed, 20 Nov 2013 08:53:55 -0500
Subject: Fwd: Fun with skimage
In-Reply-To: <CABDkGQnqmQiLjjQtoRcmASJumsuFaN9xiWWe8ufsni-uXZ6rMQ@mail.gmail.com>
References: <CABDkGQnqmQiLjjQtoRcmASJumsuFaN9xiWWe8ufsni-uXZ6rMQ@mail.gmail.com>
Message-ID: <528CBEF3.1010901@sciunto.org>

Le 20/11/2013 05:16, St?fan van der Walt a ?crit :
> How cool is this?
>
>

the coffee cup! :)

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



From jsch at demuc.de  Wed Nov 20 04:06:04 2013
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Wed, 20 Nov 2013 10:06:04 +0100
Subject: scikit-image paper
In-Reply-To: <CAEym_Hpj8X2E9aw-Z37Am_2hJouci0eY4zUi=cP1b13bjmg5JA@mail.gmail.com>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com> <CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com> <CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com> <CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com> <bf9ff28b-cb0a-4f18-9184-34679c31dbe8@googlegroups.com> <CAEym_Hpj8X2E9aw-Z37Am_2hJouci0eY4zUi=cP1b13bjmg5JA@mail.gmail.com>
Message-ID: <D66D4574-6D37-4C6B-A051-8062C5325BCE@demuc.de>

So, how should we get started with this? Any roadmap / plan?

Am 19.11.2013 um 05:49 schrieb Tony Yu <tsyu80 at gmail.com>:

> 
> 
> 
> On Mon, Nov 18, 2013 at 8:50 PM, Marianne Corvellec <marianne.corvellec at ens-lyon.org> wrote:
> Hello all,
> 
> What an exciting project!
> 
> 
> On Monday, November 18, 2013 3:59:22 AM UTC-5, Stefan van der Walt wrote:
> Let's get started on some content! 
> 
> I think we would do well to emphasize the following in the paper: 
> 
> - Pythonic API 
> - Building block for reproducible research, use in academic world (we 
> need a list of publications of work that used skimage) 
> - Educational aspects (skimage.novice) 
> - Google Summer of Code contributions 
> - Use in industry (do we have examples here?) 
> - ... other ideas?
> 
> I believe it would be fitting to cite Dharhas Pothina's recent work.
> St?fan (and possibly others) know more about it than I do, but it could be considered both academic and industrial.
> 
> I believe Tony S Yu would have lots to share as well. :)
>  
> Thanks for pinging me.
> 
> Unfortunately, the current project I'm working on isn't public (at least when I last checked). There's another enthought project that is public: I'll ask around to see if it's OK to make a direct reference to the project.
> 
> -T
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.



From jschull at gmail.com  Wed Nov 20 13:38:32 2013
From: jschull at gmail.com (Jon Schull)
Date: Wed, 20 Nov 2013 10:38:32 -0800 (PST)
Subject: match_template confidence > 3 ?
Message-ID: <8580c00d-9bdf-429b-9921-ff14cdf83207@googlegroups.com>

Greetings, we're using SciKit template_matching and getting confidence 
values   > 3.   Does that make sense?

A simple example with test images is attached.

Thanks for the fine work!

import numpy, sys
from skimage import data
from skimage import io
from skimage.feature import match_template

def containsLikelyhood(needleLoc, haystackLoc):
haystack = data.imread(haystackLoc, as_grey=True)
needle = data.imread(needleLoc, as_grey=True)
greyLoc  = match_template(haystack, needle)

ij = numpy.unravel_index(numpy.argmax(greyLoc), greyLoc.shape)
x, y = ij[::-1]

height, width = needle.shape
return greyLoc[y][x], (x, y, width, height)


if __name__ == "__main__":
print containsLikelyhood("locatedStar.PNG", "screenshot.PNG")
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From jsch at demuc.de  Wed Nov 20 04:55:12 2013
From: jsch at demuc.de (=?UTF-8?Q?Johannes_Sch=C3=B6nberger?=)
Date: Wed, 20 Nov 2013 10:55:12 +0100
Subject: scikit-image paper
In-Reply-To: <198541117.38971.1384941228713.open-xchange@app04>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com> <CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com> <CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com> <CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com> <bf9ff28b-cb0a-4f18-9184-34679c31dbe8@googlegroups.com> <CAEym_Hpj8X2E9aw-Z37Am_2hJouci0eY4zUi=cP1b13bjmg5JA@mail.gmail.com> <D66D4574-6D37-4C6B-A051-8062C5325BCE@demuc.de> <198541117.38971.1384941228713.open-xchange@app04>
Message-ID: <840462143.39041.1384941314158.open-xchange@app04.ox.hosteurope.de>

Maybe a feature / speed comparison with other libs (primarily Matlab, maybe Mahotas,...)?

> Am 20.11.2013 um 10:50 schrieb "St?fan van der Walt" <stefan at sun.ac.za>:
> 
>> On Wed, Nov 20, 2013 at 11:06 AM, Johannes Sch?nberger <jsch at demuc.de> wrote:
>> So, how should we get started with this? Any roadmap / plan?
> 
> Shall we split the paper into sections, and each take responsiblity
> for part of it?
> 
> Something like:
> 
> 1. Introduction and motivation
> 2. Purpose
>  a) Research
>  b) Education
>  c) Industry
> 3. Gallery of examples
> 4. Development practices
> 5. Conclusion
> 
> Ideas welcome.  A slightly more exciting structure could be more fun
> to write, but this will get the job done.
> 
> 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.
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> 

From bricklemacho at gmail.com  Tue Nov 19 22:01:54 2013
From: bricklemacho at gmail.com (Brickle Macho)
Date: Wed, 20 Nov 2013 11:01:54 +0800
Subject: Surface Curvature from Range Images (or Depth Maps)
In-Reply-To: <CABDkGQmYcWtH6UyCAvwvTW4a-_hUH6C4Mez1UFD8bSB26z292Q@mail.gmail.com>
References: <52837C70.20101@gmail.com> <CABDkGQmYcWtH6UyCAvwvTW4a-_hUH6C4Mez1UFD8bSB26z292Q@mail.gmail.com>
Message-ID: <528C2622.5010106@gmail.com>

Hi  St??????fan and others,

As requested.

Depth maps provide data on non-flat surfaces.  Curvature is the amount 
by which a object/surface deviates from being flat.  Using differential 
geometry, we can find the compute the curvature of the surfaces in an 
image.  Due to the structure of a depth map (essentially a Monge Patch 
see: http://mathworld.wolfram.com/MongePatch.html), numerical 
computation of the surface curvature map only requires the first and 
second partial derivative estimates at each surface point and can be 
estimated using np.gradient() function.  Here is example output form the 
provided code:  http://i.imgur.com/kyMaR1F.jpg If interested, slightly 
more detail provided after my signature block.

I have no ego over this, so if not appropriate to skimage that is ok.  
Heck, someone else can take control and include this into skimage, but I 
suspect like me, everyone is busy with life and other side projects.

Michael.
--


What follows is a more detailed version of above.  Apologies if some of 
the following is obvious some.

In my current research, my focus is on depth maps or range images. 
Others in our research ground are using point clouds.   The benefit of 
depth maps is that they are basically a structured point cloud but allow 
me to use common 2D image processing algorithms on the depth maps, and 
not worry about a specific point cloud library or algorithms.   For 
example applying some simple morphological operations (from skimge) I 
have been segment objects at varying depths, i.e segment objects that 
standout.

A depth map is gray-scale image which encodes the distance for a certain 
view or perspective.  Depth maps record the first surface seen and 
(obviously) cannot display information about occluded surfaces, surfaces 
seen or refracted through transparent object or reflected in mirrors.  I 
also have an aligned with the color view of the same scene, but not 
directly relevant to this post.

Curvature is the amount by which a object/surface deviates from being 
flat.    Curvature can be used to describe a surface. Either using the 
curvature pixel value itself as the feature or calculating one of eight 
surface primitives are: peak, pit, ridge, valley, flat, minimal, saddle 
ridge, and saddle valley surfaces. In the code provided in the original 
post I just calculate the the curvature value of each pixel, resulting 
in a curvature feature map.  Technically the code provided can be 
applied to any grey-scale image, but really only makes sense when 
applied to range iamges.

Depth maps provide data on non-flat surfaces.  Differential geometry can 
be used to process and analyse data on non-flat surfaces.  Using 
differential geometry, we can find the compute the curvature of the 
surfaces in an image.    A depth or range value at a point (x, y ) is 
given by a single-valued function z(x,y), essentially a Monge Patch see: 
http://mathworld.wolfram.com/MongePatch.html.     Because of this the 
Gaussian and mean curvatures are only related to the first and second 
partial derivatives of the function z with respect to x and y.    Thus 
the numerical computation of the surface curvature map only requires the 
first and second partial derivative estimates at each surface point.   
These can be estimated using np.gradient() function.  Once we have these 
estimates, it is simply a mater of substituting into the equations from 
the various papers.

Here is the code applied to a range image from the Middlebury data set 
(http://vision.middlebury.edu/stereo/data/).  The linked image shows he 
original range image, mean and guassian curvature, and simplified mean 
and guassian curvature. The RGB imagery is included for completeness but 
is not used in the calculation. Curvature Example: 
http://i.imgur.com/kyMaR1F.jpg





On 19/11/2013 11:37 pm, St??????fan van der Walt wrote:
> Dear Michael
>
> On Wed, Nov 13, 2013 at 3:19 PM, Brickle Macho <bricklemacho at gmail.com> wrote:
>> I have implemented mean and gaussian curvature methods in python and thought
>> they may be appropriate for inclusion to skimage.  An outline of the code is
>> provided below.  It assumes a surface defined as a function of two
>> coordinates, e.g. z = Z(x, y).  The curvature calculations are from the
>> following two papers
> Thank you for your post, and sorry for not responding earlier: I was
> hoping someone more knowledgeable would jump in.  Since I am not that
> person, would you mind explaining to me the gist of this work, and
> what it aims to do, perhaps with some example images?
>
> Thanks!
> St??????fan
>



From jsch at demuc.de  Wed Nov 20 05:41:26 2013
From: jsch at demuc.de (=?windows-1252?Q?Johannes_Sch=F6nberger?=)
Date: Wed, 20 Nov 2013 11:41:26 +0100
Subject: scikit-image paper
In-Reply-To: <CABDkGQnP3XzYOWPuoWCjZ7xwdjrvOEKK1ocx6wPgiUuLZBPDBA@mail.gmail.com>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com> <CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com> <CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com> <CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com> <bf9ff28b-cb0a-4f18-9184-34679c31dbe8@googlegroups.com> <CAEym_Hpj8X2E9aw-Z37Am_2hJouci0eY4zUi=cP1b13bjmg5JA@mail.gmail.com> <D66D4574-6D37-4C6B-A051-8062C5325BCE@demuc.de> <198541117.38971.1384941228713.open-xchange@app04> <840462143.39041.1384941314158.open-xchange@app04.ox.hosteurope.de> <CABDkGQnP3XzYOWPuoWCjZ7xwdjrvOEKK1ocx6wPgiUuLZBPDBA@mail.gmail.com>
Message-ID: <D68B22F1-0BC8-4433-BC30-139C28D851ED@demuc.de>

> I am hesitant to do that, because we expressly decided not have
> feature-hunting as a goal.  Speed comparisons are fine: it will
> probably show that we are comparable, but not the fastest (not
> currently one of our primary aims--but that could change in the
> future).

Just an idea? I?m also hesitant as it is always very difficult to compare functions, which itself have different parameters and options.

> 1. Introduction and motivation
> 2. Purpose
> a) Research
> b) Education
> c) Industry
> 3. Gallery of examples
> 4. Development practices
> 5. Conclusion

Looks like a sane choice. Another idea: ?Outlook & Future roadmap??

Splitting up the sections is a good idea, I think, although the text may sound a bit conglomerate as everyone has a different style and level of writing. So, I absolutely encourage you to correct me.

Johannes


From jsch at demuc.de  Wed Nov 20 05:46:40 2013
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Wed, 20 Nov 2013 11:46:40 +0100
Subject: scikit-image paper
In-Reply-To: <CABDkGQnKvTQJYVGZs=h-+VbFxO83L_a7gODyN27eATv6sEbpCA@mail.gmail.com>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com> <CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com> <CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com> <CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com> <bf9ff28b-cb0a-4f18-9184-34679c31dbe8@googlegroups.com> <CAEym_Hpj8X2E9aw-Z37Am_2hJouci0eY4zUi=cP1b13bjmg5JA@mail.gmail.com> <D66D4574-6D37-4C6B-A051-8062C5325BCE@demuc.de> <198541117.38971.1384941228713.open-xchange@app04> <840462143.39041.1384941314158.open-xchange@app04.ox.hosteurope.de> <CABDkGQnP3XzYOWPuoWCjZ7xwdjrvOEKK1ocx6wPgiUuLZBPDBA@mail.gmail.com> <D68B22F1-0BC8-4433-BC30-139C28D851ED@demuc.de> <CABDkGQnKvTQJYVGZs=h-+VbFxO83L_a7gODyN27eATv6sEbpCA@mail.gmail.com>
Message-ID: <4D73B4CD-DE2B-41D1-8444-D0CFD6E6E0AB@demuc.de>

> Let's do first drafts, and then review and rework one another's sections?

+1


From jsch at demuc.de  Wed Nov 20 05:46:59 2013
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Wed, 20 Nov 2013 11:46:59 +0100
Subject: scikit-image paper
In-Reply-To: <4D73B4CD-DE2B-41D1-8444-D0CFD6E6E0AB@demuc.de>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com> <CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com> <CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com> <CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com> <bf9ff28b-cb0a-4f18-9184-34679c31dbe8@googlegroups.com> <CAEym_Hpj8X2E9aw-Z37Am_2hJouci0eY4zUi=cP1b13bjmg5JA@mail.gmail.com> <D66D4574-6D37-4C6B-A051-8062C5325BCE@demuc.de> <198541117.38971.1384941228713.open-xchange@app04> <840462143.39041.1384941314158.open-xchange@app04.ox.hosteurope.de> <CABDkGQnP3XzYOWPuoWCjZ7xwdjrvOEKK1ocx6wPgiUuLZBPDBA@mail.gmail.com> <D68B22F1-0BC8-4433-BC30-139C28D851ED@demuc.de> <CABDkGQnKvTQJYVGZs=h-+VbFxO83L_a7gODyN27eATv6sEbpCA@mail.gmail.com> <4D73B4CD-DE2B-41D1-8444-D0CFD6E6E0AB@demuc.de>
Message-ID: <069149A0-AE51-481C-B140-96F6ED4C68A6@demuc.de>

Any plans on how long each of those sections and the whole article should be?


From stefan at sun.ac.za  Wed Nov 20 04:50:21 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 20 Nov 2013 11:50:21 +0200
Subject: scikit-image paper
In-Reply-To: <D66D4574-6D37-4C6B-A051-8062C5325BCE@demuc.de>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com>
 <CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com>
 <CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com>
 <CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com>
 <bf9ff28b-cb0a-4f18-9184-34679c31dbe8@googlegroups.com> <CAEym_Hpj8X2E9aw-Z37Am_2hJouci0eY4zUi=cP1b13bjmg5JA@mail.gmail.com>
 <D66D4574-6D37-4C6B-A051-8062C5325BCE@demuc.de>
Message-ID: <CABDkGQn5LAP-e0ZiKCbOeX2EzgCaQEELhtnoCFURzzwjX-0GFw@mail.gmail.com>

On Wed, Nov 20, 2013 at 11:06 AM, Johannes Sch?nberger <jsch at demuc.de> wrote:
> So, how should we get started with this? Any roadmap / plan?

Shall we split the paper into sections, and each take responsiblity
for part of it?

Something like:

1. Introduction and motivation
2. Purpose
  a) Research
  b) Education
  c) Industry
3. Gallery of examples
4. Development practices
5. Conclusion

Ideas welcome.  A slightly more exciting structure could be more fun
to write, but this will get the job done.

St?fan


From stefan at sun.ac.za  Wed Nov 20 04:57:39 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 20 Nov 2013 11:57:39 +0200
Subject: scikit-image paper
In-Reply-To: <840462143.39041.1384941314158.open-xchange@app04.ox.hosteurope.de>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com>
 <CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com>
 <CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com>
 <CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com>
 <bf9ff28b-cb0a-4f18-9184-34679c31dbe8@googlegroups.com> <CAEym_Hpj8X2E9aw-Z37Am_2hJouci0eY4zUi=cP1b13bjmg5JA@mail.gmail.com>
 <D66D4574-6D37-4C6B-A051-8062C5325BCE@demuc.de> <198541117.38971.1384941228713.open-xchange@app04>
 <840462143.39041.1384941314158.open-xchange@app04.ox.hosteurope.de>
Message-ID: <CABDkGQnP3XzYOWPuoWCjZ7xwdjrvOEKK1ocx6wPgiUuLZBPDBA@mail.gmail.com>

On Wed, Nov 20, 2013 at 11:55 AM, Johannes Sch?nberger <jsch at demuc.de> wrote:
> Maybe a feature / speed comparison with other libs (primarily Matlab, maybe Mahotas,...)?

I am hesitant to do that, because we expressly decided not have
feature-hunting as a goal.  Speed comparisons are fine: it will
probably show that we are comparable, but not the fastest (not
currently one of our primary aims--but that could change in the
future).

St?fan


From jsch at demuc.de  Wed Nov 20 05:57:48 2013
From: jsch at demuc.de (=?UTF-8?Q?Johannes_Sch=C3=B6nberger?=)
Date: Wed, 20 Nov 2013 11:57:48 +0100
Subject: scikit-image paper
In-Reply-To: <1805755143.42688.1384944805739.open-xchange@app04>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com> <CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com> <CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com> <CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com> <bf9ff28b-cb0a-4f18-9184-34679c31dbe8@googlegroups.com> <CAEym_Hpj8X2E9aw-Z37Am_2hJouci0eY4zUi=cP1b13bjmg5JA@mail.gmail.com> <D66D4574-6D37-4C6B-A051-8062C5325BCE@demuc.de> <198541117.38971.1384941228713.open-xchange@app04> <840462143.39041.1384941314158.open-xchange@app04.ox.hosteurope.de> <CABDkGQnP3XzYOWPuoWCjZ7xwdjrvOEKK1ocx6wPgiUuLZBPDBA@mail.gmail.com> <D68B22F1-0BC8-4433-BC30-139C28D851ED@demuc.de> <CABDkGQnKvTQJYVGZs=h-+VbFxO83L_a7gODyN27eATv6sEbpCA@mail.gmail.com> <4D73B4CD-DE2B-41D1-8444-D0CFD6E6E0AB@demuc.de> <069149A0-AE51-481C-B140-96F6ED4C68A6@demuc.de> <1805755143.42688.1384944805739.open-xchange@app04>
Message-ID: <903304904.43000.1384945069980.open-xchange@app04.ox.hosteurope.de>

> I was thinking around 4 to 5 pages or so?

Probably also a question of funding and if the journal charges for excessive page lengths...?

> Volunteering for sections: I will do the big picture overview
> (introduction + motivation) for now.
> 

I could do the Development practice and parts of the gallery?


From stefan at sun.ac.za  Wed Nov 20 05:16:49 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 20 Nov 2013 12:16:49 +0200
Subject: Fwd: Fun with skimage
Message-ID: <CABDkGQnqmQiLjjQtoRcmASJumsuFaN9xiWWe8ufsni-uXZ6rMQ@mail.gmail.com>

How cool is this?

---------- Forwarded message ----------
From: Brian Granger
Date: Fri, Nov 1, 2013 at 11:43 PM
Subject: Fun with skimage

I am working on some demos of the new IPython widget stuff and wrote a
simple skimage one. Thought you might find this interesting. Should be
pretty trivial to re-write the skimage viewer/plugin stuff using
this...

Cheers,

Brian

--
Brian E. Granger
Cal Poly State University, San Luis Obispo
bgranger at calpoly.edu and ellisonbg at gmail.com
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From stefan at sun.ac.za  Wed Nov 20 05:44:39 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 20 Nov 2013 12:44:39 +0200
Subject: scikit-image paper
In-Reply-To: <D68B22F1-0BC8-4433-BC30-139C28D851ED@demuc.de>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com>
 <CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com>
 <CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com>
 <CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com>
 <bf9ff28b-cb0a-4f18-9184-34679c31dbe8@googlegroups.com> <CAEym_Hpj8X2E9aw-Z37Am_2hJouci0eY4zUi=cP1b13bjmg5JA@mail.gmail.com>
 <D66D4574-6D37-4C6B-A051-8062C5325BCE@demuc.de> <198541117.38971.1384941228713.open-xchange@app04>
 <840462143.39041.1384941314158.open-xchange@app04.ox.hosteurope.de>
 <CABDkGQnP3XzYOWPuoWCjZ7xwdjrvOEKK1ocx6wPgiUuLZBPDBA@mail.gmail.com> <D68B22F1-0BC8-4433-BC30-139C28D851ED@demuc.de>
Message-ID: <CABDkGQnKvTQJYVGZs=h-+VbFxO83L_a7gODyN27eATv6sEbpCA@mail.gmail.com>

On Wed, Nov 20, 2013 at 12:41 PM, Johannes Sch?nberger <jsch at demuc.de> wrote:
> Splitting up the sections is a good idea, I think, although the text may sound a bit conglomerate as everyone has a different style and level of writing. So, I absolutely encourage you to correct me.

Let's do first drafts, and then review and rework one another's sections?

