From tsyu80 at gmail.com  Sat May  3 10:32:44 2014
From: tsyu80 at gmail.com (Tony Yu)
Date: Sat, 3 May 2014 09:32:44 -0500
Subject: SciPy 2014, revisited
In-Reply-To: <CA+JHcKQWMwkRtMO3OFjdum-jRkxPYWj7a-V0LsR3w2pfcPHYxQ@mail.gmail.com>
References: <CA+JHcKQWMwkRtMO3OFjdum-jRkxPYWj7a-V0LsR3w2pfcPHYxQ@mail.gmail.com>
Message-ID: <CAEym_HoOyvwHc0MVAECMJYxJ0h9TPFrGOQEDtOV-ty2GF0kUXw@mail.gmail.com>

Strange, I didn't get any emails about the talk getting accepted. That's
great news! I guess we'll have to figure out what were going to present :)

-Tony


On Fri, May 2, 2014 at 10:26 PM, Juan Nunez-Iglesias <jni.soma at gmail.com>wrote:

> Hi scikit-imagers!
>
> So, both my and Tony's scikit-image tutorial and my talk have been
> accepted to SciPy 2014, so it is confirmed that I will be there! Anyone
> else? Would be great to have a significant skimage contingent there!
>
> 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/d/optout.
>
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From jsch at demuc.de  Sat May  3 11:26:27 2014
From: jsch at demuc.de (=?windows-1252?Q?Johannes_Sch=0F=F6nberger?=)
Date: Sat, 3 May 2014 11:26:27 -0400
Subject: SciPy 2014, revisited
In-Reply-To: <CAEym_HoOyvwHc0MVAECMJYxJ0h9TPFrGOQEDtOV-ty2GF0kUXw@mail.gmail.com>
References: <CA+JHcKQWMwkRtMO3OFjdum-jRkxPYWj7a-V0LsR3w2pfcPHYxQ@mail.gmail.com> <CAEym_HoOyvwHc0MVAECMJYxJ0h9TPFrGOQEDtOV-ty2GF0kUXw@mail.gmail.com>
Message-ID: <DD282EB6-AED6-41FB-ABBD-9AE31E8C7F43@demuc.de>

Congratulations. Unfortunately, I?ll not be able to come.

On May 3, 2014, at 10:32 AM, Tony Yu <tsyu80 at gmail.com> wrote:

> Strange, I didn't get any emails about the talk getting accepted. That's great news! I guess we'll have to figure out what were going to present :)
> 
> -Tony
> 
> 
> On Fri, May 2, 2014 at 10:26 PM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> Hi scikit-imagers!
> 
> So, both my and Tony's scikit-image tutorial and my talk have been accepted to SciPy 2014, so it is confirmed that I will be there! Anyone else? Would be great to have a significant skimage contingent there!
> 
> 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/d/optout.
> 
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.



From jni.soma at gmail.com  Fri May  2 23:26:20 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Sat, 3 May 2014 13:26:20 +1000
Subject: SciPy 2014, revisited
Message-ID: <CA+JHcKQWMwkRtMO3OFjdum-jRkxPYWj7a-V0LsR3w2pfcPHYxQ@mail.gmail.com>

Hi scikit-imagers!

So, both my and Tony's scikit-image tutorial and my talk have been accepted
to SciPy 2014, so it is confirmed that I will be there! Anyone else? Would
be great to have a significant skimage contingent there!

Juan.
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From jni.soma at gmail.com  Sat May  3 21:49:27 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Sun, 4 May 2014 11:49:27 +1000
Subject: SciPy 2014, revisited
In-Reply-To: <DD282EB6-AED6-41FB-ABBD-9AE31E8C7F43@demuc.de>
References: <CA+JHcKQWMwkRtMO3OFjdum-jRkxPYWj7a-V0LsR3w2pfcPHYxQ@mail.gmail.com>
 <CAEym_HoOyvwHc0MVAECMJYxJ0h9TPFrGOQEDtOV-ty2GF0kUXw@mail.gmail.com> <DD282EB6-AED6-41FB-ABBD-9AE31E8C7F43@demuc.de>
Message-ID: <CA+JHcKRfkRL1eaCSnvJnnkVJ9ijLK73TW8eUK20Xy9bDMoW7dQ@mail.gmail.com>

@Tony, I guess they only bothered to notify the submitter, all PeerJ-like.
=P

Sometime next week (after the paper mods), we can make a new repo for the
tutorial with a skeleton notebook that we can flesh out.