St?fan


From stefan at sun.ac.za  Wed Nov 20 05:48:53 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 20 Nov 2013 12:48:53 +0200
Subject: scikit-image paper
In-Reply-To: <069149A0-AE51-481C-B140-96F6ED4C68A6@demuc.de>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com>
 <CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com>
 <CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com>
 <CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com>
 <bf9ff28b-cb0a-4f18-9184-34679c31dbe8@googlegroups.com> <CAEym_Hpj8X2E9aw-Z37Am_2hJouci0eY4zUi=cP1b13bjmg5JA@mail.gmail.com>
 <D66D4574-6D37-4C6B-A051-8062C5325BCE@demuc.de> <198541117.38971.1384941228713.open-xchange@app04>
 <840462143.39041.1384941314158.open-xchange@app04.ox.hosteurope.de>
 <CABDkGQnP3XzYOWPuoWCjZ7xwdjrvOEKK1ocx6wPgiUuLZBPDBA@mail.gmail.com>
 <D68B22F1-0BC8-4433-BC30-139C28D851ED@demuc.de> <CABDkGQnKvTQJYVGZs=h-+VbFxO83L_a7gODyN27eATv6sEbpCA@mail.gmail.com>
 <4D73B4CD-DE2B-41D1-8444-D0CFD6E6E0AB@demuc.de> <069149A0-AE51-481C-B140-96F6ED4C68A6@demuc.de>
Message-ID: <CABDkGQ=CP4aBomeCRCULYTORSHdkSZ4jhH+7BVhhVKC-c5XNMA@mail.gmail.com>

On Wed, Nov 20, 2013 at 12:46 PM, Johannes Sch?nberger <jsch at demuc.de> wrote:
> Any plans on how long each of those sections and the whole article should be?

I was thinking around 4 to 5 pages or so?

Volunteering for sections: I will do the big picture overview
(introduction + motivation) for now.

St?fan


From hughesadam87 at gmail.com  Wed Nov 20 12:52:47 2013
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Wed, 20 Nov 2013 12:52:47 -0500
Subject: scikit-image paper
In-Reply-To: <8BEFCBCC-0225-4FA5-9CA6-A1C5E76D9FBD@demuc.de>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com>
	<CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com>
	<CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com>
	<CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com>
	<bf9ff28b-cb0a-4f18-9184-34679c31dbe8@googlegroups.com>
	<CAEym_Hpj8X2E9aw-Z37Am_2hJouci0eY4zUi=cP1b13bjmg5JA@mail.gmail.com>
	<D66D4574-6D37-4C6B-A051-8062C5325BCE@demuc.de>
	<198541117.38971.1384941228713.open-xchange@app04>
	<840462143.39041.1384941314158.open-xchange@app04.ox.hosteurope.de>
	<CABDkGQnP3XzYOWPuoWCjZ7xwdjrvOEKK1ocx6wPgiUuLZBPDBA@mail.gmail.com>
	<D68B22F1-0BC8-4433-BC30-139C28D851ED@demuc.de>
	<CABDkGQnKvTQJYVGZs=h-+VbFxO83L_a7gODyN27eATv6sEbpCA@mail.gmail.com>
	<4D73B4CD-DE2B-41D1-8444-D0CFD6E6E0AB@demuc.de>
	<069149A0-AE51-481C-B140-96F6ED4C68A6@demuc.de>
	<1805755143.42688.1384944805739.open-xchange@app04>
	<903304904.43000.1384945069980.open-xchange@app04.ox.hosteurope.de>
	<CA+JHcKSxjRJWZGZSLa3OQX=L+WvWK+FnQrfs0mMwVOd9zuq8=A@mail.gmail.com>
	<8BEFCBCC-0225-4FA5-9CA6-A1C5E76D9FBD@demuc.de>
Message-ID: <CAMHV+dCXmNzLD8tbGGzRHg2tvKb-kPNiZ1Zug7Lrt5n4Q07W3A@mail.gmail.com>

Is there currently a preferred way to cite scikit image while this paper is
in the works?


On Wed, Nov 20, 2013 at 9:03 AM, Johannes Sch?nberger <jsch at demuc.de> wrote:

> > Speaking of development practices, I've recently noticed that there's a
> bit of heterogeneity in the API, with some parts being object-oriented in
> style and others (most) being functional, which is my preference. Do we
> want to emphasise that this is the preferred style?
>
> The functional style is imo the preferred style, especially for raw image
> processing functionality, which only takes some image and produces some
> output.
>
> But there are parts where object-oriented style makes a lot of sense. I
> only know of the following excessive cases:
>
>  - skimage.transform.GeometricTransforms
>  - skimage.measure.fit.*Models
>  - skimage.viewer
>
> And in some places internally, mostly where actually appropriate. But only
> the interface is relevant in my opinion.
>
> I can only speak for the estimation functionality in skimage, where
> objects help a lot to make a sane implementation - a purely functional
> interface would be horribly complicated.
>
> Maybe it?s easier to keep track of the status of the discussion for
> everyone with a new PR:
> https://github.com/scikit-image/scikit-image-paper/pull/3
>
> Please, raise your voice for more ideas and if you are volunteering for a
> section :-)
>
> --
> 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/ReKcHGSaATU/unsubscribe.
> To unsubscribe from this group and all of its topics, send an email to
> scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>
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From hughesadam87 at gmail.com  Wed Nov 20 13:04:46 2013
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Wed, 20 Nov 2013 13:04:46 -0500
Subject: Advice on improving a analysis on images of nanoparticles
In-Reply-To: <CA+JHcKRE4Rr1QxqfhQy36W-BBfX0OVt4o+yxO8MF1ygQiob0vw@mail.gmail.com>
References: <656876a4-8696-4f8a-b963-8ad42997db68@googlegroups.com>
	<CABDkGQ=Syt_z6UEYChpMo3F9GeuKnz9DWJtyfYG1MsWJNXskbw@mail.gmail.com>
	<f45c0b91-fd22-460c-b961-0bf05d7537bb@googlegroups.com>
	<CA+JHcKRE4Rr1QxqfhQy36W-BBfX0OVt4o+yxO8MF1ygQiob0vw@mail.gmail.com>
Message-ID: <CAMHV+dDL9Gd-iLRhX-kqrxpJaja4uaTcOM--_w5DW4uu=j7qQw@mail.gmail.com>

Hi Juan, thanks for your helpful response.  See my replies inline:


On Tue, Nov 19, 2013 at 9:39 PM, Juan Nunez-Iglesias <jni.soma at gmail.com>wrote:

> Adam,
>
> On Wed, Nov 20, 2013 at 7:44 AM, Adam Hughes <hughesadam87 at gmail.com>wrote:
>
>> To download without an account, I am not familiar with any hosting
>> solution, but if you guys have any recommendations I'd love to hear them.
>>
>
> Dropbox can be used for this...
>

I tried this but to share a link, it asks for the emails of the recipients.
 You have used Dropbox to host a publicly accessible link?  If so, I will
certainly start doing this, thanks.


>
> Thank you for you help, I will test out the methods you suggested
>>
>
> Is the goal only to count particles? In that case, I think a local
> thresholding (threshold_adaptive) would work on all these images. Then,
> just do a labelling (scipy.ndimage.label) and draw a histogram of particle
> sizes. You'll get a sharp peak around the true particle size, with bigger
> peaks for clumps. Once you have the mean particle size you can estimate the
> number of particles in each clump (barring occlusion in 3D, in which case
> you're stuffed anyway), and then the total number of particles in your
> image.
>

Yes, that is the goal.  We had done a similar process ImageJ, but did
thersholding manually.  I will read into the adaptive threshold a bit more.
 We had hoped that some of these corrections, such as histogram
equilization, would make the automatic threshold more likely to give
correct results.


>
> Looking at your images, I don't think watershed (or anything else that I
> know) will do very well with the clumps. The contrast between adjacent
> particles is too low.
>

Hmm I see.   I will still try it out, but thanks for the heads up.  I'll
feel better now if it doesn't work well.


>
> Low-contrast-4 looks tricky... Are the smaller "points" particles of
> different sizes or just image noise?
>
> Finally, Watershed-f3 also looks hard, because it appears all the
> particles are touching... Again, I don't think watershed will help you
> here, nor anything else that doesn't have an a-priori knowledge of the
> particle size.
>

We do have an a-prior knowledge actually.  What I've been doing already is
putting a lower limit on particle size, with anything under it being noise.
 After doing particle counts and binning the data, we fit it with a
guassian, and optionally scale the data so that the guassian is centered
around the mean partitcle diameter (which believe we know to about 3nm
based on TEM imaging and indirect spectroscopic techniques).  Based on the
size distribution, we try to further bin the data into small
(dimers/trimers) and large aggregates.  For all the particles that are
large enough to be considered an aggregate, we *assume *that they fill a
half-sphere volume, and then we infer the true particle due to these
aggregates.  It's pretty ad-hoc, but we certainly apply some knowledge of
the expected particle size distributions.  I realize watershedding won't
split up huge clumps, but maybe could assist in the dimers and trimers?  In
any case, even if it doesn't significantly enhance our results, it would
still be helpful to explore that option and I'll try it out.

Thanks for this, and other examples!


> Juan.
>
> --
> 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/EbS7o2HvcUc/unsubscribe.
> To unsubscribe from this group and all of its topics, send an email to
> scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>
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From hughesadam87 at gmail.com  Wed Nov 20 13:11:31 2013
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Wed, 20 Nov 2013 13:11:31 -0500
Subject: Advice on improving a analysis on images of nanoparticles
In-Reply-To: <CAMHV+dDL9Gd-iLRhX-kqrxpJaja4uaTcOM--_w5DW4uu=j7qQw@mail.gmail.com>
References: <656876a4-8696-4f8a-b963-8ad42997db68@googlegroups.com>
	<CABDkGQ=Syt_z6UEYChpMo3F9GeuKnz9DWJtyfYG1MsWJNXskbw@mail.gmail.com>
	<f45c0b91-fd22-460c-b961-0bf05d7537bb@googlegroups.com>
	<CA+JHcKRE4Rr1QxqfhQy36W-BBfX0OVt4o+yxO8MF1ygQiob0vw@mail.gmail.com>
	<CAMHV+dDL9Gd-iLRhX-kqrxpJaja4uaTcOM--_w5DW4uu=j7qQw@mail.gmail.com>
Message-ID: <CAMHV+dAWmFwbQsj-M43VdLj12sKDJH1bWvsT_pP92eLC1=sn6A@mail.gmail.com>

Hey guys,

One last thing to add to this thread.  We also have the issue that some
images were taken at low resolution, or low magnification.  As a result, it
becomes quite difficult to ascertain particle distributions.   Unto this
point, I mostly just made sure to get high quality images, but sometimes
this is not possible due to microscope-induced artifacts at long image
times.  Have you any suggestions or examples for improving low res images
of small particles?  Otherwise I'll just note the limitations in resolution
and leave it at that in my writeup.


On Wed, Nov 20, 2013 at 1:04 PM, Adam Hughes <hughesadam87 at gmail.com> wrote:

> Hi Juan, thanks for your helpful response.  See my replies inline:
>
>
> On Tue, Nov 19, 2013 at 9:39 PM, Juan Nunez-Iglesias <jni.soma at gmail.com>wrote:
>
>> Adam,
>>
>> On Wed, Nov 20, 2013 at 7:44 AM, Adam Hughes <hughesadam87 at gmail.com>wrote:
>>
>>> To download without an account, I am not familiar with any hosting
>>> solution, but if you guys have any recommendations I'd love to hear them.
>>>
>>
>> Dropbox can be used for this...
>>
>
> I tried this but to share a link, it asks for the emails of the
> recipients.  You have used Dropbox to host a publicly accessible link?  If
> so, I will certainly start doing this, thanks.
>
>
>>
>>  Thank you for you help, I will test out the methods you suggested
>>>
>>
>> Is the goal only to count particles? In that case, I think a local
>> thresholding (threshold_adaptive) would work on all these images. Then,
>> just do a labelling (scipy.ndimage.label) and draw a histogram of particle
>> sizes. You'll get a sharp peak around the true particle size, with bigger
>> peaks for clumps. Once you have the mean particle size you can estimate the
>> number of particles in each clump (barring occlusion in 3D, in which case
>> you're stuffed anyway), and then the total number of particles in your
>> image.
>>
>
> Yes, that is the goal.  We had done a similar process ImageJ, but did
> thersholding manually.  I will read into the adaptive threshold a bit more.
>  We had hoped that some of these corrections, such as histogram
> equilization, would make the automatic threshold more likely to give
> correct results.
>
>
>>
>> Looking at your images, I don't think watershed (or anything else that I
>> know) will do very well with the clumps. The contrast between adjacent
>> particles is too low.
>>
>
> Hmm I see.   I will still try it out, but thanks for the heads up.  I'll
> feel better now if it doesn't work well.
>
>
>>
>> Low-contrast-4 looks tricky... Are the smaller "points" particles of
>> different sizes or just image noise?
>>
>> Finally, Watershed-f3 also looks hard, because it appears all the
>> particles are touching... Again, I don't think watershed will help you
>> here, nor anything else that doesn't have an a-priori knowledge of the
>> particle size.
>>
>
> We do have an a-prior knowledge actually.  What I've been doing already is
> putting a lower limit on particle size, with anything under it being noise.
>  After doing particle counts and binning the data, we fit it with a
> guassian, and optionally scale the data so that the guassian is centered
> around the mean partitcle diameter (which believe we know to about 3nm
> based on TEM imaging and indirect spectroscopic techniques).  Based on the
> size distribution, we try to further bin the data into small
> (dimers/trimers) and large aggregates.  For all the particles that are
> large enough to be considered an aggregate, we *assume *that they fill a
> half-sphere volume, and then we infer the true particle due to these
> aggregates.  It's pretty ad-hoc, but we certainly apply some knowledge of
> the expected particle size distributions.  I realize watershedding won't
> split up huge clumps, but maybe could assist in the dimers and trimers?  In
> any case, even if it doesn't significantly enhance our results, it would
> still be helpful to explore that option and I'll try it out.
>
> Thanks for this, and other examples!
>
>
>> Juan.
>>
>> --
>> 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/EbS7o2HvcUc/unsubscribe.
>> To unsubscribe from this group and all of its topics, send an email to
>> scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>
>
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From hughesadam87 at gmail.com  Wed Nov 20 13:21:32 2013
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Wed, 20 Nov 2013 13:21:32 -0500
Subject: Advice on improving a analysis on images of nanoparticles
In-Reply-To: <CABDkGQk1r8NBXdxFt2NYotukE-mVtjE93WDqM=Q4ZZPG1oEcsg@mail.gmail.com>
References: <656876a4-8696-4f8a-b963-8ad42997db68@googlegroups.com>
	<CABDkGQ=Syt_z6UEYChpMo3F9GeuKnz9DWJtyfYG1MsWJNXskbw@mail.gmail.com>
	<f45c0b91-fd22-460c-b961-0bf05d7537bb@googlegroups.com>
	<CA+JHcKRE4Rr1QxqfhQy36W-BBfX0OVt4o+yxO8MF1ygQiob0vw@mail.gmail.com>
	<CAMHV+dDL9Gd-iLRhX-kqrxpJaja4uaTcOM--_w5DW4uu=j7qQw@mail.gmail.com>
	<CAMHV+dAWmFwbQsj-M43VdLj12sKDJH1bWvsT_pP92eLC1=sn6A@mail.gmail.com>
	<CABDkGQk1r8NBXdxFt2NYotukE-mVtjE93WDqM=Q4ZZPG1oEcsg@mail.gmail.com>
Message-ID: <CAMHV+dDwokgQNR4zRyE-HLrhdHgTotmob1nPYkgk=wrQHC-i1w@mail.gmail.com>

Cool suggestions, thanks!  Although I don't have multiple images of the
same region of one of our surfaces, I will try it out next time we take
images.


On Wed, Nov 20, 2013 at 1:15 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> Hi Adam
>
> On Wed, Nov 20, 2013 at 8:11 PM, Adam Hughes <hughesadam87 at gmail.com>
> wrote:
> > One last thing to add to this thread.  We also have the issue that some
> > images were taken at low resolution, or low magnification.  As a result,
> it
> > becomes quite difficult to ascertain particle distributions.   Unto this
> > point, I mostly just made sure to get high quality images, but sometimes
> > this is not possible due to microscope-induced artifacts at long image
> > times.  Have you any suggestions or examples for improving low res
> images of
> > small particles?  Otherwise I'll just note the limitations in resolution
> and
> > leave it at that in my writeup.
>
> If you have multiple images of the same object, you could do
> super-resolution.  If you only have one image, you could try
> single-frame super-resolution, which is essentially dictionary
> learning on a large set of similar photos, used to update
> high-frequency information in the current image.
>
> 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/EbS7o2HvcUc/unsubscribe.
> To unsubscribe from this group and all of its topics, send an email to
> scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>
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From jni.soma at gmail.com  Tue Nov 19 21:39:47 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Wed, 20 Nov 2013 13:39:47 +1100
Subject: Advice on improving a analysis on images of nanoparticles
In-Reply-To: <f45c0b91-fd22-460c-b961-0bf05d7537bb@googlegroups.com>
References: <656876a4-8696-4f8a-b963-8ad42997db68@googlegroups.com>
 <CABDkGQ=Syt_z6UEYChpMo3F9GeuKnz9DWJtyfYG1MsWJNXskbw@mail.gmail.com> <f45c0b91-fd22-460c-b961-0bf05d7537bb@googlegroups.com>
Message-ID: <CA+JHcKRE4Rr1QxqfhQy36W-BBfX0OVt4o+yxO8MF1ygQiob0vw@mail.gmail.com>

Adam,

On Wed, Nov 20, 2013 at 7:44 AM, Adam Hughes <hughesadam87 at gmail.com> wrote:

> To download without an account, I am not familiar with any hosting
> solution, but if you guys have any recommendations I'd love to hear them.
>

Dropbox can be used for this...

Thank you for you help, I will test out the methods you suggested
>

Is the goal only to count particles? In that case, I think a local
thresholding (threshold_adaptive) would work on all these images. Then,
just do a labelling (scipy.ndimage.label) and draw a histogram of particle
sizes. You'll get a sharp peak around the true particle size, with bigger
peaks for clumps. Once you have the mean particle size you can estimate the
number of particles in each clump (barring occlusion in 3D, in which case
you're stuffed anyway), and then the total number of particles in your
image.

Looking at your images, I don't think watershed (or anything else that I
know) will do very well with the clumps. The contrast between adjacent
particles is too low.

Low-contrast-4 looks tricky... Are the smaller "points" particles of
different sizes or just image noise?

Finally, Watershed-f3 also looks hard, because it appears all the particles
are touching... Again, I don't think watershed will help you here, nor
anything else that doesn't have an a-priori knowledge of the particle size.

Juan.
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From jsch at demuc.de  Wed Nov 20 09:03:41 2013
From: jsch at demuc.de (=?windows-1252?Q?Johannes_Sch=F6nberger?=)
Date: Wed, 20 Nov 2013 15:03:41 +0100
Subject: scikit-image paper
In-Reply-To: <CA+JHcKSxjRJWZGZSLa3OQX=L+WvWK+FnQrfs0mMwVOd9zuq8=A@mail.gmail.com>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com> <CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com> <CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com> <CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com> <bf9ff28b-cb0a-4f18-9184-34679c31dbe8@googlegroups.com> <CAEym_Hpj8X2E9aw-Z37Am_2hJouci0eY4zUi=cP1b13bjmg5JA@mail.gmail.com> <D66D4574-6D37-4C6B-A051-8062C5325BCE@demuc.de> <198541117.38971.1384941228713.open-xchange@app04> <840462143.39041.1384941314158.open-xchange@app04.ox.hosteurope.de> <CABDkGQnP3XzYOWPuoWCjZ7xwdjrvOEKK1ocx6wPgiUuLZBPDBA@mail.gmail.com> <D68B22F1-0BC8-4433-BC30-139C28D851ED@demuc.de> <CABDkGQnKvTQJYVGZs=h-+VbFxO83L_a7gODyN27eATv6sEbpCA@mail.gmail.com> <4D73B4CD-DE2B-41D1-8444-D0CFD6E6E0AB@demuc.de> <069149A0-AE51-481C-B140-96F6ED4C68A6@demuc.de> <1805755143.42688.1384944805739.open-xchange@app04> <903304904.43000.1384945069980.open-xchange@app04.ox.hosteurope.de> <CA+JHcKSxjRJWZGZSLa3OQX=L+WvWK+FnQrfs0mMwVOd9zuq8=A@mail.gmail.com>
Message-ID: <8BEFCBCC-0225-4FA5-9CA6-A1C5E76D9FBD@demuc.de>

> Speaking of development practices, I've recently noticed that there's a bit of heterogeneity in the API, with some parts being object-oriented in style and others (most) being functional, which is my preference. Do we want to emphasise that this is the preferred style?

The functional style is imo the preferred style, especially for raw image processing functionality, which only takes some image and produces some output.

But there are parts where object-oriented style makes a lot of sense. I only know of the following excessive cases:

 - skimage.transform.GeometricTransforms
 - skimage.measure.fit.*Models
 - skimage.viewer

And in some places internally, mostly where actually appropriate. But only the interface is relevant in my opinion.

I can only speak for the estimation functionality in skimage, where objects help a lot to make a sane implementation - a purely functional interface would be horribly complicated.

Maybe it?s easier to keep track of the status of the discussion for everyone with a new PR: https://github.com/scikit-image/scikit-image-paper/pull/3

Please, raise your voice for more ideas and if you are volunteering for a section :-)


From stefan at sun.ac.za  Wed Nov 20 09:03:12 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 20 Nov 2013 16:03:12 +0200
Subject: scikit-image paper
In-Reply-To: <CA+JHcKSxjRJWZGZSLa3OQX=L+WvWK+FnQrfs0mMwVOd9zuq8=A@mail.gmail.com>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com>
 <CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com>
 <CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com>
 <CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com>
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 <D66D4574-6D37-4C6B-A051-8062C5325BCE@demuc.de> <198541117.38971.1384941228713.open-xchange@app04>
 <840462143.39041.1384941314158.open-xchange@app04.ox.hosteurope.de>
 <CABDkGQnP3XzYOWPuoWCjZ7xwdjrvOEKK1ocx6wPgiUuLZBPDBA@mail.gmail.com>
 <D68B22F1-0BC8-4433-BC30-139C28D851ED@demuc.de> <CABDkGQnKvTQJYVGZs=h-+VbFxO83L_a7gODyN27eATv6sEbpCA@mail.gmail.com>
 <4D73B4CD-DE2B-41D1-8444-D0CFD6E6E0AB@demuc.de> <069149A0-AE51-481C-B140-96F6ED4C68A6@demuc.de>
 <1805755143.42688.1384944805739.open-xchange@app04> <903304904.43000.1384945069980.open-xchange@app04.ox.hosteurope.de>
 <CA+JHcKSxjRJWZGZSLa3OQX=L+WvWK+FnQrfs0mMwVOd9zuq8=A@mail.gmail.com>
Message-ID: <CABDkGQnOugP6qnYaV4a+T-ynzouHdQQcVahC-6wQrkMdCkWtNQ@mail.gmail.com>

Hi Juan

On Wed, Nov 20, 2013 at 3:19 PM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
>
> @stefanv, I've found a flaw in your structure:
>

I don't quite get the joke (doh).

> I think it's worth spending a bit of time on the actual outline (e.g. bullet points on each section), before launching into writing, to avoid redundancy. We can do this directly on the github template. For example, I would add my chromosome finding example (with code) to the gallery/science applications.

Sure, make a few suggestions here then we can pen down the outline.

> Speaking of development practices, I've recently noticed that there's a bit of heterogeneity in the API, with some parts being object-oriented in style and others (most) being functional, which is my preference. Do we want to emphasise that this is the preferred style?

I think the majority of the library consists of functions, unless
there is a big benefit to doing it differently.  Can you elaborate?

St?fan


From stefan at sun.ac.za  Wed Nov 20 09:10:27 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 20 Nov 2013 16:10:27 +0200
Subject: Advice on improving a analysis on images of nanoparticles
In-Reply-To: <528C9406.6080605@gmail.com>
References: <656876a4-8696-4f8a-b963-8ad42997db68@googlegroups.com>
 <CABDkGQ=Syt_z6UEYChpMo3F9GeuKnz9DWJtyfYG1MsWJNXskbw@mail.gmail.com>
 <f45c0b91-fd22-460c-b961-0bf05d7537bb@googlegroups.com> <CA+JHcKRE4Rr1QxqfhQy36W-BBfX0OVt4o+yxO8MF1ygQiob0vw@mail.gmail.com>
 <9964284d-a6e4-439f-b32b-ef6f07d13992@googlegroups.com> <CA+JHcKSh3F_d4Ugzmn7VhEpXr-hdrkWfTEYYvq=wFX-TX8UTcA@mail.gmail.com>
 <CABDkGQmzMar1SCBaEvnWCiL8tqN0T=sMsrLEg3-fK3JmYBOwQA@mail.gmail.com> <528C9406.6080605@gmail.com>
Message-ID: <CABDkGQmKoqOh_8rm+i-t3b7aHHNEmC=X4=KZ1wO-ReXHV25RAQ@mail.gmail.com>

On Wed, Nov 20, 2013 at 12:50 PM, Brickle Macho <bricklemacho at gmail.com> wrote:
> I can always adapt this example (http://pythonvision.org/basic-tutorial)
> which uses pymorph and mahotaos to counting nuceli and segments the image as
> a gallery example for skimage (obviously acknowledging the original
> tutorial).  Or is it bad form to copy/use another example.

I think you should ask Luis for permission, just to be on the safe side.

But this reminds me: someone needs to implement voronoi!  Should be
quite fun, actually.

St?fan


From jni.soma at gmail.com  Wed Nov 20 00:33:19 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Wed, 20 Nov 2013 16:33:19 +1100
Subject: Advice on improving a analysis on images of nanoparticles
In-Reply-To: <9964284d-a6e4-439f-b32b-ef6f07d13992@googlegroups.com>
References: <656876a4-8696-4f8a-b963-8ad42997db68@googlegroups.com>
 <CABDkGQ=Syt_z6UEYChpMo3F9GeuKnz9DWJtyfYG1MsWJNXskbw@mail.gmail.com>
 <f45c0b91-fd22-460c-b961-0bf05d7537bb@googlegroups.com> <CA+JHcKRE4Rr1QxqfhQy36W-BBfX0OVt4o+yxO8MF1ygQiob0vw@mail.gmail.com>
 <9964284d-a6e4-439f-b32b-ef6f07d13992@googlegroups.com>
Message-ID: <CA+JHcKSh3F_d4Ugzmn7VhEpXr-hdrkWfTEYYvq=wFX-TX8UTcA@mail.gmail.com>

Hi Evelyn,

I'm guessing you are applying label() directly to your image, which is not
the right way to use it. label() connects all neighboring *nonzero* points
together. Since images are rarely zero (rather than some very small
intensity value), you are simply connecting all the pixels of your image
together into one label.

The correct way to do this is to threshold your image, eg using:
http://scikit-image.org/docs/dev/api/skimage.filter.html#threshold-adaptive

So:

>>> from skimage.filter import threshold_adaptive
>>> from scipy import ndimage as nd
>>> diam = 51
>>> # "51" is a guess, you might have to fiddle with this parameter.
>>> image_t = (image > threshold_adaptive(image, diam))
>>> image_labeled = nd.label(image_t)[0]
>>> particle_sizes = np.bincount(image_labeled.ravel())[1:]
>>> # [1:] is to select only the foreground labels

Hope this helps!

Juan.



On Wed, Nov 20, 2013 at 3:45 PM, Evelyn Liu <evelzw at gmail.com> wrote:

> Hi Juan,
>
> On Tuesday, November 19, 2013 9:39:47 PM UTC-5, Juan Nunez-Iglesias wrote:
>>
>> Is the goal only to count particles? In that case, I think a local
>> thresholding (threshold_adaptive) would work on all these images. Then,
>> just do a labelling (scipy.ndimage.label) and draw a histogram of particle
>> sizes. You'll get a sharp peak around the true particle size, with bigger
>> peaks for clumps
>>
>
> I'd like to use scikit to plot the size distribution histogram of
> particles in an image, which is similar with Adam's. I tried
> scipy.ndimage.measurements.label(image), which I thought would give an
> array about particle sizes. However, the output array is with all 1,
> obviously nothing about size. I must get something wrong...So which
> function should i call for the size distribution? Thanks Juan!
>
>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
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From marianne.corvellec at ens-lyon.org  Wed Nov 20 20:30:00 2013
From: marianne.corvellec at ens-lyon.org (Marianne Corvellec)
Date: Wed, 20 Nov 2013 17:30:00 -0800 (PST)
Subject: Fwd: Fun with skimage
In-Reply-To: <528CBEF3.1010901@sciunto.org>
References: <CABDkGQnqmQiLjjQtoRcmASJumsuFaN9xiWWe8ufsni-uXZ6rMQ@mail.gmail.com>
 <528CBEF3.1010901@sciunto.org>
Message-ID: <b5152afe-02f4-4fce-abec-d335c9e265c7@googlegroups.com>

Yes, the coffee cup! ;)

Maybe we could add a "Fun" subsection to the draft structure under 
"Purpose" (scikit-image paper)... :p

I think the matplotlib people mentioned the most popular part of the 
matplotlib gallery was the XKCD-stylification of plots...  I quite like 
that.

On Wednesday, November 20, 2013 8:53:55 AM UTC-5, Fran?ois Boulogne wrote:
>
> Le 20/11/2013 05:16, St?fan van der Walt a ?crit : 
> > How cool is this? 
> > 
> > 
>
> the coffee cup! :) 
>
> -- 
> Fran?ois Boulogne. 
> http://www.sciunto.org 
> GPG fingerprint: 25F6 C971 4875 A6C1 EDD1  75C8 1AA7 216E 32D5 F22F 
>
>
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From stuart at mumford.me.uk  Wed Nov 20 13:00:52 2013
From: stuart at mumford.me.uk (Stuart Mumford)
Date: Wed, 20 Nov 2013 18:00:52 +0000
Subject: scikit-image paper
In-Reply-To: <CABDkGQ=KeoCpzURQMSKkMTdzVzpptZxhq8+WPx=g=2c8zCAo3w@mail.gmail.com>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com>
	<CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com>
	<CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com>
	<CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com>
	<bf9ff28b-cb0a-4f18-9184-34679c31dbe8@googlegroups.com>
	<CAEym_Hpj8X2E9aw-Z37Am_2hJouci0eY4zUi=cP1b13bjmg5JA@mail.gmail.com>
	<D66D4574-6D37-4C6B-A051-8062C5325BCE@demuc.de>
	<198541117.38971.1384941228713.open-xchange@app04>
	<840462143.39041.1384941314158.open-xchange@app04.ox.hosteurope.de>
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	<CABDkGQnKvTQJYVGZs=h-+VbFxO83L_a7gODyN27eATv6sEbpCA@mail.gmail.com>
	<4D73B4CD-DE2B-41D1-8444-D0CFD6E6E0AB@demuc.de>
	<069149A0-AE51-481C-B140-96F6ED4C68A6@demuc.de>
	<1805755143.42688.1384944805739.open-xchange@app04>
	<903304904.43000.1384945069980.open-xchange@app04.ox.hosteurope.de>
	<CA+JHcKSxjRJWZGZSLa3OQX=L+WvWK+FnQrfs0mMwVOd9zuq8=A@mail.gmail.com>
	<8BEFCBCC-0225-4FA5-9CA6-A1C5E76D9FBD@demuc.de>
	<CAMHV+dCXmNzLD8tbGGzRHg2tvKb-kPNiZ1Zug7Lrt5n4Q07W3A@mail.gmail.com>
	<CABDkGQ=KeoCpzURQMSKkMTdzVzpptZxhq8+WPx=g=2c8zCAo3w@mail.gmail.com>
Message-ID: <CAJ3G1JoETb=+YUskneRVZMjAJhTUz59P1g_7NaEVzP7MCm=BHA@mail.gmail.com>

The paper I have contributed to that uses skimage references the website.

Stuart
On 20 Nov 2013 17:58, "St?fan van der Walt" <stefan at sun.ac.za> wrote:

> On Wed, Nov 20, 2013 at 7:52 PM, Adam Hughes <hughesadam87 at gmail.com>
> wrote:
> > Is there currently a preferred way to cite scikit image while this paper
> is
> > in the works?
>
> I think unfortunately not until we at least upload the pre-print on arxiv.
>
> 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.
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From bricklemacho at gmail.com  Wed Nov 20 05:50:46 2013
From: bricklemacho at gmail.com (Brickle Macho)
Date: Wed, 20 Nov 2013 18:50:46 +0800
Subject: Advice on improving a analysis on images of nanoparticles
In-Reply-To: <CABDkGQmzMar1SCBaEvnWCiL8tqN0T=sMsrLEg3-fK3JmYBOwQA@mail.gmail.com>
References: <656876a4-8696-4f8a-b963-8ad42997db68@googlegroups.com>	<CABDkGQ=Syt_z6UEYChpMo3F9GeuKnz9DWJtyfYG1MsWJNXskbw@mail.gmail.com>	<f45c0b91-fd22-460c-b961-0bf05d7537bb@googlegroups.com>	<CA+JHcKRE4Rr1QxqfhQy36W-BBfX0OVt4o+yxO8MF1ygQiob0vw@mail.gmail.com>	<9964284d-a6e4-439f-b32b-ef6f07d13992@googlegroups.com>	<CA+JHcKSh3F_d4Ugzmn7VhEpXr-hdrkWfTEYYvq=wFX-TX8UTcA@mail.gmail.com> <CABDkGQmzMar1SCBaEvnWCiL8tqN0T=sMsrLEg3-fK3JmYBOwQA@mail.gmail.com>
Message-ID: <528C9406.6080605@gmail.com>

I can always adapt this example (http://pythonvision.org/basic-tutorial) 
which uses pymorph and mahotaos to counting nuceli and segments the 
image as a gallery example for skimage (obviously acknowledging the 
original tutorial).  Or is it bad form to copy/use another example.

Michael.
--



On 20/11/2013 2:13 pm, St??????fan van der Walt wrote:
>
> On 20 Nov 2013 07:33, "Juan Nunez-Iglesias" <jni.soma at gmail.com 
> <mailto:jni.soma at gmail.com>> wrote:
> >
> > I'm guessing you are applying label() directly to your image, which 
> is not the right way to use it.
>
> Looks like isolating objects is a common problem. Time for another 
> gallery example? We already have the coins, but perhaps something more 
> realistic with some biological data.
>
> St??????fan
>
> -- 
> You received this message because you are subscribed to the Google 
> Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send 
> an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.

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From stefan at sun.ac.za  Wed Nov 20 12:58:32 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 20 Nov 2013 19:58:32 +0200
Subject: scikit-image paper
In-Reply-To: <CAMHV+dCXmNzLD8tbGGzRHg2tvKb-kPNiZ1Zug7Lrt5n4Q07W3A@mail.gmail.com>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com>
 <CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com>
 <CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com>
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 <CABDkGQnP3XzYOWPuoWCjZ7xwdjrvOEKK1ocx6wPgiUuLZBPDBA@mail.gmail.com>
 <D68B22F1-0BC8-4433-BC30-139C28D851ED@demuc.de> <CABDkGQnKvTQJYVGZs=h-+VbFxO83L_a7gODyN27eATv6sEbpCA@mail.gmail.com>
 <4D73B4CD-DE2B-41D1-8444-D0CFD6E6E0AB@demuc.de> <069149A0-AE51-481C-B140-96F6ED4C68A6@demuc.de>
 <1805755143.42688.1384944805739.open-xchange@app04> <903304904.43000.1384945069980.open-xchange@app04.ox.hosteurope.de>
 <CA+JHcKSxjRJWZGZSLa3OQX=L+WvWK+FnQrfs0mMwVOd9zuq8=A@mail.gmail.com>
 <8BEFCBCC-0225-4FA5-9CA6-A1C5E76D9FBD@demuc.de> <CAMHV+dCXmNzLD8tbGGzRHg2tvKb-kPNiZ1Zug7Lrt5n4Q07W3A@mail.gmail.com>
Message-ID: <CABDkGQ=KeoCpzURQMSKkMTdzVzpptZxhq8+WPx=g=2c8zCAo3w@mail.gmail.com>

On Wed, Nov 20, 2013 at 7:52 PM, Adam Hughes <hughesadam87 at gmail.com> wrote:
> Is there currently a preferred way to cite scikit image while this paper is
> in the works?

I think unfortunately not until we at least upload the pre-print on arxiv.

St?fan


From stefan at sun.ac.za  Wed Nov 20 13:15:31 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 20 Nov 2013 20:15:31 +0200
Subject: Advice on improving a analysis on images of nanoparticles
In-Reply-To: <CAMHV+dAWmFwbQsj-M43VdLj12sKDJH1bWvsT_pP92eLC1=sn6A@mail.gmail.com>
References: <656876a4-8696-4f8a-b963-8ad42997db68@googlegroups.com>
 <CABDkGQ=Syt_z6UEYChpMo3F9GeuKnz9DWJtyfYG1MsWJNXskbw@mail.gmail.com>
 <f45c0b91-fd22-460c-b961-0bf05d7537bb@googlegroups.com> <CA+JHcKRE4Rr1QxqfhQy36W-BBfX0OVt4o+yxO8MF1ygQiob0vw@mail.gmail.com>
 <CAMHV+dDL9Gd-iLRhX-kqrxpJaja4uaTcOM--_w5DW4uu=j7qQw@mail.gmail.com> <CAMHV+dAWmFwbQsj-M43VdLj12sKDJH1bWvsT_pP92eLC1=sn6A@mail.gmail.com>
Message-ID: <CABDkGQk1r8NBXdxFt2NYotukE-mVtjE93WDqM=Q4ZZPG1oEcsg@mail.gmail.com>

Hi Adam

On Wed, Nov 20, 2013 at 8:11 PM, Adam Hughes <hughesadam87 at gmail.com> wrote:
> One last thing to add to this thread.  We also have the issue that some
> images were taken at low resolution, or low magnification.  As a result, it
> becomes quite difficult to ascertain particle distributions.   Unto this
> point, I mostly just made sure to get high quality images, but sometimes
> this is not possible due to microscope-induced artifacts at long image
> times.  Have you any suggestions or examples for improving low res images of
> small particles?  Otherwise I'll just note the limitations in resolution and
> leave it at that in my writeup.

If you have multiple images of the same object, you could do
super-resolution.  If you only have one image, you could try
single-frame super-resolution, which is essentially dictionary
learning on a large set of similar photos, used to update
high-frequency information in the current image.

St?fan


From stefan at sun.ac.za  Wed Nov 20 13:45:03 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 20 Nov 2013 20:45:03 +0200
Subject: Test coverage
Message-ID: <CABDkGQnZvbEgtJ9W7PWq68HDDPMFsc99TDAGXw_ZVQOVskJuZg@mail.gmail.com>

Hello, everyone

We now have automated test coverage for scikit-image:

https://coveralls.io/r/scikit-image/scikit-image

Most of the newer modules (those that went through rigorous PR
review!) did pretty well, but we are still only at 82%.  If ever you
find yourself with a bit of spare time on your hands, please hunt down
some of these corner cases and write tests for them so that we can
start making our way towards 100%.

Thanks!
St?fan


From tsyu80 at gmail.com  Wed Nov 20 23:39:57 2013
From: tsyu80 at gmail.com (Tony Yu)
Date: Wed, 20 Nov 2013 22:39:57 -0600
Subject: scikit-image paper
In-Reply-To: <CAEym_Hpj8X2E9aw-Z37Am_2hJouci0eY4zUi=cP1b13bjmg5JA@mail.gmail.com>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com>
 <CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com>
 <CA+JHcKS9Q=agH6iz1NcdFcqcpmUNX2V=7y9BybdPo_rsQDhS2g@mail.gmail.com>
 <CABDkGQmjRZgLK0dDt2Wo8+7uxBPe6ONrmRQmOY-eB6VoKUu1dw@mail.gmail.com>
 <bf9ff28b-cb0a-4f18-9184-34679c31dbe8@googlegroups.com> <CAEym_Hpj8X2E9aw-Z37Am_2hJouci0eY4zUi=cP1b13bjmg5JA@mail.gmail.com>
Message-ID: <CAEym_HqMxaNb9KspKeC9KivcuQnFxw0bTqjxaWPut=G9bvt0DQ@mail.gmail.com>

On Mon, Nov 18, 2013 at 10:49 PM, Tony Yu <tsyu80 at gmail.com> wrote:

>
>
>
> On Mon, Nov 18, 2013 at 8:50 PM, Marianne Corvellec <
> marianne.corvellec at ens-lyon.org> wrote:
>
>>
>> <snip>

> I believe Tony S Yu would have lots to share as well. :)
>>
>
> Thanks for pinging me.
>
> Unfortunately, the current project I'm working on isn't public (at least
> when I last checked). There's another enthought project that is public:
> I'll ask around to see if it's OK to make a direct reference to the project.
>

Unfortunately, it's a no-go on mentioning the specific companies we've
worked with, but its OK to say something like "Enthought, Inc uses
scikit-image extensively in their consulting projects related to geophysics
and microscopy".

-T
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From jni.soma at gmail.com  Wed Nov 20 07:55:37 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Wed, 20 Nov 2013 23:55:37 +1100
Subject: Advice on improving a analysis on images of nanoparticles
In-Reply-To: <528C9406.6080605@gmail.com>
References: <656876a4-8696-4f8a-b963-8ad42997db68@googlegroups.com>
 <CABDkGQ=Syt_z6UEYChpMo3F9GeuKnz9DWJtyfYG1MsWJNXskbw@mail.gmail.com>
 <f45c0b91-fd22-460c-b961-0bf05d7537bb@googlegroups.com> <CA+JHcKRE4Rr1QxqfhQy36W-BBfX0OVt4o+yxO8MF1ygQiob0vw@mail.gmail.com>
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Message-ID: <CA+JHcKQnFZ-da5v8JL-=JUS4dprf_bJmB2gPAki7mwtF1gzmYg@mail.gmail.com>

@Guillaume, please contribute the example ASAP because I'm struggling with
the exact same problem! =D In particular, the nuclei example from
pythonvision is not ideal because they gloss over a lot of parameter tuning
that is much easier to deal with in 2D than 3D. I'll be happy to hear about
your experience!

Juan.


On Wed, Nov 20, 2013 at 9:50 PM, Brickle Macho <bricklemacho at gmail.com>wrote:

>  I can always adapt this example (http://pythonvision.org/basic-tutorial)
> which uses pymorph and mahotaos to counting nuceli and segments the image
> as a gallery example for skimage (obviously acknowledging the original
> tutorial).  Or is it bad form to copy/use another example.
>
> Michael.
> --
>
>
>
>
> On 20/11/2013 2:13 pm, St?fan van der Walt wrote:
>
> On 20 Nov 2013 07:33, "Juan Nunez-Iglesias" <jni.soma at gmail.com> wrote:
> >
> > I'm guessing you are applying label() directly to your image, which is
> not the right way to use it.
>
> Looks like isolating objects is a common problem. Time for another gallery
> example? We already have the coins, but perhaps something more realistic
> with some biological data.
>
> St?fan
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>
>
>  --
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From jni.soma at gmail.com  Wed Nov 20 08:01:41 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Thu, 21 Nov 2013 00:01:41 +1100
Subject: Fun with skimage
In-Reply-To: <CABDkGQnqmQiLjjQtoRcmASJumsuFaN9xiWWe8ufsni-uXZ6rMQ@mail.gmail.com>
References: <CABDkGQnqmQiLjjQtoRcmASJumsuFaN9xiWWe8ufsni-uXZ6rMQ@mail.gmail.com>
Message-ID: <CA+JHcKRxtuHXiqOzeJPHg0pXzR06KRzH67s1oK9wuqOjit5j1w@mail.gmail.com>

Haha it took me a while to realise that it was within a notebook!!! I was
like, looks pretty much identical to the viewer to me... =P

That's bloody awesome, can't wait to use it!

Juan.

PS: Brian, please look at my recent
PR<https://github.com/scikit-image/scikit-image/pull/810>for the
viewer to get output from overlays. Would be excellent to get the
same capability from this!