Juan.



On Sun, May 4, 2014 at 1:26 AM, Johannes Sch ?nberger <jsch at demuc.de> wrote:

> Congratulations. Unfortunately, I'll not be able to come.
>
> On May 3, 2014, at 10:32 AM, Tony Yu <tsyu80 at gmail.com> wrote:
>
> > Strange, I didn't get any emails about the talk getting accepted. That's
> great news! I guess we'll have to figure out what were going to present :)
> >
> > -Tony
> >
> >
> > On Fri, May 2, 2014 at 10:26 PM, Juan Nunez-Iglesias <jni.soma at gmail.com>
> wrote:
> > Hi scikit-imagers!
> >
> > So, both my and Tony's scikit-image tutorial and my talk have been
> accepted to SciPy 2014, so it is confirmed that I will be there! Anyone
> else? Would be great to have a significant skimage contingent there!
> >
> > 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/d/optout.
> >
> >
> > --
> > You received this message because you are subscribed to the Google
> Groups "scikit-image" group.
> > To unsubscribe from this group and stop receiving emails from it, send
> an email to scikit-image+unsubscribe at googlegroups.com.
> > For more options, visit https://groups.google.com/d/optout.
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From msarahan at gmail.com  Sun May  4 23:21:56 2014
From: msarahan at gmail.com (Michael Sarahan)
Date: Sun, 4 May 2014 20:21:56 -0700
Subject: Potential contribution: subpixel cross correlation
In-Reply-To: <CA+JHcKSnMeyvdiXNugZRbKyubNYyWE98Yd6VFxfJnVzca6YFpA@mail.gmail.com>
References: <ef1461b6-aced-44d9-8d25-e2c195d389bf@googlegroups.com>
 <CABDkGQn0t+Jo2nuDPLB2FUa5RpKH=vtBOtxP9owQ3Oqn90GFSA@mail.gmail.com>
 <CAB9hrOoqwE3ZZo2fZ0hNC9y0+9yTMKag5YmogMmnZejNLrJggQ@mail.gmail.com>
 <CABDkGQn=Tfq-VVDm9X27GxjFaUEsJkxQcyox6yH--zV47CcBvg@mail.gmail.com>
 <CAB9hrOq-5YegcCnRi+vz4uXXeq824QTJMfHY4nK63dhoty4z9g@mail.gmail.com>
 <CABDkGQno3DAR4iFYKOkSSU+HU+EEV-nTZ-0DpNfnEQyJeoVkyQ@mail.gmail.com> <CA+JHcKSnMeyvdiXNugZRbKyubNYyWE98Yd6VFxfJnVzca6YFpA@mail.gmail.com>
Message-ID: <CAB9hrOpaU2jsi6pc+xv+HNUihPbdA69c4QwdxjhE_s5oWJzo1A@mail.gmail.com>

Sorry guys, things aren't looking good for the license.  Manuel was kind
enough to reply to me and to forward my message to James Fienup, but it
seems the license (or lack thereof) was already a point of contention
between Manuel and James.

I'm going to leave my branch open for anyone wanting to use the code, but I
think it's better to not include officially until a license is determined
for the parent work.
https://github.com/msarahan/scikit-image/tree/PhaseCorrelation

Best,
Michael


On Mon, Apr 28, 2014 at 8:49 PM, Juan Nunez-Iglesias <jni.soma at gmail.com>wrote:

> On Sun, Apr 27, 2014 at 10:53 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:
>>
>> Perhaps Juan can answer this one--he is our most vocal 3D proponent!
>>
>
> Haha, 3D is not the same as 2D+c! I'm actually also used to grayscale EM
> images, but in 3D. For that case, I think the generalisation would be
> straightforward. For 2D+c, I have no idea!
>
> In the meanwhile, getting a version up and running with tests in 2D is
>> a great start.
>>
>
> Or 3D grayscale. Just a suggestion. ;)
>
> 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/d/optout.
>
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From stefan at sun.ac.za  Mon May  5 06:00:32 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Mon, 5 May 2014 12:00:32 +0200
Subject: Potential contribution: subpixel cross correlation
In-Reply-To: <CAB9hrOpaU2jsi6pc+xv+HNUihPbdA69c4QwdxjhE_s5oWJzo1A@mail.gmail.com>
References: <ef1461b6-aced-44d9-8d25-e2c195d389bf@googlegroups.com>
 <CABDkGQn0t+Jo2nuDPLB2FUa5RpKH=vtBOtxP9owQ3Oqn90GFSA@mail.gmail.com>
 <CAB9hrOoqwE3ZZo2fZ0hNC9y0+9yTMKag5YmogMmnZejNLrJggQ@mail.gmail.com>
 <CABDkGQn=Tfq-VVDm9X27GxjFaUEsJkxQcyox6yH--zV47CcBvg@mail.gmail.com>
 <CAB9hrOq-5YegcCnRi+vz4uXXeq824QTJMfHY4nK63dhoty4z9g@mail.gmail.com>
 <CABDkGQno3DAR4iFYKOkSSU+HU+EEV-nTZ-0DpNfnEQyJeoVkyQ@mail.gmail.com>
 <CA+JHcKSnMeyvdiXNugZRbKyubNYyWE98Yd6VFxfJnVzca6YFpA@mail.gmail.com> <CAB9hrOpaU2jsi6pc+xv+HNUihPbdA69c4QwdxjhE_s5oWJzo1A@mail.gmail.com>
Message-ID: <CABDkGQnHrm3NxY+7g-JES55b6eftZHfB=wm1Tei=Fv7cGt4C7g@mail.gmail.com>

Hi Michael

On Mon, May 5, 2014 at 5:21 AM, Michael Sarahan <msarahan at gmail.com> wrote:
> Sorry guys, things aren't looking good for the license.  Manuel was kind
> enough to reply to me and to forward my message to James Fienup, but it
> seems the license (or lack thereof) was already a point of contention
> between Manuel and James.

Did James sound like he was willing to negotiate on the license terms?
 If not, is this work published and unpatented?

St?fan


From stefan at sun.ac.za  Mon May  5 19:59:01 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Tue, 6 May 2014 01:59:01 +0200
Subject: SciPy 2014, revisited
In-Reply-To: <CA+JHcKQWMwkRtMO3OFjdum-jRkxPYWj7a-V0LsR3w2pfcPHYxQ@mail.gmail.com>
References: <CA+JHcKQWMwkRtMO3OFjdum-jRkxPYWj7a-V0LsR3w2pfcPHYxQ@mail.gmail.com>
Message-ID: <CABDkGQkALFgXVFmZoP42_Nb3+MW8YKSuGiLiZ8UDp0tf_j1n_Q@mail.gmail.com>

On Sat, May 3, 2014 at 5:26 AM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> So, both my and Tony's scikit-image tutorial and my talk have been accepted
> to SciPy 2014, so it is confirmed that I will be there! Anyone else? Would
> be great to have a significant skimage contingent there!

Thanks for giving us such a strong presence at the conference!
Unfortunately, I won't be at the conference this year, but I will be
supporting enthusiastically from the side.

St?fan


From jsch at demuc.de  Tue May  6 11:34:25 2014
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=0F=F6nberger?=)
Date: Tue, 6 May 2014 11:34:25 -0400
Subject: Help with Windows buildbot errors
In-Reply-To: <CABDkGQnaWrVhvNcUvb1HcOyPGMDCeE988p0hVpTj2ReGK5_wPw@mail.gmail.com>
References: <CABDkGQnaWrVhvNcUvb1HcOyPGMDCeE988p0hVpTj2ReGK5_wPw@mail.gmail.com>
Message-ID: <091BFB3F-B8B0-4329-84BD-35CDF3F44765@demuc.de>

I am not sure, where I read it, but I think the pillow plugin in conda is broken on Windows.

On May 6, 2014, at 11:31 AM, St?fan van der Walt <stefan at sun.ac.za> wrote:

> Hi, everyone
> 
> Continuous integration for Windows is almost ready, but the test suite
> is failing:
> 
> https://ci.appveyor.com/project/stefanv/scikit-image-494/build/1.0.39
> 
> Has anyone seen those errors before, and do you have suggestions on
> how to fix them?
> 
> Thanks
> St?fan
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.



From stefan at sun.ac.za  Tue May  6 11:31:54 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Tue, 6 May 2014 17:31:54 +0200
Subject: Help with Windows buildbot errors
Message-ID: <CABDkGQnaWrVhvNcUvb1HcOyPGMDCeE988p0hVpTj2ReGK5_wPw@mail.gmail.com>

Hi, everyone

Continuous integration for Windows is almost ready, but the test suite
is failing:

https://ci.appveyor.com/project/stefanv/scikit-image-494/build/1.0.39

Has anyone seen those errors before, and do you have suggestions on
how to fix them?