On Wed, Nov 20, 2013 at 9:16 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> How cool is this?
>
> ---------- Forwarded message ----------
> From: Brian Granger
> Date: Fri, Nov 1, 2013 at 11:43 PM
> Subject: Fun with skimage
>
> I am working on some demos of the new IPython widget stuff and wrote a
> simple skimage one. Thought you might find this interesting. Should be
> pretty trivial to re-write the skimage viewer/plugin stuff using
> this...
>
> Cheers,
>
> Brian
>
> --
> Brian E. Granger
> Cal Poly State University, San Luis Obispo
> bgranger at calpoly.edu and ellisonbg at gmail.com
>
> --
> 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
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From jni.soma at gmail.com  Wed Nov 20 08:19:16 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Thu, 21 Nov 2013 00:19:16 +1100
Subject: scikit-image paper
In-Reply-To: <903304904.43000.1384945069980.open-xchange@app04.ox.hosteurope.de>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com>
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 <CABDkGQnP3XzYOWPuoWCjZ7xwdjrvOEKK1ocx6wPgiUuLZBPDBA@mail.gmail.com>
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 <4D73B4CD-DE2B-41D1-8444-D0CFD6E6E0AB@demuc.de> <069149A0-AE51-481C-B140-96F6ED4C68A6@demuc.de>
 <1805755143.42688.1384944805739.open-xchange@app04> <903304904.43000.1384945069980.open-xchange@app04.ox.hosteurope.de>
Message-ID: <CA+JHcKSxjRJWZGZSLa3OQX=L+WvWK+FnQrfs0mMwVOd9zuq8=A@mail.gmail.com>

@stefanv, I've found a flaw in your structure:

[image: Inline image 1]

=P

Section 2 sounds to me like it would be made of examples, maybe merged with
3?

I think it's worth spending a bit of time on the actual outline (e.g.
bullet points on each section), before launching into writing, to avoid
redundancy. We can do this directly on the github template. For example, I
would add my chromosome finding example (with code) to the gallery/science
applications.

Speaking of development practices, I've recently noticed that there's a bit
of heterogeneity in the API, with some parts being object-oriented in style
and others (most) being functional, which is my preference. Do we want to
emphasise that this is the preferred style?

+1 for a roadmap section.

Juan.



On Wed, Nov 20, 2013 at 9:57 PM, Johannes Sch?nberger <jsch at demuc.de> wrote:

> > I was thinking around 4 to 5 pages or so?
>
> Probably also a question of funding and if the journal charges for
> excessive page lengths...?
>
> > Volunteering for sections: I will do the big picture overview
> > (introduction + motivation) for now.
> >
>
> I could do the Development practice and parts of the gallery?
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
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From aaaagrawal at gmail.com  Wed Nov 20 15:01:28 2013
From: aaaagrawal at gmail.com (Ankit Agrawal)
Date: Thu, 21 Nov 2013 01:31:28 +0530
Subject: Test coverage
In-Reply-To: <CABDkGQnZvbEgtJ9W7PWq68HDDPMFsc99TDAGXw_ZVQOVskJuZg@mail.gmail.com>
References: <CABDkGQnZvbEgtJ9W7PWq68HDDPMFsc99TDAGXw_ZVQOVskJuZg@mail.gmail.com>
Message-ID: <CAON2ciJMOovXf5JLNUnEopVBzUt7CvWeTOb4zys=iwGTZs+O2A@mail.gmail.com>

Hi Stefan,

      Can you elaborate briefly what the coverage percentage exactly
represents? Is it the fraction of API functions that have tests to cover
their back? Or something else?

Regards,
Ankit Agrawal,
Communication and Signal Processing,
IIT Bombay.


On Thu, Nov 21, 2013 at 12:15 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> Hello, everyone
>
> We now have automated test coverage for scikit-image:
>
> https://coveralls.io/r/scikit-image/scikit-image
>
> Most of the newer modules (those that went through rigorous PR
> review!) did pretty well, but we are still only at 82%.  If ever you
> find yourself with a bit of spare time on your hands, please hunt down
> some of these corner cases and write tests for them so that we can
> start making our way towards 100%.
>
> 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.
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From chintaksheth at gmail.com  Wed Nov 20 15:06:55 2013
From: chintaksheth at gmail.com (Chintak Sheth)
Date: Thu, 21 Nov 2013 01:36:55 +0530
Subject: Test coverage
In-Reply-To: <CAON2ciJMOovXf5JLNUnEopVBzUt7CvWeTOb4zys=iwGTZs+O2A@mail.gmail.com>
References: <CABDkGQnZvbEgtJ9W7PWq68HDDPMFsc99TDAGXw_ZVQOVskJuZg@mail.gmail.com>
	<CAON2ciJMOovXf5JLNUnEopVBzUt7CvWeTOb4zys=iwGTZs+O2A@mail.gmail.com>
Message-ID: <CAKAks=E7wbMG_ewE9LBQ5+urSYOGKA5V31sARgJLwtnyAydE_A@mail.gmail.com>

Hi Ankit

Yes, the number of function calls and the lines (?) that have tests for
them. Tests are for ensuring that all the lines of code that is written is
checked against test cases and are correct.

Chintak
On Nov 21, 2013 1:31 AM, "Ankit Agrawal" <aaaagrawal at gmail.com> wrote:

> Hi Stefan,
>
>       Can you elaborate briefly what the coverage percentage exactly
> represents? Is it the fraction of API functions that have tests to cover
> their back? Or something else?
>
> Regards,
> Ankit Agrawal,
> Communication and Signal Processing,
> IIT Bombay.
>
>
> On Thu, Nov 21, 2013 at 12:15 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:
>
>> Hello, everyone
>>
>> We now have automated test coverage for scikit-image:
>>
>> https://coveralls.io/r/scikit-image/scikit-image
>>
>> Most of the newer modules (those that went through rigorous PR
>> review!) did pretty well, but we are still only at 82%.  If ever you
>> find yourself with a bit of spare time on your hands, please hunt down
>> some of these corner cases and write tests for them so that we can
>> start making our way towards 100%.
>>
>> Thanks!
>> St?fan
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
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From stefan at sun.ac.za  Thu Nov 21 01:30:17 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 21 Nov 2013 08:30:17 +0200
Subject: scikit-image paper
In-Reply-To: <CAEym_HqMxaNb9KspKeC9KivcuQnFxw0bTqjxaWPut=G9bvt0DQ@mail.gmail.com>
References: <CA+JHcKRP=__zHNXa+ErKvQNdRWneZWCmO1OXj0PWk6we=QQ5Rw@mail.gmail.com>
 <CABDkGQkxusWuX=YFBb=PCBnvCM=wPD3tkiK03sXCRAg5yUK_kA@mail.gmail.com>
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 <CAEym_HqMxaNb9KspKeC9KivcuQnFxw0bTqjxaWPut=G9bvt0DQ@mail.gmail.com>
Message-ID: <CABDkGQnS51Zb=63QSHoz6U8=MYuVWML_PCnOomvrMn2gSdk1=w@mail.gmail.com>

On Thu, Nov 21, 2013 at 6:39 AM, Tony Yu <tsyu80 at gmail.com> wrote:
> Unfortunately, it's a no-go on mentioning the specific companies we've
> worked with, but its OK to say something like "Enthought, Inc uses
> scikit-image extensively in their consulting projects related to geophysics
> and microscopy".

That's great, thank you!  Could I use [1] as a reference?

St?fan

[1] Personal communications with Tony S Yu, <insert title> [or insert
other name here]


From jni.soma at gmail.com  Wed Nov 20 20:45:20 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Thu, 21 Nov 2013 12:45:20 +1100
Subject: Advice on improving a analysis on images of nanoparticles
In-Reply-To: <CAMHV+dDL9Gd-iLRhX-kqrxpJaja4uaTcOM--_w5DW4uu=j7qQw@mail.gmail.com>
References: <656876a4-8696-4f8a-b963-8ad42997db68@googlegroups.com>
 <CABDkGQ=Syt_z6UEYChpMo3F9GeuKnz9DWJtyfYG1MsWJNXskbw@mail.gmail.com>
 <f45c0b91-fd22-460c-b961-0bf05d7537bb@googlegroups.com> <CA+JHcKRE4Rr1QxqfhQy36W-BBfX0OVt4o+yxO8MF1ygQiob0vw@mail.gmail.com>
 <CAMHV+dDL9Gd-iLRhX-kqrxpJaja4uaTcOM--_w5DW4uu=j7qQw@mail.gmail.com>
Message-ID: <CA+JHcKT44YVStKuWk4CgmZ-enSX6QsP4=EX6B6LukaDri5nxBg@mail.gmail.com>

Hi Adam, more responses inline below. =)


On Thu, Nov 21, 2013 at 5:04 AM, Adam Hughes <hughesadam87 at gmail.com> wrote:
>
> I tried this but to share a link, it asks for the emails of the
> recipients.  You have used Dropbox to host a publicly accessible link?  If
> so, I will certainly start doing this, thanks.
>

The web interface is a bit wonky that way, but it's certainly possible,
it's called something like "copy share link". Then you get a URL that has a
random token embedded in it, which anyone with the link can open. In OSX,
you can just right-click > share dropbox link to have the link copied to
your clipboard. That's how I got this:
https://www.dropbox.com/s/ic04w1d0x98gnop/suspension%20bridge.jpg

=)

(You can add a "?dl=1" to the end to go straight to the file.)

Yes, that is the goal.  We had done a similar process ImageJ, but did
> thersholding manually.  I will read into the adaptive threshold a bit more.
>  We had hoped that some of these corrections, such as histogram
> equilization, would make the automatic threshold more likely to give
> correct results.
>

adaptive is automatic, but adjusts the threshold individually for each
pixel based on surrounding pixels. This should help e.g. for your image
warped_f2_b1, where the background is not uniform and no single threshold
may work for your entire image.

 Hmm I see.   I will still try it out, but thanks for the heads up.  I'll
> feel better now if it doesn't work well.
>

Great strategy. =D

We do have an a-prior knowledge actually.  What I've been doing already is
> putting a lower limit on particle size, with anything under it being noise.
>  After doing particle counts and binning the data, we fit it with a
> guassian, and optionally scale the data so that the guassian is centered
> around the mean partitcle diameter (which believe we know to about 3nm
> based on TEM imaging and indirect spectroscopic techniques).  Based on the
> size distribution, we try to further bin the data into small
> (dimers/trimers) and large aggregates.  For all the particles that are
> large enough to be considered an aggregate, we *assume *that they fill a
> half-sphere volume, and then we infer the true particle due to these
> aggregates.  It's pretty ad-hoc, but we certainly apply some knowledge of
> the expected particle size distributions.  I realize watershedding won't
> split up huge clumps, but maybe could assist in the dimers and trimers?  In
> any case, even if it doesn't significantly enhance our results, it would
> still be helpful to explore that option and I'll try it out.
>

That's the strategy I would suggest, but my point is that in some images,
such as your last one, you have more of a carpet of particles, and no
single particle will separate, so you will need knowledge from different
images. If you have that, no problem! =)

If you want to publish the result of your explorations as an IPython
notebook, we won't stop you. =D

Juan.
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From guillaume at mitotic-machine.org  Thu Nov 21 08:29:30 2013
From: guillaume at mitotic-machine.org (Guillaume Gay)
Date: Thu, 21 Nov 2013 14:29:30 +0100
Subject: Advice on improving a analysis on images of nanoparticles
In-Reply-To: <CA+JHcKQnFZ-da5v8JL-=JUS4dprf_bJmB2gPAki7mwtF1gzmYg@mail.gmail.com>
References: <656876a4-8696-4f8a-b963-8ad42997db68@googlegroups.com> <CABDkGQ=Syt_z6UEYChpMo3F9GeuKnz9DWJtyfYG1MsWJNXskbw@mail.gmail.com> <f45c0b91-fd22-460c-b961-0bf05d7537bb@googlegroups.com> <CA+JHcKRE4Rr1QxqfhQy36W-BBfX0OVt4o+yxO8MF1ygQiob0vw@mail.gmail.com> <9964284d-a6e4-439f-b32b-ef6f07d13992@googlegroups.com> <CA+JHcKSh3F_d4Ugzmn7VhEpXr-hdrkWfTEYYvq=wFX-TX8UTcA@mail.gmail.com> <CABDkGQmzMar1SCBaEvnWCiL8tqN0T=sMsrLEg3-fK3JmYBOwQA@mail.gmail.com> <528C9406.6080605@gmail.com> <CA+JHcKQnFZ-da5v8JL-=JUS4dprf_bJmB2gPAki7mwtF1gzmYg@mail.gmail.com>
Message-ID: <528E0ABA.5020902@mitotic-machine.org>

Hi,

This:
http://damcb.com/posts/segmenting-nuclei-with-skimage.html

links to a notebook where I expose what I'm doing for the segmentation. 
It won't be too much work to turn it into an example if needed.
Also feel free to comment on the post... As you'll see I kind of go 
around the 3D part by clustering strategies, more that by doing real 3D 
stuff...

Cheers.

Guillaume

PS: I'll try to have syntax highlighting in nikola soon, so that this 
code is more readable.

On 20/11/2013 13:55, Juan Nunez-Iglesias wrote:
> @Guillaume, please contribute the example ASAP because I'm struggling 
> with the exact same problem! =D In particular, the nuclei example from 
> pythonvision is not ideal because they gloss over a lot of parameter 
> tuning that is much easier to deal with in 2D than 3D. I'll be happy 
> to hear about your experience!
>
> Juan.
>
>
> On Wed, Nov 20, 2013 at 9:50 PM, Brickle Macho <bricklemacho at gmail.com 
> <mailto:bricklemacho at gmail.com>> wrote:
>
>     I can always adapt this example
>     (http://pythonvision.org/basic-tutorial) which uses pymorph and
>     mahotaos to counting nuceli and segments the image as a gallery
>     example for skimage (obviously acknowledging the original
>     tutorial).  Or is it bad form to copy/use another example.
>
>     Michael.
>     -- 
>
>
>
>
>     On 20/11/2013 2:13 pm, St?fan van der Walt wrote:
>>
>>     On 20 Nov 2013 07:33, "Juan Nunez-Iglesias" <jni.soma at gmail.com
>>     <mailto:jni.soma at gmail.com>> wrote:
>>     >
>>     > I'm guessing you are applying label() directly to your image,
>>     which is not the right way to use it.
>>
>>     Looks like isolating objects is a common problem. Time for
>>     another gallery example? We already have the coins, but perhaps
>>     something more realistic with some biological data.
>>
>>     St?fan
>>
>>     -- 
>>     You received this message because you are subscribed to the
>>     Google Groups "scikit-image" group.
>>     To unsubscribe from this group and stop receiving emails from it,
>>     send an email to scikit-image+unsubscribe at googlegroups.com
>>     <mailto:scikit-image+unsubscribe at googlegroups.com>.
>>     For more options, visit https://groups.google.com/groups/opt_out.
>
>     -- 
>     You received this message because you are subscribed to the Google
>     Groups "scikit-image" group.
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>
>
> -- 
> You received this message because you are subscribed to the Google 
> Groups "scikit-image" group.
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From jni.soma at gmail.com  Wed Nov 20 23:28:57 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Thu, 21 Nov 2013 15:28:57 +1100
Subject: Fwd: Fun with skimage
In-Reply-To: <b5152afe-02f4-4fce-abec-d335c9e265c7@googlegroups.com>
References: <CABDkGQnqmQiLjjQtoRcmASJumsuFaN9xiWWe8ufsni-uXZ6rMQ@mail.gmail.com>
 <528CBEF3.1010901@sciunto.org> <b5152afe-02f4-4fce-abec-d335c9e265c7@googlegroups.com>
Message-ID: <CA+JHcKSde-K_t1JxGerdR0B6LdxppmsM0Oq8BL5VHibAsq+83w@mail.gmail.com>

On Thu, Nov 21, 2013 at 12:30 PM, Marianne Corvellec <
marianne.corvellec at ens-lyon.org> wrote:

> Maybe we could add a "Fun" subsection to the draft structure under
> "Purpose" (scikit-image paper)... :p
>
> I think the matplotlib people mentioned the most popular part of the
> matplotlib gallery was the XKCD-stylification of plots...  I quite like
> that.
>

+1! Maybe that embedded face detection example could go in there. =)
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From silvertrumpet999 at gmail.com  Thu Nov 21 18:42:21 2013
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Thu, 21 Nov 2013 15:42:21 -0800 (PST)
Subject: Fwd: Fun with skimage
In-Reply-To: <CA+JHcKSde-K_t1JxGerdR0B6LdxppmsM0Oq8BL5VHibAsq+83w@mail.gmail.com>
References: <CABDkGQnqmQiLjjQtoRcmASJumsuFaN9xiWWe8ufsni-uXZ6rMQ@mail.gmail.com>
 <528CBEF3.1010901@sciunto.org> <b5152afe-02f4-4fce-abec-d335c9e265c7@googlegroups.com>
 <CA+JHcKSde-K_t1JxGerdR0B6LdxppmsM0Oq8BL5VHibAsq+83w@mail.gmail.com>
Message-ID: <88f48aef-1dce-4188-a669-b35bd21ec6bd@googlegroups.com>

If we want popular exposure, stuff like 

   - Small snippets that can create Instagram-like filters in a few lines.
   - Fiddling with transforms to yield some interesting effects.
   - Perhaps combination face detection + transforms?

would probably track quite well.

On Wednesday, November 20, 2013 10:28:57 PM UTC-6, Juan Nunez-Iglesias 
wrote:
>
> On Thu, Nov 21, 2013 at 12:30 PM, Marianne Corvellec <
> marianne.... at ens-lyon.org <javascript:>> wrote:
>
>> Maybe we could add a "Fun" subsection to the draft structure under 
>> "Purpose" (scikit-image paper)... :p
>>
>> I think the matplotlib people mentioned the most popular part of the 
>> matplotlib gallery was the XKCD-stylification of plots...  I quite like 
>> that.
>>
>
> +1! Maybe that embedded face detection example could go in there. =)
>
>
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From hughesadam87 at gmail.com  Thu Nov 21 16:50:41 2013
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Thu, 21 Nov 2013 16:50:41 -0500
Subject: Advice on improving a analysis on images of nanoparticles
In-Reply-To: <528E0ABA.5020902@mitotic-machine.org>
References: <656876a4-8696-4f8a-b963-8ad42997db68@googlegroups.com>
	<CABDkGQ=Syt_z6UEYChpMo3F9GeuKnz9DWJtyfYG1MsWJNXskbw@mail.gmail.com>
	<f45c0b91-fd22-460c-b961-0bf05d7537bb@googlegroups.com>
	<CA+JHcKRE4Rr1QxqfhQy36W-BBfX0OVt4o+yxO8MF1ygQiob0vw@mail.gmail.com>
	<9964284d-a6e4-439f-b32b-ef6f07d13992@googlegroups.com>
	<CA+JHcKSh3F_d4Ugzmn7VhEpXr-hdrkWfTEYYvq=wFX-TX8UTcA@mail.gmail.com>
	<CABDkGQmzMar1SCBaEvnWCiL8tqN0T=sMsrLEg3-fK3JmYBOwQA@mail.gmail.com>
	<528C9406.6080605@gmail.com>
	<CA+JHcKQnFZ-da5v8JL-=JUS4dprf_bJmB2gPAki7mwtF1gzmYg@mail.gmail.com>
	<528E0ABA.5020902@mitotic-machine.org>
Message-ID: <CAMHV+dBEoA=5YZOc2YURR7P4A6jyiL_jVs2i+FqHiB1auHS1ag@mail.gmail.com>

Thanks Juan,

I will followup and get a NB or two returned to the list.


On Thu, Nov 21, 2013 at 8:29 AM, Guillaume Gay <
guillaume at mitotic-machine.org> wrote:

>  Hi,
>
> This:
> http://damcb.com/posts/segmenting-nuclei-with-skimage.html
>
> links to a notebook where I expose what I'm doing for the segmentation. It
> won't be too much work to turn it into an example if needed.
> Also feel free to comment on the post... As you'll see I kind of go around
> the 3D part by clustering strategies, more that by doing real 3D stuff...
>
> Cheers.
>
> Guillaume
>
> PS: I'll try to have syntax highlighting in nikola soon, so that this code
> is more readable.
>
>
> On 20/11/2013 13:55, Juan Nunez-Iglesias wrote:
>
> @Guillaume, please contribute the example ASAP because I'm struggling with
> the exact same problem! =D In particular, the nuclei example from
> pythonvision is not ideal because they gloss over a lot of parameter tuning
> that is much easier to deal with in 2D than 3D. I'll be happy to hear about
> your experience!
>
>  Juan.
>
>
> On Wed, Nov 20, 2013 at 9:50 PM, Brickle Macho <bricklemacho at gmail.com>wrote:
>
>>  I can always adapt this example (http://pythonvision.org/basic-tutorial)
>> which uses pymorph and mahotaos to counting nuceli and segments the image
>> as a gallery example for skimage (obviously acknowledging the original
>> tutorial).  Or is it bad form to copy/use another example.
>>
>> Michael.
>> --
>>
>>
>>
>>
>> On 20/11/2013 2:13 pm, St?fan van der Walt wrote:
>>
>> On 20 Nov 2013 07:33, "Juan Nunez-Iglesias" <jni.soma at gmail.com> wrote:
>> >
>> > I'm guessing you are applying label() directly to your image, which is
>> not the right way to use it.
>>
>> Looks like isolating objects is a common problem. Time for another
>> gallery example? We already have the coins, but perhaps something more
>> realistic with some biological data.
>>
>> St?fan
>>  --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>>
>>    --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>
>
>  --
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From hughesadam87 at gmail.com  Fri Nov 22 14:03:04 2013
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Fri, 22 Nov 2013 14:03:04 -0500
Subject: Advice on basic operations: zoom, crop and splice
Message-ID: <CAMHV+dBXfWk8Pd221ZC7S-gYtjbAHOR5=McAC1wGB3_L+s8Qjg@mail.gmail.com>

Hi everyone,

I'm used to working with big images of lots of particles.  In the notebook,
I'd like to be able to look at a full image, and then at a zoomed in region
of interest.  A few basic questions come to mind:

 Is there a zoom/crop function or preffered approach to basic manipulations
of zooming and cropping, or would I have to do this at the numpy or
matplotlib level?  I saw that there's a rectangle function that probably
would be useful here.  Does anyone have any examples or personal code built
for doing some of these common manipulations?   Ideally, I want to take the
fastest approach to:

1.  Selecting a rectangular region of interest (ROI).
2.  Cropping or zooming in on this region, and storing the ROI as its own
array/image.
3.  If possible, removing the ROI from the original image, and splicing the
original image back together.  If this is possible, that would be amazing.
 This would allow us to effectively cut out regions of our images that are
obviously contaminates.

Thanks.
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From silvertrumpet999 at gmail.com  Fri Nov 22 18:19:42 2013
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Fri, 22 Nov 2013 15:19:42 -0800 (PST)
Subject: Advice on basic operations: zoom, crop and splice
In-Reply-To: <CAMHV+dBXfWk8Pd221ZC7S-gYtjbAHOR5=McAC1wGB3_L+s8Qjg@mail.gmail.com>
References: <CAMHV+dBXfWk8Pd221ZC7S-gYtjbAHOR5=McAC1wGB3_L+s8Qjg@mail.gmail.com>
Message-ID: <94a3186a-11a5-4a95-938e-9c3ffc79baa2@googlegroups.com>

The backend functionality for all of this exists. I believe all of this can 
be accomplished with masks and NumPy array slicing.

The problem is that generally speaking, these are not interactive or GUI 
level operations. For example, if you want a zoomed-in ROI you can slice 
that region out and then `plt.imshow(sliced_img)`, but this requires 
manually entering the ROI corners in the slicing operation.

`skimage.viewer` includes a method to select and save rectangular regions 
interactively, and could probably be extended to allow clipping them out as 
well. However, the viewer requires PyQt or PySide and cannot be embedded in 
an iPython notebook.

Are you specifically looking for iPython notebook capable solutions? Or 
would a tweaked Viewer plugin be sufficient?

On Friday, November 22, 2013 1:03:04 PM UTC-6, Adam Hughes wrote:
>
> Hi everyone,
>
> I'm used to working with big images of lots of particles.  In the 
> notebook, I'd like to be able to look at a full image, and then at a zoomed 
> in region of interest.  A few basic questions come to mind:
>     
>  Is there a zoom/crop function or preffered approach to basic 
> manipulations of zooming and cropping, or would I have to do this at the 
> numpy or matplotlib level?  I saw that there's a rectangle function that 
> probably would be useful here.  Does anyone have any examples or personal 
> code built for doing some of these common manipulations?   Ideally, I want 
> to take the fastest approach to:
>
> 1.  Selecting a rectangular region of interest (ROI).
> 2.  Cropping or zooming in on this region, and storing the ROI as its own 
> array/image.
> 3.  If possible, removing the ROI from the original image, and splicing 
> the original image back together.  If this is possible, that would be 
> amazing.  This would allow us to effectively cut out regions of our images 
> that are obviously contaminates. 
>
> Thanks.
>
>
>
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From kmichael.aye at gmail.com  Fri Nov 22 21:00:07 2013
From: kmichael.aye at gmail.com (Michael Aye)
Date: Fri, 22 Nov 2013 18:00:07 -0800 (PST)
Subject: Kakadu JP2000 reader
In-Reply-To: <234fcb19-bb64-430a-bb72-1bce3f577035@googlegroups.com>
References: <b0ab6704-f2c2-48c9-9fde-d904f198c59c@googlegroups.com>
 <234fcb19-bb64-430a-bb72-1bce3f577035@googlegroups.com>
Message-ID: <c1058003-0f34-419d-aa48-7fb695053033@googlegroups.com>



On Sunday, November 17, 2013 8:57:56 PM UTC-8, Pierre Villeneuve wrote:
>
> What about the OpenJPEG library: http://www.openjpeg.org<http://www.google.com/url?q=http%3A%2F%2Fwww.openjpeg.org&sa=D&sntz=1&usg=AFQjCNER3CcvIjOEzdDID3pyA5Q1ks5LPw>. 
>  Could that be an alternative?


If this is the driver that is exposed by GDAL, it's far too slow and crashy 
for HiRISE images.
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From kmichael.aye at gmail.com  Sat Nov 23 00:34:48 2013
From: kmichael.aye at gmail.com (Michael Aye)
Date: Fri, 22 Nov 2013 21:34:48 -0800 (PST)
Subject: Test coverage
In-Reply-To: <CAKAks=E7wbMG_ewE9LBQ5+urSYOGKA5V31sARgJLwtnyAydE_A@mail.gmail.com>
References: <CABDkGQnZvbEgtJ9W7PWq68HDDPMFsc99TDAGXw_ZVQOVskJuZg@mail.gmail.com>
 <CAON2ciJMOovXf5JLNUnEopVBzUt7CvWeTOb4zys=iwGTZs+O2A@mail.gmail.com>
 <CAKAks=E7wbMG_ewE9LBQ5+urSYOGKA5V31sARgJLwtnyAydE_A@mail.gmail.com>
Message-ID: <bf204d55-ea53-4e7a-abd2-677897312b17@googlegroups.com>

I'd like to help here. Can somebody line out briefly how to find/identify 
uncovered code? Can this website generate a list and paths to the relevant 
code?

Cheers,
Michael

On Wednesday, November 20, 2013 12:06:55 PM UTC-8, Chintak Sheth wrote:
>
> Hi Ankit
>
> Yes, the number of function calls and the lines (?) that have tests for 
> them. Tests are for ensuring that all the lines of code that is written is 
> checked against test cases and are correct.
>
> Chintak
> On Nov 21, 2013 1:31 AM, "Ankit Agrawal" <aaaag... at gmail.com <javascript:>> 
> wrote:
>
>> Hi Stefan,
>>
>>       Can you elaborate briefly what the coverage percentage exactly 
>> represents? Is it the fraction of API functions that have tests to cover 
>> their back? Or something else?
>>
>> Regards, 
>> Ankit Agrawal,
>> Communication and Signal Processing,
>> IIT Bombay.
>>
>>
>> On Thu, Nov 21, 2013 at 12:15 AM, St?fan van der Walt <ste... at sun.ac.za<javascript:>
>> > wrote:
>>
>>> Hello, everyone
>>>
>>> We now have automated test coverage for scikit-image:
>>>
>>> https://coveralls.io/r/scikit-image/scikit-image<https://www.google.com/url?q=https%3A%2F%2Fcoveralls.io%2Fr%2Fscikit-image%2Fscikit-image&sa=D&sntz=1&usg=AFQjCNGspHczhppUHiAhoLNZ62ZEVcziJQ>
>>>
>>> Most of the newer modules (those that went through rigorous PR
>>> review!) did pretty well, but we are still only at 82%.  If ever you
>>> find yourself with a bit of spare time on your hands, please hunt down
>>> some of these corner cases and write tests for them so that we can
>>> start making our way towards 100%.
>>>
>>> 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/groups/opt_out.
>>>
>>
>>  -- 
>> You received this message because you are subscribed to the Google Groups 
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an 
>> email to scikit-image... at googlegroups.com <javascript:>.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>
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From stefan at sun.ac.za  Fri Nov 22 21:10:52 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sat, 23 Nov 2013 04:10:52 +0200
Subject: Kakadu JP2000 reader
In-Reply-To: <c1058003-0f34-419d-aa48-7fb695053033@googlegroups.com>
References: <b0ab6704-f2c2-48c9-9fde-d904f198c59c@googlegroups.com>
 <234fcb19-bb64-430a-bb72-1bce3f577035@googlegroups.com> <c1058003-0f34-419d-aa48-7fb695053033@googlegroups.com>
Message-ID: <CABDkGQnHWe2c333NN2s-6WMXXB6cU5=Ga94U2M9bpFU3Gv6pUg@mail.gmail.com>

On Sat, Nov 23, 2013 at 4:00 AM, Michael Aye <kmichael.aye at gmail.com> wrote:
> If this is the driver that is exposed by GDAL, it's far too slow and crashy
> for HiRISE images.

These images look like they're about 1GB in size.  Do you want to read
the entire image into memory?  How large would that NumPy array be?
Are you interested in only loading a specific portion of the image?

St?fan


From chintaksheth at gmail.com  Sat Nov 23 01:16:31 2013
From: chintaksheth at gmail.com (Chintak Sheth)
Date: Sat, 23 Nov 2013 11:46:31 +0530
Subject: Advice on basic operations: zoom, crop and splice
In-Reply-To: <CAMHV+dBXfWk8Pd221ZC7S-gYtjbAHOR5=McAC1wGB3_L+s8Qjg@mail.gmail.com>
References: <CAMHV+dBXfWk8Pd221ZC7S-gYtjbAHOR5=McAC1wGB3_L+s8Qjg@mail.gmail.com>
Message-ID: <CAKAks=Eo3NF+-Wg_tTy70XuzsUTHxGWEHh9EGTAn=rnba48xmA@mail.gmail.com>

Hi Adam

On Nov 23, 2013 12:33 AM, "Adam Hughes" <hughesadam87 at gmail.com> wrote:
>
> 3.  If possible, removing the ROI from the original image, and splicing
the original image back together.  If this is possible, that would be
amazing.  This would allow us to effectively cut out regions of our images
that are obviously contaminates.

Yes, this is possible. It is also known as Image Inpainting. There are two
algorithm implementations for the same, although they haven't yet been
merged.

Fast Marching Algorithm: (Fast, introduce some blurriness)
Here is the dev branch: https://github.com/chintak/scikit-image/tree/inpaint
PR for it: https://github.com/scikit-image/scikit-image/pull/663

Exemplar based Inpainting: (Slower, very accurate for repeating patterns,
reconstructs using sample image patches from the image)
Dev branch: https://github.com/chintak/scikit-image/tree/inpaint_exemplar
PR: https://github.com/scikit-image/scikit-image/pull/706

For the first one, a skimage.viewer plugin is also
there: ``viewer_examples/plugins/demo_inpaint.py``

Regarding your first 2 points, Josh shed some light on how you can do this
using `skim age.viewer`. An interesting thread regarding interactive image
manipulation in iPython notebook came up lately which might interest you:
https://groups.google.com/forum/#!topic/scikit-image/vrPzanJ42rs. I'm not
sure if you can select an ROI in the image, but that'd be worth checking
out. If we can't directly select a rectangular region then probably
defining 4 sliders in the widget: left, right, top, bottom, and moving them
around to select the ROI.

Chintak
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From stefan at sun.ac.za  Sat Nov 23 05:04:19 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sat, 23 Nov 2013 12:04:19 +0200
Subject: Advice on basic operations: zoom, crop and splice
In-Reply-To: <CAKAks=Eo3NF+-Wg_tTy70XuzsUTHxGWEHh9EGTAn=rnba48xmA@mail.gmail.com>
References: <CAMHV+dBXfWk8Pd221ZC7S-gYtjbAHOR5=McAC1wGB3_L+s8Qjg@mail.gmail.com>
 <CAKAks=Eo3NF+-Wg_tTy70XuzsUTHxGWEHh9EGTAn=rnba48xmA@mail.gmail.com>
Message-ID: <CABDkGQmhDc9nQQopw34tFt9o4Oz-KNFMPBhU=erQiM71p9433Q@mail.gmail.com>

On Sat, Nov 23, 2013 at 8:16 AM, Chintak Sheth <chintaksheth at gmail.com> wrote:
> An interesting thread regarding interactive image
> manipulation in iPython notebook came up lately which might interest you:
> https://groups.google.com/forum/#!topic/scikit-image/vrPzanJ42rs.

I spoke to Brian Granger about the possibility of building the viewer
described above in IPython.  Here is his response:

"""
Definitely possible - shouldn't be too bad.  Here is a rough sketch:

* You can define a Python object with traitlets.
* You get a JavaScript object that has the same exact attributes as
the Python object - we keep those attributes completely synchronized
on the two sides automatically. When the JavaScript side (through UI
control changes) changes the attributes we sync the python side and
all of the traitlets callbacks will fire. When the Python side makes
changes, the JS side is updated and the UI will refresh. The time
scale for all of this is super fast - at least running on localhost.
* You can then create arbitrary "view" code for the JavaScript side.
You get a div to put the UI in and can do whatever you want.
* The JavaScript and Python objects also have methods for sending
arbitrary JSON messages at any time, so you can stream data, etc.

To get familiar with how it all works, have a look at the notebooks in
this branch:

https://github.com/jdfreder/ipython/tree/widget-msg/examples/widgets

They show how to develop new widgets from scratch as well as how all
of the existing ones can be used.
"""

I am really keen to try this out next week, although I may have to up
my Javascript-foo a bit.

St?fan


From stefan at sun.ac.za  Sat Nov 23 05:13:39 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sat, 23 Nov 2013 12:13:39 +0200
Subject: Test coverage
In-Reply-To: <bf204d55-ea53-4e7a-abd2-677897312b17@googlegroups.com>
References: <CABDkGQnZvbEgtJ9W7PWq68HDDPMFsc99TDAGXw_ZVQOVskJuZg@mail.gmail.com>
 <CAON2ciJMOovXf5JLNUnEopVBzUt7CvWeTOb4zys=iwGTZs+O2A@mail.gmail.com>
 <CAKAks=E7wbMG_ewE9LBQ5+urSYOGKA5V31sARgJLwtnyAydE_A@mail.gmail.com> <bf204d55-ea53-4e7a-abd2-677897312b17@googlegroups.com>
Message-ID: <CABDkGQmv6JsjaF_TLfUm34Mfq9==UxZfxkvrQg-Vz8-RXT5wFw@mail.gmail.com>

Hi Michael

On Sat, Nov 23, 2013 at 7:34 AM, Michael Aye <kmichael.aye at gmail.com> wrote:
> I'd like to help here. Can somebody line out briefly how to find/identify
> uncovered code? Can this website generate a list and paths to the relevant
> code?

There are a few things to be done:

1. Our website [1] needs to be updated with a Coveralls badge.
2. The development guidelines [2] need to indicate that a person
should check the coverage report there.
3. Coverage should be improved based on the report at [3].

Thanks for helping out!

St?fan

[1]: https://github.com/scikit-image/scikit-image-web
[2]: https://github.com/scikit-image/scikit-image/blob/master/CONTRIBUTING.txt#L136
[3]: https://coveralls.io/r/scikit-image/scikit-image


From m.p.romaniuk at gmail.com  Sat Nov 23 16:28:17 2013
From: m.p.romaniuk at gmail.com (Michal Romaniuk)
Date: Sat, 23 Nov 2013 13:28:17 -0800 (PST)
Subject: SLICO
Message-ID: <717ead1b-0435-462c-83e5-45f534b5a886@googlegroups.com>

Hi everyone,

I'm wondering if anyone is working on implementing SLICO, the more recent 
version of SLIC which doesn't require the compactness parameter?

Michal
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From jni.soma at gmail.com  Sat Nov 23 20:17:33 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Sun, 24 Nov 2013 12:17:33 +1100
Subject: SLICO
In-Reply-To: <717ead1b-0435-462c-83e5-45f534b5a886@googlegroups.com>
References: <717ead1b-0435-462c-83e5-45f534b5a886@googlegroups.com>
Message-ID: <CA+JHcKSEhSrMqy=DuTKbqPfitO+GrueCdhgAsnfD1GaTZRz=Qg@mail.gmail.com>

Hi Michal,

(You have to join the list first to be able to post without moderation.
Otherwise, one of the list moderators has to approve your message. I've
approved this one and closed your follow-up.)

I saw SLICO but haven't had time to dive in their code and port it to
skimage. Pull requests with implementations are always welcome. =) As far
as I know, no one else is working on this at the moment.

Juan.



On Sun, Nov 24, 2013 at 8:28 AM, Michal Romaniuk <m.p.romaniuk at gmail.com>wrote:

> Hi everyone,
>
> I'm wondering if anyone is working on implementing SLICO, the more recent
> version of SLIC which doesn't require the compactness parameter?
>
> Michal
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
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>
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From kevin.keraudren at googlemail.com  Sun Nov 24 17:45:53 2013
From: kevin.keraudren at googlemail.com (Kevin Keraudren)
Date: Sun, 24 Nov 2013 22:45:53 +0000
Subject: Template matching for 3D image
Message-ID: <529281A1.6020707@googlemail.com>

Hi,

I adapted the 2D code from:
https://github.com/scikit-image/scikit-image/blob/master/skimage/feature/template.py

to 3D:
https://github.com/kevin-keraudren/template-matching-3d

I use it in my work, I have manual segmentation experts performed on 
cropped data, and I need the template matching to realign the cropped 
image with the full image (3D medical images). So thanks a lot for the 
2D code!

If you think it is of use, I could fork scikit-image and add the 3D 
version next to the 2D version.

I understand there should be as little duplicated code as necessary, but 
shall I create a function match_template3D or shall match_template check 
the shape of the input image?

Kind regards,

Kevin






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From evelzw at gmail.com  Mon Nov 25 02:49:04 2013
From: evelzw at gmail.com (Evelyn Liu)
Date: Sun, 24 Nov 2013 23:49:04 -0800 (PST)
Subject: Advice on improving a analysis on images of nanoparticles
In-Reply-To: <CA+JHcKSh3F_d4Ugzmn7VhEpXr-hdrkWfTEYYvq=wFX-TX8UTcA@mail.gmail.com>
References: <656876a4-8696-4f8a-b963-8ad42997db68@googlegroups.com>
 <CABDkGQ=Syt_z6UEYChpMo3F9GeuKnz9DWJtyfYG1MsWJNXskbw@mail.gmail.com>
 <f45c0b91-fd22-460c-b961-0bf05d7537bb@googlegroups.com> <CA+JHcKRE4Rr1QxqfhQy36W-BBfX0OVt4o+yxO8MF1ygQiob0vw@mail.gmail.com>
 <9964284d-a6e4-439f-b32b-ef6f07d13992@googlegroups.com>
 <CA+JHcKSh3F_d4Ugzmn7VhEpXr-hdrkWfTEYYvq=wFX-TX8UTcA@mail.gmail.com>
Message-ID: <c9bc61ba-0ba2-4cbc-954e-8dbbc399b48f@googlegroups.com>

Thanks for your helpful response Juan. But I have the issue with choosing 
parameter for threshold_adaptive.. Some of my images have uneven contrast, 
like the lower part of image has darker background compared to the upper 
part. So if the threshold is proper for the upper part, some 
neighboring particles will be taken as a cluster even they are individual. 
I tried different diam, but none of them leads to good threshold in terms 
of the full image. Is there any other thresholding methods for those uneven 
contrast images? 

I also tried the edge operator *filter.sobel *and it looks good for drawing 
up particles' edges(the attached image). I wonder if i can fill these 
circles up to get the thresholding image?  I tried *ndimage.**binary_fill_holes 
*but it gives me either blank or total total black pic..

<https://lh6.googleusercontent.com/-89xSmEmy7Wc/UpL_fNubbSI/AAAAAAAAAB8/0N-N1cf-374/s1600/edge_invert_wraped1.png>



On Wednesday, November 20, 2013 12:33:19 AM UTC-5, Juan Nunez-Iglesias 
wrote:
>
> Hi Evelyn,
>
> I'm guessing you are applying label() directly to your image, which is not 
> the right way to use it. label() connects all neighboring *nonzero*points together. Since images are rarely zero (rather than some very small 
> intensity value), you are simply connecting all the pixels of your image 
> together into one label.
>
> The correct way to do this is to threshold your image, eg using:
> http://scikit-image.org/docs/dev/api/skimage.filter.html#threshold-adaptive<http://www.google.com/url?q=http%3A%2F%2Fscikit-image.org%2Fdocs%2Fdev%2Fapi%2Fskimage.filter.html%23threshold-adaptive&sa=D&sntz=1&usg=AFQjCNG3r7Y-dZ9r6IBjOojwF1eoEgwp1Q>
>
> So:
>
> >>> from skimage.filter import threshold_adaptive
> >>> from scipy import ndimage as nd
> >>> diam = 51
> >>> # "51" is a guess, you might have to fiddle with this parameter.
> >>> image_t = (image > threshold_adaptive(image, diam))
> >>> image_labeled = nd.label(image_t)[0]
> >>> particle_sizes = np.bincount(image_labeled.ravel())[1:]
> >>> # [1:] is to select only the foreground labels
>
> Hope this helps!
>
> Juan.
>
>
>
> On Wed, Nov 20, 2013 at 3:45 PM, Evelyn Liu <eve... at gmail.com<javascript:>
> > wrote:
>
>> Hi Juan,
>>
>> On Tuesday, November 19, 2013 9:39:47 PM UTC-5, Juan Nunez-Iglesias wrote:
>>>
>>> Is the goal only to count particles? In that case, I think a local 
>>> thresholding (threshold_adaptive) would work on all these images. Then, 
>>> just do a labelling (scipy.ndimage.label) and draw a histogram of particle 
>>> sizes. You'll get a sharp peak around the true particle size, with bigger 
>>> peaks for clumps
>>>
>>
>> I'd like to use scikit to plot the size distribution histogram of 
>> particles in an image, which is similar with Adam's. I tried 
>> scipy.ndimage.measurements.label(image), which I thought would give an 
>> array about particle sizes. However, the output array is with all 1, 
>> obviously nothing about size. I must get something wrong...So which 
>> function should i call for the size distribution? Thanks Juan!
>>
>>
>>  -- 
>> You received this message because you are subscribed to the Google Groups 
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an 
>> email to scikit-image... at googlegroups.com <javascript:>.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>
>
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From jsch at demuc.de  Sun Nov 24 18:41:44 2013
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Mon, 25 Nov 2013 00:41:44 +0100
Subject: Template matching for 3D image
In-Reply-To: <529281A1.6020707@googlemail.com>
References: <529281A1.6020707@googlemail.com>
Message-ID: <1A7BE6BF-A6AA-4D9D-930D-E7BF03311B1F@demuc.de>

Support for 3D images would be great!

Imo checking for 3D images in the same function is the best option.

Johannes

Am 24.11.2013 um 23:45 schrieb Kevin Keraudren <kevin.keraudren at googlemail.com>:

> Hi,
> 
> I adapted the 2D code from:
> https://github.com/scikit-image/scikit-image/blob/master/skimage/feature/template.py
> 
> to 3D:
> https://github.com/kevin-keraudren/template-matching-3d
> 
> I use it in my work, I have manual segmentation experts performed on cropped data, and I need the template matching to realign the cropped image with the full image (3D medical images). So thanks a lot for the 2D code!
> 
> If you think it is of use, I could fork scikit-image and add the 3D version next to the 2D version.
> 
> I understand there should be as little duplicated code as necessary, but shall I create a function match_template3D or shall match_template check the shape of the input image?
> 
> Kind regards,
> 
> Kevin
> 
> 
> 
> 
> 
> 
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.