Thanks
St?fan


From stefan at sun.ac.za  Tue May  6 14:41:08 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Tue, 6 May 2014 20:41:08 +0200
Subject: Help with Windows buildbot errors
In-Reply-To: <091BFB3F-B8B0-4329-84BD-35CDF3F44765@demuc.de>
References: <CABDkGQnaWrVhvNcUvb1HcOyPGMDCeE988p0hVpTj2ReGK5_wPw@mail.gmail.com>
	<091BFB3F-B8B0-4329-84BD-35CDF3F44765@demuc.de>
Message-ID: <CABDkGQkEQ7F0066F79U9ugHbpTpEOTPtybMfZ=k3sC6WwNWXnQ@mail.gmail.com>

On May 6, 2014 5:34 PM, "Johannes Sch ?nberger" <jsch at demuc.de> wrote:
>
> I am not sure, where I read it, but I think the pillow plugin in conda is
broken on Windows.

I don't think I installed Pillow. Is it installed by default?

St?fan
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From jsch at demuc.de  Wed May  7 10:01:54 2014
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=0F=F6nberger?=)
Date: Wed, 7 May 2014 10:01:54 -0400
Subject: 0.10
Message-ID: <F1A1D555-4AF0-4804-BC04-93BF279B8D96@demuc.de>

Hi everyone,

I think, we are finally close to release 0.10. Does anyone have any outstanding issues? Otherwise I could arrange some time to finish up the release (which would also be good for the paper, as we can then refer to version 0.10).

Johannes


From stefan at sun.ac.za  Wed May  7 20:06:13 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Thu, 8 May 2014 02:06:13 +0200
Subject: 0.10
In-Reply-To: <F1A1D555-4AF0-4804-BC04-93BF279B8D96@demuc.de>
References: <F1A1D555-4AF0-4804-BC04-93BF279B8D96@demuc.de>
Message-ID: <CABDkGQmhfHXT=1A54EgzCRP4km0tfwQ7Bp8rAaFVW2xBj3KCkQ@mail.gmail.com>

On Wed, May 7, 2014 at 4:01 PM, Johannes Sch ?nberger <jsch at demuc.de> wrote:
> I think, we are finally close to release 0.10. Does anyone have any outstanding issues? Otherwise I could arrange some time to finish up the release (which would also be good for the paper, as we can then refer to version 0.10).

We're good to go, apart from the one ticket left in the milestone.

I'm happy to also work on this over the weekend--let me know.

St?fan


From msarahan at gmail.com  Tue May 13 00:02:17 2014
From: msarahan at gmail.com (Michael Sarahan)
Date: Mon, 12 May 2014 21:02:17 -0700
Subject: Potential contribution: subpixel cross correlation
In-Reply-To: <CABDkGQnHrm3NxY+7g-JES55b6eftZHfB=wm1Tei=Fv7cGt4C7g@mail.gmail.com>
References: <ef1461b6-aced-44d9-8d25-e2c195d389bf@googlegroups.com>
 <CABDkGQn0t+Jo2nuDPLB2FUa5RpKH=vtBOtxP9owQ3Oqn90GFSA@mail.gmail.com>
 <CAB9hrOoqwE3ZZo2fZ0hNC9y0+9yTMKag5YmogMmnZejNLrJggQ@mail.gmail.com>
 <CABDkGQn=Tfq-VVDm9X27GxjFaUEsJkxQcyox6yH--zV47CcBvg@mail.gmail.com>
 <CAB9hrOq-5YegcCnRi+vz4uXXeq824QTJMfHY4nK63dhoty4z9g@mail.gmail.com>
 <CABDkGQno3DAR4iFYKOkSSU+HU+EEV-nTZ-0DpNfnEQyJeoVkyQ@mail.gmail.com>
 <CA+JHcKSnMeyvdiXNugZRbKyubNYyWE98Yd6VFxfJnVzca6YFpA@mail.gmail.com>
 <CAB9hrOpaU2jsi6pc+xv+HNUihPbdA69c4QwdxjhE_s5oWJzo1A@mail.gmail.com> <CABDkGQnHrm3NxY+7g-JES55b6eftZHfB=wm1Tei=Fv7cGt4C7g@mail.gmail.com>
Message-ID: <CAB9hrOqOBgZU5X=RcO2LHryHZND5o-r80Xo-EfjtesDgCF0t3A@mail.gmail.com>

Hi Stefan,

I wrote to Prof. Fienup last Tuesday, but haven't heard back.  The work is
published, and to the best of my knowledge unpatented (Google patent search
turns up nothing.)  Let me know if you'd still be up for a PR.