From guillaume at mitotic-machine.org  Mon Nov 25 03:27:17 2013
From: guillaume at mitotic-machine.org (Guillaume Gay)
Date: Mon, 25 Nov 2013 09:27:17 +0100
Subject: Advice on improving a analysis on images of nanoparticles
In-Reply-To: <c9bc61ba-0ba2-4cbc-954e-8dbbc399b48f@googlegroups.com>
References: <656876a4-8696-4f8a-b963-8ad42997db68@googlegroups.com> <CABDkGQ=Syt_z6UEYChpMo3F9GeuKnz9DWJtyfYG1MsWJNXskbw@mail.gmail.com> <f45c0b91-fd22-460c-b961-0bf05d7537bb@googlegroups.com> <CA+JHcKRE4Rr1QxqfhQy36W-BBfX0OVt4o+yxO8MF1ygQiob0vw@mail.gmail.com> <9964284d-a6e4-439f-b32b-ef6f07d13992@googlegroups.com> <CA+JHcKSh3F_d4Ugzmn7VhEpXr-hdrkWfTEYYvq=wFX-TX8UTcA@mail.gmail.com> <c9bc61ba-0ba2-4cbc-954e-8dbbc399b48f@googlegroups.com>
Message-ID: <529309E5.8010403@mitotic-machine.org>

For the uneven background issue, you can always filter out the low 
frequency parts of the image. You can do this in Fourrier space, or just 
subtract a Gaussian filtered version of the image:

|from  skimageimport  img_as_float
from  scipyimport  ndimage

def  preprocess_highpass(image, filter_width=100):
     '''Emulates a highpass filter by subtracted a smoothed version
     of the image from the image.

     Parameters:
     ----------------
     image: a ndarray
     filter_width: an int, should be much bigger than the relevant features in the image,
         and about the scale of the background variations

     Returns:
     -----------
     f_image: ndarray with the same shape as the input image, with float dtype, the filtered image,
         with minimum at 0.
     '''

     image = img_as_float(image)
     lowpass = ndimage.gaussian_filter(image, filter_width)
     f_image = image - lowpass
     f_image -= f_image.min()
     return  f_image|

On 25/11/2013 08:49, Evelyn Liu wrote:

> Thanks for your helpful response Juan. But I have the issue with 
> choosing parameter for threshold_adaptive.. Some of my images have 
> uneven contrast, like the lower part of image has darker background 
> compared to the upper part. So if the threshold is proper for the 
> upper part, some neighboring particles will be taken as a cluster even 
> they are individual. I tried different diam, but none of them leads to 
> good threshold in terms of the full image. Is there any other 
> thresholding methods for those uneven contrast images?
>
> I also tried the edge operator /filter.sobel /and it looks good for 
> drawing up particles' edges(the attached image). I wonder if i can 
> fill these circles up to get the thresholding image?  I tried 
> /ndimage.//binary_fill_holes /but it gives me either blank or total 
> total black pic..
>
> <https://lh6.googleusercontent.com/-89xSmEmy7Wc/UpL_fNubbSI/AAAAAAAAAB8/0N-N1cf-374/s1600/edge_invert_wraped1.png>
>
>
>
>
> On Wednesday, November 20, 2013 12:33:19 AM UTC-5, Juan Nunez-Iglesias 
> wrote:
>
>     Hi Evelyn,
>
>     I'm guessing you are applying label() directly to your image,
>     which is not the right way to use it. label() connects all
>     neighboring *nonzero* points together. Since images are rarely
>     zero (rather than some very small intensity value), you are simply
>     connecting all the pixels of your image together into one label.
>
>     The correct way to do this is to threshold your image, eg using:
>     http://scikit-image.org/docs/dev/api/skimage.filter.html#threshold-adaptive
>     <http://www.google.com/url?q=http%3A%2F%2Fscikit-image.org%2Fdocs%2Fdev%2Fapi%2Fskimage.filter.html%23threshold-adaptive&sa=D&sntz=1&usg=AFQjCNG3r7Y-dZ9r6IBjOojwF1eoEgwp1Q>
>
>     So:
>
>     >>> from skimage.filter import threshold_adaptive
>     >>> from scipy import ndimage as nd
>     >>> diam = 51
>     >>> # "51" is a guess, you might have to fiddle with this parameter.
>     >>> image_t = (image > threshold_adaptive(image, diam))
>     >>> image_labeled = nd.label(image_t)[0]
>     >>> particle_sizes = np.bincount(image_labeled.ravel())[1:]
>     >>> # [1:] is to select only the foreground labels
>
>     Hope this helps!
>
>     Juan.
>
>
>
>     On Wed, Nov 20, 2013 at 3:45 PM, Evelyn Liu <eve... at gmail.com
>     <javascript:>> wrote:
>
>         Hi Juan,
>
>         On Tuesday, November 19, 2013 9:39:47 PM UTC-5, Juan
>         Nunez-Iglesias wrote:
>
>             Is the goal only to count particles? In that case, I think
>             a local thresholding (threshold_adaptive) would work on
>             all these images. Then, just do a labelling
>             (scipy.ndimage.label) and draw a histogram of particle
>             sizes. You'll get a sharp peak around the true particle
>             size, with bigger peaks for clumps
>
>
>         I'd like to use scikit to plot the size distribution histogram
>         of particles in an image, which is similar with Adam's. I
>         tried scipy.ndimage.measurements.label(image), which I thought
>         would give an array about particle sizes. However, the output
>         array is with all 1, obviously nothing about size. I must get
>         something wrong...So which function should i call for the size
>         distribution? Thanks Juan!
>
>
>         -- 
>         You received this message because you are subscribed to the
>         Google Groups "scikit-image" group.
>         To unsubscribe from this group and stop receiving emails from
>         it, send an email to scikit-image... at googlegroups.com
>         <javascript:>.
>         For more options, visit
>         https://groups.google.com/groups/opt_out
>         <https://groups.google.com/groups/opt_out>.
>
>
> -- 
> You received this message because you are subscribed to the Google 
> Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send 
> an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.

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From m.p.romaniuk at gmail.com  Mon Nov 25 13:25:44 2013
From: m.p.romaniuk at gmail.com (Michal Romaniuk)
Date: Mon, 25 Nov 2013 10:25:44 -0800 (PST)
Subject: SLICO
In-Reply-To: <CA+JHcKSEhSrMqy=DuTKbqPfitO+GrueCdhgAsnfD1GaTZRz=Qg@mail.gmail.com>
References: <717ead1b-0435-462c-83e5-45f534b5a886@googlegroups.com>
 <CA+JHcKSEhSrMqy=DuTKbqPfitO+GrueCdhgAsnfD1GaTZRz=Qg@mail.gmail.com>
Message-ID: <4a9d8a9d-dae6-4083-81c9-fc6fcee859a5@googlegroups.com>

Hi Juan,

I'll see what I can do about SLICO, although I might need some help with 
Cython.

I also noticed that the scikit-image version doesn't do the seed 
perturbation step in preprocessing, and doesn't seem to do the connected 
components step in post-processing. Was there any reason for omitting them?

Michal

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From pierre.villeneuve at gmail.com  Mon Nov 25 13:27:39 2013
From: pierre.villeneuve at gmail.com (Pierre Villeneuve)
Date: Mon, 25 Nov 2013 10:27:39 -0800 (PST)
Subject: Kakadu JP2000 reader
In-Reply-To: <c1058003-0f34-419d-aa48-7fb695053033@googlegroups.com>
References: <b0ab6704-f2c2-48c9-9fde-d904f198c59c@googlegroups.com>
 <234fcb19-bb64-430a-bb72-1bce3f577035@googlegroups.com>
 <c1058003-0f34-419d-aa48-7fb695053033@googlegroups.com>
Message-ID: <256a0354-56f9-4298-8389-1944ab102eb0@googlegroups.com>

It looks to me from this link http://www.gdal.org/frmt_jp2kak.html that 
GDAL uses Kakadu, not OpenJPEG.

On Friday, November 22, 2013 6:00:07 PM UTC-8, Michael Aye wrote:
>
>
>
> On Sunday, November 17, 2013 8:57:56 PM UTC-8, Pierre Villeneuve wrote:
>>
>> What about the OpenJPEG library: http://www.openjpeg.org<http://www.google.com/url?q=http%3A%2F%2Fwww.openjpeg.org&sa=D&sntz=1&usg=AFQjCNER3CcvIjOEzdDID3pyA5Q1ks5LPw>. 
>>  Could that be an alternative?
>
>
> If this is the driver that is exposed by GDAL, it's far too slow and 
> crashy for HiRISE images.
>
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From kevin.keraudren at googlemail.com  Mon Nov 25 06:57:26 2013
From: kevin.keraudren at googlemail.com (Kevin Keraudren)
Date: Mon, 25 Nov 2013 11:57:26 +0000
Subject: Template matching for 3D image
In-Reply-To: <CA+JHcKQFwV-A_4ky_uZZTGpo2UuZPf5z8GDTCq3Gv_21hCM6ug@mail.gmail.com>
References: <529281A1.6020707@googlemail.com> <1A7BE6BF-A6AA-4D9D-930D-E7BF03311B1F@demuc.de> <CA+JHcKQFwV-A_4ky_uZZTGpo2UuZPf5z8GDTCq3Gv_21hCM6ug@mail.gmail.com>
Message-ID: <52933B26.5090907@googlemail.com>

I had a look at the SLIC code and I'll try this approach then, replace 
the 2D code by 3D code and consider 2D images as special cases.
Cheers,
Kevin


Le 25/11/2013 04:02, Juan Nunez-Iglesias a ??????crit :
> On Mon, Nov 25, 2013 at 10:41 AM, Johannes Sch??????nberger <jsch at demuc.de 
> <mailto:jsch at demuc.de>> wrote:
>
>     Imo checking for 3D images in the same function is the best option.
>
>
> +1
>
> Sorry if I betray my ignorance about template matching, but can the 2D 
> case not be considered a special case of the 3D with z=1? In other 
> code (such as SLIC), when we get a 2D image we simply go:
>
> im = im[np.newaxis, ...]
>
> and feed that to the 3D code. Can the same be done for template matching?
>
> Thanks for this, Kevin!
>
> Juan.
>
> -- 
> You received this message because you are subscribed to the Google 
> Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send 
> an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.

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From kmichael.aye at gmail.com  Mon Nov 25 17:15:39 2013
From: kmichael.aye at gmail.com (Michael Aye)
Date: Mon, 25 Nov 2013 14:15:39 -0800 (PST)
Subject: Kakadu JP2000 reader
In-Reply-To: <256a0354-56f9-4298-8389-1944ab102eb0@googlegroups.com>
References: <b0ab6704-f2c2-48c9-9fde-d904f198c59c@googlegroups.com>
 <234fcb19-bb64-430a-bb72-1bce3f577035@googlegroups.com>
 <c1058003-0f34-419d-aa48-7fb695053033@googlegroups.com>
 <256a0354-56f9-4298-8389-1944ab102eb0@googlegroups.com>
Message-ID: <6a02140d-bd0a-4fe3-9105-2102c1e239d9@googlegroups.com>

Read on, it says:

"However, it is not free, and so normally builds of GDAL from source will 
not include support for this driver unless the builder purchases a license 
for the library and configures accordingly. GDAL includes another JPEG2000 
driver <http://www.gdal.org/frmt_jpeg2000.html> based on the free JasPer 
library."


On Monday, November 25, 2013 10:27:39 AM UTC-8, Pierre Villeneuve wrote:
>
> It looks to me from this link http://www.gdal.org/frmt_jp2kak.html<http://www.google.com/url?q=http%3A%2F%2Fwww.gdal.org%2Ffrmt_jp2kak.html&sa=D&sntz=1&usg=AFQjCNFhmMQ2uUwufLDGTt3oLA9HOmpUyw>that GDAL uses Kakadu, not OpenJPEG.
>
> On Friday, November 22, 2013 6:00:07 PM UTC-8, Michael Aye wrote:
>>
>>
>>
>> On Sunday, November 17, 2013 8:57:56 PM UTC-8, Pierre Villeneuve wrote:
>>>
>>> What about the OpenJPEG library: http://www.openjpeg.org<http://www.google.com/url?q=http%3A%2F%2Fwww.openjpeg.org&sa=D&sntz=1&usg=AFQjCNER3CcvIjOEzdDID3pyA5Q1ks5LPw>. 
>>>  Could that be an alternative?
>>
>>
>> If this is the driver that is exposed by GDAL, it's far too slow and 
>> crashy for HiRISE images.
>>
>
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From kmichael.aye at gmail.com  Mon Nov 25 17:16:30 2013
From: kmichael.aye at gmail.com (Michael Aye)
Date: Mon, 25 Nov 2013 14:16:30 -0800 (PST)
Subject: Kakadu JP2000 reader
In-Reply-To: <6a02140d-bd0a-4fe3-9105-2102c1e239d9@googlegroups.com>
References: <b0ab6704-f2c2-48c9-9fde-d904f198c59c@googlegroups.com>
 <234fcb19-bb64-430a-bb72-1bce3f577035@googlegroups.com>
 <c1058003-0f34-419d-aa48-7fb695053033@googlegroups.com>
 <256a0354-56f9-4298-8389-1944ab102eb0@googlegroups.com>
 <6a02140d-bd0a-4fe3-9105-2102c1e239d9@googlegroups.com>
Message-ID: <5e741745-e070-4390-972f-ac9f197e4339@googlegroups.com>

In general, the GDAL framework supports more than 1 driver per image format 
and uses whatever is first in the loaded queue, I believe.


On Monday, November 25, 2013 2:15:39 PM UTC-8, Michael Aye wrote:
>
> Read on, it says:
>
> "However, it is not free, and so normally builds of GDAL from source will 
> not include support for this driver unless the builder purchases a license 
> for the library and configures accordingly. GDAL includes another 
> JPEG2000 driver<http://www.google.com/url?q=http%3A%2F%2Fwww.gdal.org%2Ffrmt_jpeg2000.html&sa=D&sntz=1&usg=AFQjCNHdAkE6m_v28BbHHbf3BW0aMpjBSg> based 
> on the free JasPer library."
>
>
> On Monday, November 25, 2013 10:27:39 AM UTC-8, Pierre Villeneuve wrote:
>>
>> It looks to me from this link http://www.gdal.org/frmt_jp2kak.html<http://www.google.com/url?q=http%3A%2F%2Fwww.gdal.org%2Ffrmt_jp2kak.html&sa=D&sntz=1&usg=AFQjCNFhmMQ2uUwufLDGTt3oLA9HOmpUyw>that GDAL uses Kakadu, not OpenJPEG.
>>
>> On Friday, November 22, 2013 6:00:07 PM UTC-8, Michael Aye wrote:
>>>
>>>
>>>
>>> On Sunday, November 17, 2013 8:57:56 PM UTC-8, Pierre Villeneuve wrote:
>>>>
>>>> What about the OpenJPEG library: http://www.openjpeg.org<http://www.google.com/url?q=http%3A%2F%2Fwww.openjpeg.org&sa=D&sntz=1&usg=AFQjCNER3CcvIjOEzdDID3pyA5Q1ks5LPw>. 
>>>>  Could that be an alternative?
>>>
>>>
>>> If this is the driver that is exposed by GDAL, it's far too slow and 
>>> crashy for HiRISE images.
>>>
>>
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From kmichael.aye at gmail.com  Mon Nov 25 17:24:18 2013
From: kmichael.aye at gmail.com (Michael Aye)
Date: Mon, 25 Nov 2013 14:24:18 -0800 (PST)
Subject: stupid question: Why is imshow in io module?
Message-ID: <d73961e7-44a5-4240-8c36-0cddfe61513a@googlegroups.com>

I just stumbled over the 3 lines of code on scikits' title page:


from skimage import data, io, filter
image = data.coins() # or any NumPy array!
edges = filter.sobel(image)
io.imshow(edges)

and wondered: Isn't it a bit funny to require an I/O module to show an 
image that is already loaded?

My apologies if that has been discussed before.

Michael

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From kmichael.aye at gmail.com  Mon Nov 25 17:50:44 2013
From: kmichael.aye at gmail.com (Michael Aye)
Date: Mon, 25 Nov 2013 14:50:44 -0800 (PST)
Subject: Kakadu JP2000 reader
In-Reply-To: <CABDkGQnHWe2c333NN2s-6WMXXB6cU5=Ga94U2M9bpFU3Gv6pUg@mail.gmail.com>
References: <b0ab6704-f2c2-48c9-9fde-d904f198c59c@googlegroups.com>
 <234fcb19-bb64-430a-bb72-1bce3f577035@googlegroups.com> <c1058003-0f34-419d-aa48-7fb695053033@googlegroups.com>
 <CABDkGQnHWe2c333NN2s-6WMXXB6cU5=Ga94U2M9bpFU3Gv6pUg@mail.gmail.com>
Message-ID: <a8f0c824-9065-4f94-aa7f-c3c4c0c6b577@googlegroups.com>



On Friday, November 22, 2013 6:10:52 PM UTC-8, Stefan van der Walt wrote:
>
> On Sat, Nov 23, 2013 at 4:00 AM, Michael Aye <kmicha... at gmail.com<javascript:>> 
> wrote: 
> > If this is the driver that is exposed by GDAL, it's far too slow and 
> crashy 
> > for HiRISE images. 
>
> These images look like they're about 1GB in size.  Do you want to read 
> the entire image into memory?  How large would that NumPy array be? 
> Are you interested in only loading a specific portion of the image? 
>
> Hi St?fan,
I'm usually not interested in reading the whole image into memory, but 
would like to successively scan through the image in portions. But even 
that used to crash with the HiRISE images using open source JP2000 drivers, 
maybe because they use an exceptional harsh compression algorithm.
Do I see it correctly, that the io.imread interface does not yet support 
partial reading of an image?

Michael
 

> St?fan 
>
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From kmichael.aye at gmail.com  Mon Nov 25 17:53:28 2013
From: kmichael.aye at gmail.com (Michael Aye)
Date: Mon, 25 Nov 2013 14:53:28 -0800 (PST)
Subject: stupid question: Why is imshow in io module?
In-Reply-To: <CAA48SF8cFMt3Q-ZCthOGO-ww-51NFnNRoWQ--7g_0KpVD6CnVw@mail.gmail.com>
References: <d73961e7-44a5-4240-8c36-0cddfe61513a@googlegroups.com>
 <CAA48SF8cFMt3Q-ZCthOGO-ww-51NFnNRoWQ--7g_0KpVD6CnVw@mail.gmail.com>
Message-ID: <788288e0-97a0-4663-8d65-01885ad853a5@googlegroups.com>



On Monday, November 25, 2013 2:29:26 PM UTC-8, Thomas A Caswell wrote:
>
> I would argue that showing an image is the 'out' part of I/O. 
>

I see your point. It is certainly 'some' kind of output, although I'm used 
to have the output part more dealing with a file than with a display of it, 
but YMMV.
Never mind, carry on. ;)

 

>
> On Mon, Nov 25, 2013 at 4:24 PM, Michael Aye <kmicha... at gmail.com<javascript:>> 
> wrote: 
> > I just stumbled over the 3 lines of code on scikits' title page: 
> > 
> > 
> > from skimage import data, io, filter 
> > image = data.coins() # or any NumPy array! 
> > edges = filter.sobel(image) 
> > io.imshow(edges) 
> > 
> > and wondered: Isn't it a bit funny to require an I/O module to show an 
> image 
> > that is already loaded? 
> > 
> > My apologies if that has been discussed before. 
> > 
> > Michael 
> > 
> > -- 
> > You received this message because you are subscribed to the Google 
> Groups 
> > "scikit-image" group. 
> > To unsubscribe from this group and stop receiving emails from it, send 
> an 
> > email to scikit-image... at googlegroups.com <javascript:>. 
> > For more options, visit https://groups.google.com/groups/opt_out. 
>
>
>
> -- 
> Thomas A Caswell 
> PhD Candidate University of Chicago 
> Nagel and Gardel labs 
> tcas... at uchicago.edu <javascript:> 
> jfi.uchicago.edu/~tcaswell<http://www.google.com/url?q=http%3A%2F%2Fjfi.uchicago.edu%2F~tcaswell&sa=D&sntz=1&usg=AFQjCNHcm86f2p43M5eOmhzZmuqHBRtZ0w> 
> o: 773.702.7204 
>
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From jni.soma at gmail.com  Sun Nov 24 23:02:46 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Mon, 25 Nov 2013 15:02:46 +1100
Subject: Template matching for 3D image
In-Reply-To: <1A7BE6BF-A6AA-4D9D-930D-E7BF03311B1F@demuc.de>
References: <529281A1.6020707@googlemail.com> <1A7BE6BF-A6AA-4D9D-930D-E7BF03311B1F@demuc.de>
Message-ID: <CA+JHcKQFwV-A_4ky_uZZTGpo2UuZPf5z8GDTCq3Gv_21hCM6ug@mail.gmail.com>

On Mon, Nov 25, 2013 at 10:41 AM, Johannes Sch?nberger <jsch at demuc.de>wrote:

> Imo checking for 3D images in the same function is the best option.
>

+1

Sorry if I betray my ignorance about template matching, but can the 2D case
not be considered a special case of the 3D with z=1? In other code (such as
SLIC), when we get a 2D image we simply go:

im = im[np.newaxis, ...]

and feed that to the 3D code. Can the same be done for template matching?

Thanks for this, Kevin!

Juan.
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From hughesadam87 at gmail.com  Mon Nov 25 18:09:58 2013
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Mon, 25 Nov 2013 15:09:58 -0800 (PST)
Subject: stupid question: Why is imshow in io module?
In-Reply-To: <d73961e7-44a5-4240-8c36-0cddfe61513a@googlegroups.com>
References: <d73961e7-44a5-4240-8c36-0cddfe61513a@googlegroups.com>
Message-ID: <51533474-f7c9-44c6-b4c7-3761f0d04bf8@googlegroups.com>

Working with scikit image recently has changed my perception of images. 
 While the visualization is what we normally take for granted as the image 
itself, scikit has made me appreciate that the canonical image 
datastructure is an ndarray.  I too had wondered why imshow was in IO, but 
the more I use with this excellent library, the more I can appreciate this 
design choice.

On Monday, November 25, 2013 5:24:18 PM UTC-5, Michael Aye wrote:
>
> I just stumbled over the 3 lines of code on scikits' title page:
>
>
> from skimage import data, io, filter
> image = data.coins() # or any NumPy array!
> edges = filter.sobel(image)
> io.imshow(edges)
>
> and wondered: Isn't it a bit funny to require an I/O module to show an 
> image that is already loaded?
>
> My apologies if that has been discussed before.
>
> Michael
>
>
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From hughesadam87 at gmail.com  Mon Nov 25 18:25:46 2013
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Mon, 25 Nov 2013 15:25:46 -0800 (PST)
Subject: Advice on basic operations: zoom, crop and splice
In-Reply-To: <CAMHV+dBXfWk8Pd221ZC7S-gYtjbAHOR5=McAC1wGB3_L+s8Qjg@mail.gmail.com>
References: <CAMHV+dBXfWk8Pd221ZC7S-gYtjbAHOR5=McAC1wGB3_L+s8Qjg@mail.gmail.com>
Message-ID: <482cb2b7-67a8-4cb1-b564-ba49904c8c5c@googlegroups.com>

Thanks for all of your help guys.  I was unaware of image Inpainting, so 
thank you Chintak for bringing that fascinating concept to my attention.

Josh, thanks for your help.  I am capable enough to do such manipulations 
in numpy and matplotlib; hell,I could even just save a zoomed/crop version 
of the images of interest.  I was certainly interested in doing such 
manipulations in the notebook.  I wouldn't worry about tweaking the viewer, 
as it would just be easier for me to, as I said, do the manipulations in 
and save them to separate images.

The discussion that followed was quite interesting, and in line with what I 
expected might be the case.  It's really great to see the progress of 
iPython widgets.  I'm fairly competent at traits/chaco, but don't have a 
javascript background.  Stefan, any idea how much javascript competency one 
might need to begin to approach this effort?

On Friday, November 22, 2013 2:03:04 PM UTC-5, Adam Hughes wrote:
>
> Hi everyone,
>
> I'm used to working with big images of lots of particles.  In the 
> notebook, I'd like to be able to look at a full image, and then at a zoomed 
> in region of interest.  A few basic questions come to mind:
>     
>  Is there a zoom/crop function or preffered approach to basic 
> manipulations of zooming and cropping, or would I have to do this at the 
> numpy or matplotlib level?  I saw that there's a rectangle function that 
> probably would be useful here.  Does anyone have any examples or personal 
> code built for doing some of these common manipulations?   Ideally, I want 
> to take the fastest approach to:
>
> 1.  Selecting a rectangular region of interest (ROI).
> 2.  Cropping or zooming in on this region, and storing the ROI as its own 
> array/image.
> 3.  If possible, removing the ROI from the original image, and splicing 
> the original image back together.  If this is possible, that would be 
> amazing.  This would allow us to effectively cut out regions of our images 
> that are obviously contaminates. 
>
> Thanks.
>
>
>
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From silvertrumpet999 at gmail.com  Mon Nov 25 18:45:57 2013
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Mon, 25 Nov 2013 15:45:57 -0800 (PST)
Subject: stupid question: Why is imshow in io module?
In-Reply-To: <d73961e7-44a5-4240-8c36-0cddfe61513a@googlegroups.com>
References: <d73961e7-44a5-4240-8c36-0cddfe61513a@googlegroups.com>
Message-ID: <ba1d5c7b-b454-4e94-b136-4d1f39c548b3@googlegroups.com>



To answer this question and potentially shine a bit more light on the issue:

The example images shipped with the package and exposed by skimage.dataactually are shipped as raw files in that directory. Upon import of 
skimage.data, these convenience functions (e.g. skimage.data.lena()) are 
actually wrapping skimage.io.imread for the fixed, known local path to each 
image file and returning the result.

Take a look<https://github.com/scikit-image/scikit-image/blob/master/skimage/data/__init__.py>at the 
__init__.py file for skimage.data to see what?s going on.

So, the io module *is* required - we just handle that behind the scenes for 
these examples.

Hope that helps someone,
Josh

On Monday, November 25, 2013 4:24:18 PM UTC-6, Michael Aye wrote:

I just stumbled over the 3 lines of code on scikits' title page:
>
>
> from skimage import data, io, filter
> image = data.coins() # or any NumPy array!
> edges = filter.sobel(image)
> io.imshow(edges)
>
> and wondered: Isn't it a bit funny to require an I/O module to show an 
> image that is already loaded?
>
> My apologies if that has been discussed before.
>
> Michael
>
>
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From tcaswell at uchicago.edu  Mon Nov 25 17:29:26 2013
From: tcaswell at uchicago.edu (Thomas A Caswell)
Date: Mon, 25 Nov 2013 16:29:26 -0600
Subject: stupid question: Why is imshow in io module?
In-Reply-To: <d73961e7-44a5-4240-8c36-0cddfe61513a@googlegroups.com>
References: <d73961e7-44a5-4240-8c36-0cddfe61513a@googlegroups.com>
Message-ID: <CAA48SF8cFMt3Q-ZCthOGO-ww-51NFnNRoWQ--7g_0KpVD6CnVw@mail.gmail.com>

I would argue that showing an image is the 'out' part of I/O.

On Mon, Nov 25, 2013 at 4:24 PM, Michael Aye <kmichael.aye at gmail.com> wrote:
> I just stumbled over the 3 lines of code on scikits' title page:
>
>
> from skimage import data, io, filter
> image = data.coins() # or any NumPy array!
> edges = filter.sobel(image)
> io.imshow(edges)
>
> and wondered: Isn't it a bit funny to require an I/O module to show an image
> that is already loaded?
>
> My apologies if that has been discussed before.
>
> Michael
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.



-- 
Thomas A Caswell
PhD Candidate University of Chicago
Nagel and Gardel labs
tcaswell at uchicago.edu
jfi.uchicago.edu/~tcaswell
o: 773.702.7204


From kmichael.aye at gmail.com  Mon Nov 25 19:57:10 2013
From: kmichael.aye at gmail.com (Michael Aye)
Date: Mon, 25 Nov 2013 16:57:10 -0800 (PST)
Subject: What's 'stable' version currently?
In-Reply-To: <4450C23A-D68C-4C19-A0BB-5E34F511B004@demuc.de>
References: <960f3f18-682f-4b92-aa2e-7935d093e7be@googlegroups.com> <CABDkGQmf5b8AjsiHcm0PAo1rv+GGe7VJfSnMWDxixJeM_ezvpg@mail.gmail.com> <1183972889.328452.1384258688650.open-xchange@app01> <1500375494.328830.1384258804040.open-xchange@app01.ox.hosteurope.de> <CABDkGQknCQ75PO0KkS2euJFH4CyFcBw23Q=F3ihiEuyZ2F4MWg@mail.gmail.com> <CABDkGQkhwemJdxanSwf5eG3QsZnE3aXJKJSMVpsz7R4jaK2CXA@mail.gmail.com> <114E0C33-BC10-43C7-AB5B-672846F31289@demuc.de> <CABDkGQm2ihTFUup8Sed=cJoBNo=N734Mgpn3djSLEw3PeWfBmQ@mail.gmail.com>
 <4450C23A-D68C-4C19-A0BB-5E34F511B004@demuc.de>
Message-ID: <b136f86d-bfd5-494f-9eec-805df60dbe7d@googlegroups.com>

Hi there!

The html pages themselves still show the 0.9.0 version. I am talking about 
what is shown in the title bar of the browser window. See for example here:
http://scikit-image.org/docs/0.9.x/api/skimage.io.html#imread

Michael

On Tuesday, November 12, 2013 11:21:47 PM UTC-8, Johannes Sch?nberger wrote:
>
> Stefan, would you merge and push the update to gh-pages? 
>
> Am 13.11.2013 um 06:52 schrieb St?fan van der Walt <ste... at sun.ac.za<javascript:>>: 
>
>
> > Perfect, thank you. 
> > 
> > On 12 Nov 2013 18:37, "Johannes Sch?nberger" <js... at demuc.de<javascript:>> 
> wrote: 
> > Sorry, I didn?t see that you were asking for a review, so I just merged. 
> > 
> > See https://github.com/scikit-image/scikit-image-web/pull/14<https://www.google.com/url?q=https%3A%2F%2Fgithub.com%2Fscikit-image%2Fscikit-image-web%2Fpull%2F14&sa=D&sntz=1&usg=AFQjCNG7f5hFSNoOyO-0scE_OFoUoREfTw>for a slightly modified layout and automatic release date insertion. 
> > 
> > Am 12.11.2013 um 16:31 schrieb St?fan van der Walt <ste... at sun.ac.za<javascript:>>: 
>
> > 
> > > Here's a start--this PR grabs it directly from PyPi: 
> > > 
> > > https://github.com/scikit-image/scikit-image-web/pull/13<https://www.google.com/url?q=https%3A%2F%2Fgithub.com%2Fscikit-image%2Fscikit-image-web%2Fpull%2F13&sa=D&sntz=1&usg=AFQjCNFMvLXQQNIxQ3yEmaQdLJLz_kyhVg> 
> > > 
> > > Some spacing issues etc., so some suggestions on how to tweak welcome. 
> > > 
> > > On Tue, Nov 12, 2013 at 4:55 PM, St?fan van der Walt <ste... at sun.ac.za<javascript:>> 
> wrote: 
> > >> Easiest way to do that is to just grab it from docversions.js. 
> > >> 
> > >> On 12 Nov 2013 20:20, "Johannes Sch?nberger" <js... at demuc.de<javascript:>> 
> wrote: 
> > >>> 
> > >>> Yes, but only in the documentation section and not on the home page 
> in the 
> > >>> sidebar on the top left. 
> > >>> 
> > >>> We should change this to automatically update the version number, 
> because 
> > >>> building the docs and uploading it every time is a pain... 
> > >>> 
> > >>> Am 12.11.2013 um 12:53 schrieb "Juan Nunez-Iglesias" <
> jni.... at gmail.com <javascript:>>: 
> > >>> 
> > >>> I thought we had changed the site version string to read "0.9.x"??? 
> > >>> 
> > >>> 
> > >>> On Tue, Nov 12, 2013 at 8:40 PM, St?fan van der Walt <
> ste... at sun.ac.za <javascript:>> 
> > >>> wrote: 
> > >>>> 
> > >>>> Those are all bug fix releases, but yes: the website needs an 
> update. In 
> > >>>> fact, why don't we have the website builder just query pipy? 
> > >>>> 
> > >>>> On 12 Nov 2013 14:40, "Michael Aye" <kmicha... at gmail.com<javascript:>> 
> wrote: 
> > >>>>> 
> > >>>>> I am asking because the website says 0.9.0, but pip just brought 
> me 
> > >>>>> 0.9.3? 
> > >>>>> So either 0.9.3 is stable, and the website needs an update, or pip 
> > >>>>> provides unstable versions, which would not be in line with what 
> is written 
> > >>>>> on skimage's Download page? 
> > >>>>> 
> > >>>>> Cheers, 
> > >>>>> Michael 
> > >>>>> 
> > >>>>> 
> > >>>>> -- 
> > >>>>> You received this message because you are subscribed to the Google 
> > >>>>> Groups "scikit-image" group. 
> > >>>>> To unsubscribe from this group and stop receiving emails from it, 
> send 
> > >>>>> an email to scikit-image... at googlegroups.com <javascript:>. 
> > >>>>> For more options, visit https://groups.google.com/groups/opt_out. 
> > >>>> 
> > >>>> -- 
> > >>>> You received this message because you are subscribed to the Google 
> Groups 
> > >>>> "scikit-image" group. 
> > >>>> To unsubscribe from this group and stop receiving emails from it, 
> send an 
> > >>>> email to scikit-image... at googlegroups.com <javascript:>. 
> > >>>> For more options, visit https://groups.google.com/groups/opt_out. 
> > >>> 
> > >>> 
> > >>> -- 
> > >>> You received this message because you are subscribed to the Google 
> Groups 
> > >>> "scikit-image" group. 
> > >>> To unsubscribe from this group and stop receiving emails from it, 
> send an 
> > >>> email to scikit-image... at googlegroups.com <javascript:>. 
> > >>> For more options, visit https://groups.google.com/groups/opt_out. 
> > >>> 
> > >>> -- 
> > >>> You received this message because you are subscribed to the Google 
> Groups 
> > >>> "scikit-image" group. 
> > >>> To unsubscribe from this group and stop receiving emails from it, 
> send an 
> > >>> email to scikit-image... at googlegroups.com <javascript:>. 
> > >>> For more options, visit https://groups.google.com/groups/opt_out. 
> > > 
> > > -- 
> > > You received this message because you are subscribed to the Google 
> Groups "scikit-image" group. 
> > > To unsubscribe from this group and stop receiving emails from it, send 
> an email to scikit-image... at googlegroups.com <javascript:>. 
> > > For more options, visit https://groups.google.com/groups/opt_out. 
> > > 
> > 
> > -- 
> > You received this message because you are subscribed to the Google 
> Groups "scikit-image" group. 
> > To unsubscribe from this group and stop receiving emails from it, send 
> an email to scikit-image... at googlegroups.com <javascript:>. 
> > For more options, visit https://groups.google.com/groups/opt_out. 
> > 
> > -- 
> > 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:>. 
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>
>
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From hughesadam87 at gmail.com  Mon Nov 25 21:45:38 2013
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Mon, 25 Nov 2013 18:45:38 -0800 (PST)
Subject: Advice on basic operations: zoom, crop and splice
In-Reply-To: <CAMHV+dBXfWk8Pd221ZC7S-gYtjbAHOR5=McAC1wGB3_L+s8Qjg@mail.gmail.com>
References: <CAMHV+dBXfWk8Pd221ZC7S-gYtjbAHOR5=McAC1wGB3_L+s8Qjg@mail.gmail.com>
Message-ID: <3475f22c-6a29-42c2-9afd-96700d82dd65@googlegroups.com>

I made a couple basic utilties:
  zoom, crop, and zoomplot

They're very straightforward, but there was just enough nuance involved 
that working directly with numpy and matplotlib would become a pain.

See the attached notebook and/or pdf.  The PDF was generaged with 
nbconvert, and the image quality is poor.  Feel free to use and distribute 
this; please the ignore the content claim on the title page; it defaults to 
all of our pdfs that we generate with nbconvert.

On Friday, November 22, 2013 2:03:04 PM UTC-5, Adam Hughes wrote:
>
> Hi everyone,
>
> I'm used to working with big images of lots of particles.  In the 
> notebook, I'd like to be able to look at a full image, and then at a zoomed 
> in region of interest.  A few basic questions come to mind:
>     
>  Is there a zoom/crop function or preffered approach to basic 
> manipulations of zooming and cropping, or would I have to do this at the 
> numpy or matplotlib level?  I saw that there's a rectangle function that 
> probably would be useful here.  Does anyone have any examples or personal 
> code built for doing some of these common manipulations?   Ideally, I want 
> to take the fastest approach to:
>
> 1.  Selecting a rectangular region of interest (ROI).
> 2.  Cropping or zooming in on this region, and storing the ROI as its own 
> array/image.
> 3.  If possible, removing the ROI from the original image, and splicing 
> the original image back together.  If this is possible, that would be 
> amazing.  This would allow us to effectively cut out regions of our images 
> that are obviously contaminates. 
>
> Thanks.
>
>
>
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From evelzw at gmail.com  Tue Nov 26 13:47:01 2013
From: evelzw at gmail.com (Evelyn Liu)
Date: Tue, 26 Nov 2013 10:47:01 -0800 (PST)
Subject: Advice on improving a analysis on images of nanoparticles
In-Reply-To: <529309E5.8010403@mitotic-machine.org>
References: <656876a4-8696-4f8a-b963-8ad42997db68@googlegroups.com> <CABDkGQ=Syt_z6UEYChpMo3F9GeuKnz9DWJtyfYG1MsWJNXskbw@mail.gmail.com> <f45c0b91-fd22-460c-b961-0bf05d7537bb@googlegroups.com> <CA+JHcKRE4Rr1QxqfhQy36W-BBfX0OVt4o+yxO8MF1ygQiob0vw@mail.gmail.com> <9964284d-a6e4-439f-b32b-ef6f07d13992@googlegroups.com> <CA+JHcKSh3F_d4Ugzmn7VhEpXr-hdrkWfTEYYvq=wFX-TX8UTcA@mail.gmail.com> <c9bc61ba-0ba2-4cbc-954e-8dbbc399b48f@googlegroups.com>
 <529309E5.8010403@mitotic-machine.org>
Message-ID: <9e9ae32e-2ac7-414b-87e8-7441c51bc5e8@googlegroups.com>

This is really helpful. Thanks Guillaume!

On Monday, November 25, 2013 3:27:17 AM UTC-5, Guillaume wrote:
>
>  For the uneven background issue, you can always filter out the low 
> frequency parts of the image. You can do this in Fourrier space, or just 
> subtract a Gaussian filtered version of the image:
>
> from skimage import img_as_floatfrom scipy import ndimage
> def preprocess_highpass(image, filter_width=100):
>     '''Emulates a highpass filter by subtracted a smoothed version 
>     of the image from the image.
>
>     Parameters:
>     ----------------
>     image: a ndarray
>     filter_width: an int, should be much bigger than the relevant features in the image, 
>         and about the scale of the background variations
>
>     Returns:
>     -----------
>     f_image: ndarray with the same shape as the input image, with float dtype, the filtered image,
>         with minimum at 0.
>     '''
>
>     image = img_as_float(image)
>     lowpass = ndimage.gaussian_filter(image, filter_width)
>     f_image = image - lowpass
>     f_image -= f_image.min()
>     return f_image
>
> On 25/11/2013 08:49, Evelyn Liu wrote:
>
>   Thanks for your helpful response Juan. But I have the issue with 
> choosing parameter for threshold_adaptive.. Some of my images have uneven 
> contrast, like the lower part of image has darker background compared to 
> the upper part. So if the threshold is proper for the upper part, some 
> neighboring particles will be taken as a cluster even they are individual. 
> I tried different diam, but none of them leads to good threshold in terms 
> of the full image. Is there any other thresholding methods for those uneven 
> contrast images?  
>
>  I also tried the edge operator *filter.sobel *and it looks good for 
> drawing up particles' edges(the attached image). I wonder if i can fill 
> these circles up to get the thresholding image?  I tried *ndimage.**binary_fill_holes 
> *but it gives me either blank or total total black pic..
>
>
> <https://lh6.googleusercontent.com/-89xSmEmy7Wc/UpL_fNubbSI/AAAAAAAAAB8/0N-N1cf-374/s1600/edge_invert_wraped1.png>
>
>  
>
> On Wednesday, November 20, 2013 12:33:19 AM UTC-5, Juan Nunez-Iglesias 
> wrote: 
>>
>> Hi Evelyn, 
>>
>>  I'm guessing you are applying label() directly to your image, which is 
>> not the right way to use it. label() connects all neighboring *nonzero*points together. Since images are rarely zero (rather than some very small 
>> intensity value), you are simply connecting all the pixels of your image 
>> together into one label.
>>
>>    The correct way to do this is to threshold your image, eg using:
>>
>> http://scikit-image.org/docs/dev/api/skimage.filter.html#threshold-adaptive<http://www.google.com/url?q=http%3A%2F%2Fscikit-image.org%2Fdocs%2Fdev%2Fapi%2Fskimage.filter.html%23threshold-adaptive&sa=D&sntz=1&usg=AFQjCNG3r7Y-dZ9r6IBjOojwF1eoEgwp1Q>
>>  
>>  So:
>>
>>  >>> from skimage.filter import threshold_adaptive
>> >>> from scipy import ndimage as nd
>> >>> diam = 51
>> >>> # "51" is a guess, you might have to fiddle with this parameter.
>> >>> image_t = (image > threshold_adaptive(image, diam))
>> >>> image_labeled = nd.label(image_t)[0]
>> >>> particle_sizes = np.bincount(image_labeled.ravel())[1:]
>>  >>> # [1:] is to select only the foreground labels
>>
>>  Hope this helps!
>>
>>  Juan.
>>
>>  
>>
>> On Wed, Nov 20, 2013 at 3:45 PM, Evelyn Liu <eve... at gmail.com> wrote:
>>
>>> Hi Juan, 
>>>
>>>  On Tuesday, November 19, 2013 9:39:47 PM UTC-5, Juan Nunez-Iglesias 
>>> wrote: 
>>>>
>>>>  Is the goal only to count particles? In that case, I think a local 
>>>> thresholding (threshold_adaptive) would work on all these images. Then, 
>>>> just do a labelling (scipy.ndimage.label) and draw a histogram of particle 
>>>> sizes. You'll get a sharp peak around the true particle size, with bigger 
>>>> peaks for clumps
>>>>   
>>>
>>>  I'd like to use scikit to plot the size distribution histogram of 
>>> particles in an image, which is similar with Adam's. I tried 
>>> scipy.ndimage.measurements.label(image), which I thought would give an 
>>> array about particle sizes. However, the output array is with all 1, 
>>> obviously nothing about size. I must get something wrong...So which 
>>> function should i call for the size distribution? Thanks Juan!
>>>  
>>>  
>>>   -- 
>>> You received this message because you are subscribed to the Google 
>>> Groups "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send 
>>> an email to scikit-image... at googlegroups.com.
>>> For more options, visit https://groups.google.com/groups/opt_out.
>>>  
>>  
>>    -- 
> You received this message because you are subscribed to the Google Groups 
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an 
> email to scikit-image... at googlegroups.com <javascript:>.
> For more options, visit https://groups.google.com/groups/opt_out.
>
>    
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From hughesadam87 at gmail.com  Tue Nov 26 13:30:58 2013
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Tue, 26 Nov 2013 13:30:58 -0500
Subject: Advice on basic operations: zoom, crop and splice
In-Reply-To: <3475f22c-6a29-42c2-9afd-96700d82dd65@googlegroups.com>
References: <CAMHV+dBXfWk8Pd221ZC7S-gYtjbAHOR5=McAC1wGB3_L+s8Qjg@mail.gmail.com>
	<3475f22c-6a29-42c2-9afd-96700d82dd65@googlegroups.com>
Message-ID: <CAMHV+dD4gArJyGa9YwERiRu19RkD0h-hCogEjqk1XJFDkPTNhg@mail.gmail.com>