Best,
Michael


On Mon, May 5, 2014 at 3:00 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> Hi Michael
>
> On Mon, May 5, 2014 at 5:21 AM, Michael Sarahan <msarahan at gmail.com>
> wrote:
> > Sorry guys, things aren't looking good for the license.  Manuel was kind
> > enough to reply to me and to forward my message to James Fienup, but it
> > seems the license (or lack thereof) was already a point of contention
> > between Manuel and James.
>
> Did James sound like he was willing to negotiate on the license terms?
>  If not, is this work published and unpatented?
>
> St?fan
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From stefan at sun.ac.za  Tue May 13 02:16:02 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Tue, 13 May 2014 08:16:02 +0200
Subject: Potential contribution: subpixel cross correlation
In-Reply-To: <CAB9hrOqOBgZU5X=RcO2LHryHZND5o-r80Xo-EfjtesDgCF0t3A@mail.gmail.com>
References: <ef1461b6-aced-44d9-8d25-e2c195d389bf@googlegroups.com>
 <CABDkGQn0t+Jo2nuDPLB2FUa5RpKH=vtBOtxP9owQ3Oqn90GFSA@mail.gmail.com>
 <CAB9hrOoqwE3ZZo2fZ0hNC9y0+9yTMKag5YmogMmnZejNLrJggQ@mail.gmail.com>
 <CABDkGQn=Tfq-VVDm9X27GxjFaUEsJkxQcyox6yH--zV47CcBvg@mail.gmail.com>
 <CAB9hrOq-5YegcCnRi+vz4uXXeq824QTJMfHY4nK63dhoty4z9g@mail.gmail.com>
 <CABDkGQno3DAR4iFYKOkSSU+HU+EEV-nTZ-0DpNfnEQyJeoVkyQ@mail.gmail.com>
 <CA+JHcKSnMeyvdiXNugZRbKyubNYyWE98Yd6VFxfJnVzca6YFpA@mail.gmail.com>
 <CAB9hrOpaU2jsi6pc+xv+HNUihPbdA69c4QwdxjhE_s5oWJzo1A@mail.gmail.com>
 <CABDkGQnHrm3NxY+7g-JES55b6eftZHfB=wm1Tei=Fv7cGt4C7g@mail.gmail.com> <CAB9hrOqOBgZU5X=RcO2LHryHZND5o-r80Xo-EfjtesDgCF0t3A@mail.gmail.com>
Message-ID: <CABDkGQmZArfBxiGV3XNuAFfC2vssF23_emEXugXM6czfRdLhgA@mail.gmail.com>

Hi Michael

On Tue, May 13, 2014 at 6:02 AM, Michael Sarahan <msarahan at gmail.com> wrote:
> I wrote to Prof. Fienup last Tuesday, but haven't heard back.  The work is
> published, and to the best of my knowledge unpatented (Google patent search
> turns up nothing.)  Let me know if you'd still be up for a PR.

I would prefer to get Prof. Fienup's approval of the work.  However,
if that cannot be obtained we can still publish code if we can show
that it was derived purely from the published information (not from
the "tainted" code the current version is based on).

Regards
St?fan


From stefan at sun.ac.za  Tue May 13 19:49:58 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Wed, 14 May 2014 01:49:58 +0200
Subject: Broken PR display
Message-ID: <CABDkGQ=DdQJo2mnO2x9grOp-YfBD-Rr-_T7gB1MfW+C4Kj2oNA@mail.gmail.com>

Hi everyone

An update from GitHub on the PR from Abid Rahman that was closed from
their side without actually being integrated into scikit-image.  The
dangers of rebase :)

Cheers
St?fan


---------- Forwarded message ----------
From: Brian Levine (GitHub Staff)
Date: Wed, May 14, 2014 at 1:36 AM
Subject: Re: Broken PR display
To: Stefan van der Walt


Hey Stefan

It looks like the head branch of that pull request was updated to
include a list of commits that already existed in master. When the
head branch of a pull request is changed, the commit list is updated
to reflect the diff between it and the base branch at that time.

In this case, the commits pushed to the head branch existed in the
upstream base branch, so the pull request was closed and marked as
merged.

I hope this helps explain things a bit. Let us know if you have any
other questions.

Brian
GitHub Support

> This PR claims that it has been merged, which it has not. Clicking on the the merged commit id at the bottom takes me to work done in an entirely different PR.


From stefan at sun.ac.za  Thu May 15 07:10:53 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Thu, 15 May 2014 13:10:53 +0200
Subject: I/O infrastructure
Message-ID: <CABDkGQmrS4vTYxrVC8zyRqjKiYLSFJxjn5T+4h=X7tzL726WZQ@mail.gmail.com>

Hi all,

Juan recently again brought to my attention the dismal state of the
scikit-image I/O infrastructure.  This needs to be fixed for 0.11
(0.10 is almost out the door--this weekend, I hope!).

We are currently relying on other libraries to do the job, and while
it allows you to do "from skimage import io; io.imread(anything)" on
almost any platform, it's just not working--we need reproducible
backends.

My current thinking is thus: make Luis's "imread" [0] a dependency,
and remove all plugins from scikit-image.  Users can, of course, still
load data using mpl, imread, astropy or whatever suits them.  In the
documentation, we may provide recipes for handling files like ITK,
gdal etc. if that proves useful.

What do you think?

St?fan

[0] https://github.com/luispedro/imread


From vighneshbirodkar at gmail.com  Thu May 15 17:56:12 2014
From: vighneshbirodkar at gmail.com (Vighnesh Birodkar)
Date: Thu, 15 May 2014 14:56:12 -0700 (PDT)
Subject: Hisotry of scikit-image in a 5min video.
Message-ID: <8aadabb5-2464-4a44-95b7-60b73cfa0e22@googlegroups.com>

Hello Everyone

code_swarm is a organic visualizer for source code history. I managed to 
create one for scikit-image. Do have a look.

scikit-image code_swarm<https://www.youtube.com/watch?v=E1bJPP38ueE&feature=youtu.be>

See Also
code_swarm project page <https://code.google.com/p/codeswarm/>
Other awesome code swarms <http://vis.cs.ucdavis.edu/~ogawa/codeswarm/>

Thanks
Vighnesh
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From stefan at sun.ac.za  Thu May 15 11:27:28 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Thu, 15 May 2014 17:27:28 +0200
Subject: I/O infrastructure
In-Reply-To: <CA+JHcKS69_4+bij+TFh7CS-b1CZ7YmDUfGS-oi6vZ2D1dFR76g@mail.gmail.com>
References: <CABDkGQmrS4vTYxrVC8zyRqjKiYLSFJxjn5T+4h=X7tzL726WZQ@mail.gmail.com>
 <CA+JHcKS69_4+bij+TFh7CS-b1CZ7YmDUfGS-oi6vZ2D1dFR76g@mail.gmail.com>
Message-ID: <CABDkGQnFL4qCS9GLLaPGm-pYa91McwbNcw-S_u7PiVR3UUg8gw@mail.gmail.com>

On Thu, May 15, 2014 at 4:11 PM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> I'm behind this 100%. (Though I want to make sure that imread supports 3D
> tiffs, as Christoph Gohlke's tifffile does.)

I thought imread already supports that, but if it doesn't we should
contribute a patch.

> Do we want to add a paragraph about this to the paper? It seems like a
> fairly trivial detail, but it also seems perverse having information there
> that we know will quickly be obsolete...

Sure, I'll add it to the future roadmap.

St?fan


From jni.soma at gmail.com  Thu May 15 10:11:29 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Fri, 16 May 2014 00:11:29 +1000
Subject: I/O infrastructure
In-Reply-To: <CABDkGQmrS4vTYxrVC8zyRqjKiYLSFJxjn5T+4h=X7tzL726WZQ@mail.gmail.com>
References: <CABDkGQmrS4vTYxrVC8zyRqjKiYLSFJxjn5T+4h=X7tzL726WZQ@mail.gmail.com>
Message-ID: <CA+JHcKS69_4+bij+TFh7CS-b1CZ7YmDUfGS-oi6vZ2D1dFR76g@mail.gmail.com>

I'm behind this 100%. (Though I want to make sure that imread supports 3D
tiffs, as Christoph Gohlke's tifffile does.)