Sorry, last post.  Here's a slightly more complete version for sake of
archiving:




On Mon, Nov 25, 2013 at 9:45 PM, Adam Hughes <hughesadam87 at gmail.com> wrote:

> I made a couple basic utilties:
>   zoom, crop, and zoomplot
>
> They're very straightforward, but there was just enough nuance involved
> that working directly with numpy and matplotlib would become a pain.
>
> See the attached notebook and/or pdf.  The PDF was generaged with
> nbconvert, and the image quality is poor.  Feel free to use and distribute
> this; please the ignore the content claim on the title page; it defaults to
> all of our pdfs that we generate with nbconvert.
>
> On Friday, November 22, 2013 2:03:04 PM UTC-5, Adam Hughes wrote:
>>
>> Hi everyone,
>>
>> I'm used to working with big images of lots of particles.  In the
>> notebook, I'd like to be able to look at a full image, and then at a zoomed
>> in region of interest.  A few basic questions come to mind:
>>
>>  Is there a zoom/crop function or preffered approach to basic
>> manipulations of zooming and cropping, or would I have to do this at the
>> numpy or matplotlib level?  I saw that there's a rectangle function that
>> probably would be useful here.  Does anyone have any examples or personal
>> code built for doing some of these common manipulations?   Ideally, I want
>> to take the fastest approach to:
>>
>> 1.  Selecting a rectangular region of interest (ROI).
>> 2.  Cropping or zooming in on this region, and storing the ROI as its own
>> array/image.
>> 3.  If possible, removing the ROI from the original image, and splicing
>> the original image back together.  If this is possible, that would be
>> amazing.  This would allow us to effectively cut out regions of our images
>> that are obviously contaminates.
>>
>> Thanks.
>>
>>
>>  --
> 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/Ke7_TwUew4U/unsubscribe.
> To unsubscribe from this group and all of its topics, send an email to
> scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>
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From jni.soma at gmail.com  Mon Nov 25 22:45:06 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Tue, 26 Nov 2013 14:45:06 +1100
Subject: SLICO
In-Reply-To: <4a9d8a9d-dae6-4083-81c9-fc6fcee859a5@googlegroups.com>
References: <717ead1b-0435-462c-83e5-45f534b5a886@googlegroups.com>
 <CA+JHcKSEhSrMqy=DuTKbqPfitO+GrueCdhgAsnfD1GaTZRz=Qg@mail.gmail.com> <4a9d8a9d-dae6-4083-81c9-fc6fcee859a5@googlegroups.com>
Message-ID: <CA+JHcKQkND44m4naBVzRWCXgodOTbSN8pOQNsW+tznQpgptDcA@mail.gmail.com>

Hey Michal,

I'll see what I can do about SLICO, although I might need some help with
> Cython.
>

My first experience with Cython was making scikit-image's SLIC 3D
compatible, so it would perhaps be a great entrypoint for you as well! =)
It now uses memoryviews instead of pointer arithmetic (thanks Stefan for
pushing me to do this! ;), so I think it should be more accessible even! =)

I also noticed that the scikit-image version doesn't do the seed
> perturbation step in preprocessing, and doesn't seem to do the connected
> components step in post-processing. Was there any reason for omitting them?
>

Nope. =) A powerful combination of simplicity and laziness. =P In my own
problems, SLIC with reasonable compactness and sigma parameters produced
very good results, so I never felt compelled to port that code. Andy, on
the other hand, got worse results with sigma > 0. I think it's because I'm
looking at objects that are intrinsically fuzzier (cell nuclei).

Anyway, adding the post-processing would also be appreciated!

Juan.
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From jni.soma at gmail.com  Mon Nov 25 22:49:25 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Tue, 26 Nov 2013 14:49:25 +1100
Subject: Kakadu JP2000 reader
In-Reply-To: <a8f0c824-9065-4f94-aa7f-c3c4c0c6b577@googlegroups.com>
References: <b0ab6704-f2c2-48c9-9fde-d904f198c59c@googlegroups.com>
 <234fcb19-bb64-430a-bb72-1bce3f577035@googlegroups.com> <c1058003-0f34-419d-aa48-7fb695053033@googlegroups.com>
 <CABDkGQnHWe2c333NN2s-6WMXXB6cU5=Ga94U2M9bpFU3Gv6pUg@mail.gmail.com> <a8f0c824-9065-4f94-aa7f-c3c4c0c6b577@googlegroups.com>
Message-ID: <CA+JHcKSogL37mt_eaopcBW1Shoezo1-aK-4swGQiJH+JLnd=hA@mail.gmail.com>

Hi Michael,

On Tue, Nov 26, 2013 at 9:50 AM, Michael Aye <kmichael.aye at gmail.com> wrote:

> Do I see it correctly, that the io.imread interface does not yet support
> partial reading of an image?
>

afaik you are correct here. In fact, we've been wanting to refactor the io
module dramatically for some time (search the list for discussions), but
other aspects have taken priority. (To my chagrin yesterday, when I was
having ludicrous amounts of imread-related errors. =\) Partial loads should
also be considered in the refactor discussions.

Juan.
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From jni.soma at gmail.com  Mon Nov 25 22:55:13 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Tue, 26 Nov 2013 14:55:13 +1100
Subject: stupid question: Why is imshow in io module?
In-Reply-To: <ba1d5c7b-b454-4e94-b136-4d1f39c548b3@googlegroups.com>
References: <d73961e7-44a5-4240-8c36-0cddfe61513a@googlegroups.com> <ba1d5c7b-b454-4e94-b136-4d1f39c548b3@googlegroups.com>
Message-ID: <CA+JHcKS6PbGWayYME+BYFv2kmX0vj9+ahKtB8gnCONmYeRspjw@mail.gmail.com>

@Josh, there's two issues here: whether the import io is wasteful (which,
as you demonstrated, it isn't), and whether it makes sense to stick imshow
under io, which is certainly not clear to me, despite the rationalisations
posted to this thread. =P

I would argue that we rename the "viewer" package to "view" and include a
simple imshow in there *in addition to* the viewer.

Juan.



On Tue, Nov 26, 2013 at 10:45 AM, Josh Warner <silvertrumpet999 at gmail.com>wrote:

> To answer this question and potentially shine a bit more light on the
> issue:
>
> The example images shipped with the package and exposed by skimage.dataactually are shipped as raw files in that directory. Upon import of
> skimage.data, these convenience functions (e.g. skimage.data.lena()) are
> actually wrapping skimage.io.imread for the fixed, known local path to
> each image file and returning the result.
>
> Take a look<https://github.com/scikit-image/scikit-image/blob/master/skimage/data/__init__.py>at the
> __init__.py file for skimage.data to see what?s going on.
>
> So, the io module *is* required - we just handle that behind the scenes
> for these examples.
>
> Hope that helps someone,
> Josh
>
> On Monday, November 25, 2013 4:24:18 PM UTC-6, Michael Aye wrote:
>
> I just stumbled over the 3 lines of code on scikits' title page:
>>
>>
>> from skimage import data, io, filter
>> image = data.coins() # or any NumPy array!
>> edges = filter.sobel(image)
>> io.imshow(edges)
>>
>> and wondered: Isn't it a bit funny to require an I/O module to show an
>> image that is already loaded?
>>
>> My apologies if that has been discussed before.
>>
>> Michael
>>
>>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>
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From kmichael.aye at gmail.com  Tue Nov 26 22:09:59 2013
From: kmichael.aye at gmail.com (Michael Aye)
Date: Tue, 26 Nov 2013 19:09:59 -0800 (PST)
Subject: Advice on basic operations: zoom, crop and splice
In-Reply-To: <CAMHV+dD4gArJyGa9YwERiRu19RkD0h-hCogEjqk1XJFDkPTNhg@mail.gmail.com>
References: <CAMHV+dBXfWk8Pd221ZC7S-gYtjbAHOR5=McAC1wGB3_L+s8Qjg@mail.gmail.com>
 <3475f22c-6a29-42c2-9afd-96700d82dd65@googlegroups.com>
 <CAMHV+dD4gArJyGa9YwERiRu19RkD0h-hCogEjqk1XJFDkPTNhg@mail.gmail.com>
Message-ID: <df969aaa-6d1e-424a-b63d-9e930ddda414@googlegroups.com>

Hey Adam, your Notebook PDF output is *sick*! ;)

Care to share how you set it up so nicely?

Michael

On Tuesday, November 26, 2013 10:30:58 AM UTC-8, Adam Hughes wrote:
>
> Sorry, last post.  Here's a slightly more complete version for sake of 
> archiving:
>
>
>
>
> On Mon, Nov 25, 2013 at 9:45 PM, Adam Hughes <hughes... at gmail.com<javascript:>
> > wrote:
>
>> I made a couple basic utilties:
>>   zoom, crop, and zoomplot
>>
>> They're very straightforward, but there was just enough nuance involved 
>> that working directly with numpy and matplotlib would become a pain.
>>
>> See the attached notebook and/or pdf.  The PDF was generaged with 
>> nbconvert, and the image quality is poor.  Feel free to use and distribute 
>> this; please the ignore the content claim on the title page; it defaults to 
>> all of our pdfs that we generate with nbconvert.
>>
>> On Friday, November 22, 2013 2:03:04 PM UTC-5, Adam Hughes wrote:
>>>
>>> Hi everyone,
>>>
>>> I'm used to working with big images of lots of particles.  In the 
>>> notebook, I'd like to be able to look at a full image, and then at a zoomed 
>>> in region of interest.  A few basic questions come to mind:
>>>     
>>>  Is there a zoom/crop function or preffered approach to basic 
>>> manipulations of zooming and cropping, or would I have to do this at the 
>>> numpy or matplotlib level?  I saw that there's a rectangle function that 
>>> probably would be useful here.  Does anyone have any examples or personal 
>>> code built for doing some of these common manipulations?   Ideally, I want 
>>> to take the fastest approach to:
>>>
>>> 1.  Selecting a rectangular region of interest (ROI).
>>> 2.  Cropping or zooming in on this region, and storing the ROI as its 
>>> own array/image.
>>> 3.  If possible, removing the ROI from the original image, and splicing 
>>> the original image back together.  If this is possible, that would be 
>>> amazing.  This would allow us to effectively cut out regions of our images 
>>> that are obviously contaminates. 
>>>
>>> Thanks.
>>>
>>>
>>>  -- 
>> 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/Ke7_TwUew4U/unsubscribe.
>> To unsubscribe from this group and all of its topics, send an email to 
>> scikit-image... at googlegroups.com <javascript:>.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>
>
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From hughesadam87 at gmail.com  Tue Nov 26 23:00:17 2013
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Tue, 26 Nov 2013 23:00:17 -0500
Subject: Advice on basic operations: zoom, crop and splice
In-Reply-To: <df969aaa-6d1e-424a-b63d-9e930ddda414@googlegroups.com>
References: <CAMHV+dBXfWk8Pd221ZC7S-gYtjbAHOR5=McAC1wGB3_L+s8Qjg@mail.gmail.com>
	<3475f22c-6a29-42c2-9afd-96700d82dd65@googlegroups.com>
	<CAMHV+dD4gArJyGa9YwERiRu19RkD0h-hCogEjqk1XJFDkPTNhg@mail.gmail.com>
	<df969aaa-6d1e-424a-b63d-9e930ddda414@googlegroups.com>
Message-ID: <CAMHV+dC7USHCUZssSh9eQdGaRLTgO_X1mLNhObx_J1xqOZeZoQ@mail.gmail.com>

Thanks!  Let me make a few adaptaions and host it proper in a day or two
On Nov 26, 2013 10:10 PM, "Michael Aye" <kmichael.aye at gmail.com> wrote:

> Hey Adam, your Notebook PDF output is *sick*! ;)
>
> Care to share how you set it up so nicely?
>
> Michael
>
> On Tuesday, November 26, 2013 10:30:58 AM UTC-8, Adam Hughes wrote:
>>
>> Sorry, last post.  Here's a slightly more complete version for sake of
>> archiving:
>>
>>
>>
>>
>> On Mon, Nov 25, 2013 at 9:45 PM, Adam Hughes <hughes... at gmail.com> wrote:
>>
>>> I made a couple basic utilties:
>>>   zoom, crop, and zoomplot
>>>
>>> They're very straightforward, but there was just enough nuance involved
>>> that working directly with numpy and matplotlib would become a pain.
>>>
>>> See the attached notebook and/or pdf.  The PDF was generaged with
>>> nbconvert, and the image quality is poor.  Feel free to use and distribute
>>> this; please the ignore the content claim on the title page; it defaults to
>>> all of our pdfs that we generate with nbconvert.
>>>
>>> On Friday, November 22, 2013 2:03:04 PM UTC-5, Adam Hughes wrote:
>>>>
>>>> Hi everyone,
>>>>
>>>> I'm used to working with big images of lots of particles.  In the
>>>> notebook, I'd like to be able to look at a full image, and then at a zoomed
>>>> in region of interest.  A few basic questions come to mind:
>>>>
>>>>  Is there a zoom/crop function or preffered approach to basic
>>>> manipulations of zooming and cropping, or would I have to do this at the
>>>> numpy or matplotlib level?  I saw that there's a rectangle function that
>>>> probably would be useful here.  Does anyone have any examples or personal
>>>> code built for doing some of these common manipulations?   Ideally, I want
>>>> to take the fastest approach to:
>>>>
>>>> 1.  Selecting a rectangular region of interest (ROI).
>>>> 2.  Cropping or zooming in on this region, and storing the ROI as its
>>>> own array/image.
>>>> 3.  If possible, removing the ROI from the original image, and splicing
>>>> the original image back together.  If this is possible, that would be
>>>> amazing.  This would allow us to effectively cut out regions of our images
>>>> that are obviously contaminates.
>>>>
>>>> Thanks.
>>>>
>>>>
>>>>  --
>>> 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/Ke7_TwUew4U/unsubscribe.
>>> To unsubscribe from this group and all of its topics, send an email to
>>> scikit-image... at googlegroups.com.
>>> For more options, visit https://groups.google.com/groups/opt_out.
>>>
>>
>>  --
> 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/Ke7_TwUew4U/unsubscribe.
> To unsubscribe from this group and all of its topics, send an email to
> scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>
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From m.p.romaniuk at gmail.com  Wed Nov 27 12:34:40 2013
From: m.p.romaniuk at gmail.com (Michal Romaniuk)
Date: Wed, 27 Nov 2013 09:34:40 -0800 (PST)
Subject: SLICO
In-Reply-To: <CA+JHcKQkND44m4naBVzRWCXgodOTbSN8pOQNsW+tznQpgptDcA@mail.gmail.com>
References: <717ead1b-0435-462c-83e5-45f534b5a886@googlegroups.com>
 <CA+JHcKSEhSrMqy=DuTKbqPfitO+GrueCdhgAsnfD1GaTZRz=Qg@mail.gmail.com> <4a9d8a9d-dae6-4083-81c9-fc6fcee859a5@googlegroups.com>
 <CA+JHcKQkND44m4naBVzRWCXgodOTbSN8pOQNsW+tznQpgptDcA@mail.gmail.com>
Message-ID: <93cdc3fc-e9dd-48b3-9536-db64fb482a05@googlegroups.com>

Hi Juan,

I made the changes to add SLIC-zero but the code has become a bit messy and 
redundant... I think it's not ready for a pull request yet but I would 
welcome some feedback :)

https://github.com/romaniukm/scikit-image/tree/slico

I also updated the plot_segmentations.py example to add SLIC-zero to the 
comparison. It's available here: 

https://gist.github.com/romaniukm/7679402

Michal

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From jni.soma at gmail.com  Wed Nov 27 21:31:42 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Thu, 28 Nov 2013 13:31:42 +1100
Subject: SLICO
In-Reply-To: <93cdc3fc-e9dd-48b3-9536-db64fb482a05@googlegroups.com>
References: <717ead1b-0435-462c-83e5-45f534b5a886@googlegroups.com>
 <CA+JHcKSEhSrMqy=DuTKbqPfitO+GrueCdhgAsnfD1GaTZRz=Qg@mail.gmail.com>
 <4a9d8a9d-dae6-4083-81c9-fc6fcee859a5@googlegroups.com> <CA+JHcKQkND44m4naBVzRWCXgodOTbSN8pOQNsW+tznQpgptDcA@mail.gmail.com>
 <93cdc3fc-e9dd-48b3-9536-db64fb482a05@googlegroups.com>
Message-ID: <CA+JHcKTvxC6GTEg+m-f_+b-RsotcfySUSoSPo55f4JqF+xyErQ@mail.gmail.com>

Hey Michal,

Cool! That was quick! =) But there's no such thing as "not ready for a pull
request", if you have already checked that it would be welcome in skimage,
and it runs. Just start the PR title with "WIP" ? work in progress. Then we
can make comments directly on the code, which is not the case here. =)

Thanks!

Juan.



On Thu, Nov 28, 2013 at 4:34 AM, Michal Romaniuk <m.p.romaniuk at gmail.com>wrote:

> Hi Juan,
>
> I made the changes to add SLIC-zero but the code has become a bit messy
> and redundant... I think it's not ready for a pull request yet but I would
> welcome some feedback :)
>
> https://github.com/romaniukm/scikit-image/tree/slico
>
> I also updated the plot_segmentations.py example to add SLIC-zero to the
> comparison. It's available here:
>
> https://gist.github.com/romaniukm/7679402
>
> Michal
>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
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>
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From stefan at sun.ac.za  Thu Nov 28 09:55:47 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 28 Nov 2013 16:55:47 +0200
Subject: Advice on basic operations: zoom, crop and splice
In-Reply-To: <3475f22c-6a29-42c2-9afd-96700d82dd65@googlegroups.com>
References: <CAMHV+dBXfWk8Pd221ZC7S-gYtjbAHOR5=McAC1wGB3_L+s8Qjg@mail.gmail.com>
 <3475f22c-6a29-42c2-9afd-96700d82dd65@googlegroups.com>
Message-ID: <CABDkGQk57okxFcBVNHO=-xwsHfSRktxEQmWo+hJ4a=yeub7vTQ@mail.gmail.com>

Hi Adam

On Tue, Nov 26, 2013 at 4:45 AM, Adam Hughes <hughesadam87 at gmail.com> wrote:
> I made a couple basic utilties:
>   zoom, crop, and zoomplot

Thanks for sharing!

A tiny IPython tip: if you end the last line of your cell with a
semi-colon, the printing of the resulting object is disabled.  Very
useful for doing plots.

Regards
St?fan


From stefan at sun.ac.za  Thu Nov 28 10:33:15 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 28 Nov 2013 17:33:15 +0200
Subject: stupid question: Why is imshow in io module?
In-Reply-To: <CA+JHcKS6PbGWayYME+BYFv2kmX0vj9+ahKtB8gnCONmYeRspjw@mail.gmail.com>
References: <d73961e7-44a5-4240-8c36-0cddfe61513a@googlegroups.com>
 <ba1d5c7b-b454-4e94-b136-4d1f39c548b3@googlegroups.com> <CA+JHcKS6PbGWayYME+BYFv2kmX0vj9+ahKtB8gnCONmYeRspjw@mail.gmail.com>
Message-ID: <CABDkGQnBKuGWZg=g+UkZdCGLnnkB2nA+3gG98PXv4mmxHTQf9g@mail.gmail.com>

On Tue, Nov 26, 2013 at 5:55 AM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> @Josh, there's two issues here: whether the import io is wasteful (which, as
> you demonstrated, it isn't), and whether it makes sense to stick imshow
> under io, which is certainly not clear to me, despite the rationalisations
> posted to this thread. =P
>
> I would argue that we rename the "viewer" package to "view" and include a
> simple imshow in there in addition to the viewer.

This wasn't as much a design decision as evolution.  Initially, we had
a module for reading, writing and displaying images, and only later
the viewer tools came along.  Since then, we've started using
matplotlib almost exclusively for displaying images (e.g. in the
gallery), so I'd opt for deprecating "imshow" in favor of standard
matplotlib.

Having a viewer in the ``viewer`` package makes some sense, because it
adds additional functionality.  But before we put more code in there,
it would be good to figure out how to test it--any ideas how to script
GUI tests?

St?fan


From hughesadam87 at gmail.com  Fri Nov 29 00:17:42 2013
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Fri, 29 Nov 2013 00:17:42 -0500
Subject: Advice on basic operations: zoom, crop and splice
In-Reply-To: <CABDkGQk57okxFcBVNHO=-xwsHfSRktxEQmWo+hJ4a=yeub7vTQ@mail.gmail.com>
References: <CAMHV+dBXfWk8Pd221ZC7S-gYtjbAHOR5=McAC1wGB3_L+s8Qjg@mail.gmail.com>
	<3475f22c-6a29-42c2-9afd-96700d82dd65@googlegroups.com>
	<CABDkGQk57okxFcBVNHO=-xwsHfSRktxEQmWo+hJ4a=yeub7vTQ@mail.gmail.com>
Message-ID: <CAMHV+dC-yNbvEceOA+O=UZWHWHTfcZoJEqfCv2hmWB+h1M9ttQ@mail.gmail.com>

Thanks Stefan, I didn't know that.  Appreciate it.


On Thu, Nov 28, 2013 at 9:55 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> Hi Adam
>
> On Tue, Nov 26, 2013 at 4:45 AM, Adam Hughes <hughesadam87 at gmail.com>
> wrote:
> > I made a couple basic utilties:
> >   zoom, crop, and zoomplot
>
> Thanks for sharing!
>
> A tiny IPython tip: if you end the last line of your cell with a
> semi-colon, the printing of the resulting object is disabled.  Very
> useful for doing plots.
>
> Regards
> St?fan
>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "scikit-image" group.
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