Do we want to add a paragraph about this to the paper? It seems like a
fairly trivial detail, but it also seems perverse having information there
that we know will quickly be obsolete...


On Thu, May 15, 2014 at 9:10 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> Hi all,
>
> Juan recently again brought to my attention the dismal state of the
> scikit-image I/O infrastructure.  This needs to be fixed for 0.11
> (0.10 is almost out the door--this weekend, I hope!).
>
> We are currently relying on other libraries to do the job, and while
> it allows you to do "from skimage import io; io.imread(anything)" on
> almost any platform, it's just not working--we need reproducible
> backends.
>
> My current thinking is thus: make Luis's "imread" [0] a dependency,
> and remove all plugins from scikit-image.  Users can, of course, still
> load data using mpl, imread, astropy or whatever suits them.  In the
> documentation, we may provide recipes for handling files like ITK,
> gdal etc. if that proves useful.
>
> What do you think?
>
> St?fan
>
> [0] https://github.com/luispedro/imread
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From stefan at sun.ac.za  Thu May 15 18:34:46 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Fri, 16 May 2014 00:34:46 +0200
Subject: Hisotry of scikit-image in a 5min video.
In-Reply-To: <8aadabb5-2464-4a44-95b7-60b73cfa0e22@googlegroups.com>
References: <8aadabb5-2464-4a44-95b7-60b73cfa0e22@googlegroups.com>
Message-ID: <CABDkGQmcWMyYZBm56sieU+7vNQxQ+GcqeE0wp1dCBV9DSZs50w@mail.gmail.com>

On Thu, May 15, 2014 at 11:56 PM, Vighnesh Birodkar
<vighneshbirodkar at gmail.com> wrote:
> code_swarm is a organic visualizer for source code history. I managed to
> create one for scikit-image. Do have a look.

I've never seen a code-swarm of skimage before--but I recognise each
and every one of those movements ;)

Do you happen to have a higher resolution version of this available?

Thanks!
St?fan


From vighneshbirodkar at gmail.com  Fri May 16 11:07:30 2014
From: vighneshbirodkar at gmail.com (Vighnesh Birodkar)
Date: Fri, 16 May 2014 08:07:30 -0700 (PDT)
Subject: Hisotry of scikit-image in a 5min video.
In-Reply-To: <CABDkGQmcWMyYZBm56sieU+7vNQxQ+GcqeE0wp1dCBV9DSZs50w@mail.gmail.com>
References: <8aadabb5-2464-4a44-95b7-60b73cfa0e22@googlegroups.com>
 <CABDkGQmcWMyYZBm56sieU+7vNQxQ+GcqeE0wp1dCBV9DSZs50w@mail.gmail.com>
Message-ID: <b252d4ec-3626-4756-b3db-c1b2a2a1a5d2@googlegroups.com>

Hello St?fan 

I can generate a high resolution ( 1920 x 1080 ) one. Should I ?

Thanks
Vighnesh

On Friday, May 16, 2014 4:04:46 AM UTC+5:30, Stefan van der Walt wrote:
>
> On Thu, May 15, 2014 at 11:56 PM, Vighnesh Birodkar 
> <vighnesh... at gmail.com <javascript:>> wrote: 
> > code_swarm is a organic visualizer for source code history. I managed to 
> > create one for scikit-image. Do have a look. 
>
> I've never seen a code-swarm of skimage before--but I recognise each 
> and every one of those movements ;) 
>
> Do you happen to have a higher resolution version of this available? 
>
> Thanks! 
> St?fan 
>
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From stefan at sun.ac.za  Fri May 16 12:05:45 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Fri, 16 May 2014 18:05:45 +0200
Subject: Hisotry of scikit-image in a 5min video.
In-Reply-To: <b252d4ec-3626-4756-b3db-c1b2a2a1a5d2@googlegroups.com>
References: <8aadabb5-2464-4a44-95b7-60b73cfa0e22@googlegroups.com>
	<CABDkGQmcWMyYZBm56sieU+7vNQxQ+GcqeE0wp1dCBV9DSZs50w@mail.gmail.com>
	<b252d4ec-3626-4756-b3db-c1b2a2a1a5d2@googlegroups.com>
Message-ID: <CABDkGQmaHmN0rMKC4ynkk-RXzzFighHHL7-+8sQ9CDtCRn+Uqg@mail.gmail.com>

Hi Vighnesh

On May 16, 2014 5:07 PM, "Vighnesh Birodkar" <vighneshbirodkar at gmail.com>
wrote:
>
> I can generate a high resolution ( 1920 x 1080 ) one. Should I ?

That would be nice, although perhaps even more handy would be the script
used to do it so we can generate it ourselves, also in the future...

Regards
St?fan
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From jni.soma at gmail.com  Sat May 17 23:14:16 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Sun, 18 May 2014 13:14:16 +1000
Subject: Hisotry of scikit-image in a 5min video.
In-Reply-To: <CABDkGQmaHmN0rMKC4ynkk-RXzzFighHHL7-+8sQ9CDtCRn+Uqg@mail.gmail.com>
References: <8aadabb5-2464-4a44-95b7-60b73cfa0e22@googlegroups.com>
 <CABDkGQmcWMyYZBm56sieU+7vNQxQ+GcqeE0wp1dCBV9DSZs50w@mail.gmail.com>
 <b252d4ec-3626-4756-b3db-c1b2a2a1a5d2@googlegroups.com> <CABDkGQmaHmN0rMKC4ynkk-RXzzFighHHL7-+8sQ9CDtCRn+Uqg@mail.gmail.com>
Message-ID: <CA+JHcKQmdJF367qXe3wn3Qo0D9tNnQ5H3rf3cKXCn99_A6rr-Q@mail.gmail.com>

Very cool! Needs an epic soundtrack from John Williams, though. =P


On Sat, May 17, 2014 at 2:05 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> Hi Vighnesh
>
> On May 16, 2014 5:07 PM, "Vighnesh Birodkar" <vighneshbirodkar at gmail.com>
> wrote:
> >
> > I can generate a high resolution ( 1920 x 1080 ) one. Should I ?
>
> That would be nice, although perhaps even more handy would be the script
> used to do it so we can generate it ourselves, also in the future...
>
> Regards
> St?fan
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From stefan at sun.ac.za  Wed May 21 03:14:15 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Wed, 21 May 2014 09:14:15 +0200
Subject: Tutorials
In-Reply-To: <CA+JHcKT=u18Y1ggA7ZNv87g-50BBLAwx_-e6fsynJQOYVYtq0g@mail.gmail.com>
References: <CA+JHcKT=u18Y1ggA7ZNv87g-50BBLAwx_-e6fsynJQOYVYtq0g@mail.gmail.com>
Message-ID: <CABDkGQkZWU9-pDtpHGfdnEmwVuer_7zR0c=6=_Sn56OjvJo0rA@mail.gmail.com>

Hey Juan

On Wed, May 21, 2014 at 7:25 AM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> I'd like to have a repo for the tutorial Tony and I are doing at SciPy, and
> all future scikit-image tutorials. I imagine it'll be a mix of markdown,
> Python, and IPython notebooks. Do you think this is a good idea (say
> github.com/scikit-image/skimage-tutorials), and if so, can you create it?
> I'd suggest all core members should have write access to it.

I think it's a great idea!

https://github.com/scikit-image/skimage-tutorials

With notebooks, I sometimes worry that the repository grows rapidly if
you don't clear out the images before storing--what do you think is
the best way to handle that?

I could perhaps add a Travis config that runs all the notebooks (then
one doesn't need to store the images because you are sure they can be
generated). Also, another idea is to deploy to readthedocs upon merge.

Thanks!
St?fan


From stuart at mumford.me.uk  Wed May 21 05:06:24 2014
From: stuart at mumford.me.uk (Stuart Mumford)
Date: Wed, 21 May 2014 10:06:24 +0100
Subject: Tutorials
In-Reply-To: <CABDkGQkZWU9-pDtpHGfdnEmwVuer_7zR0c=6=_Sn56OjvJo0rA@mail.gmail.com>
References: <CA+JHcKT=u18Y1ggA7ZNv87g-50BBLAwx_-e6fsynJQOYVYtq0g@mail.gmail.com>
 <CABDkGQkZWU9-pDtpHGfdnEmwVuer_7zR0c=6=_Sn56OjvJo0rA@mail.gmail.com>
Message-ID: <CAJ3G1JrmNKVhLPieY0KxZW2JudyTLjwfoWv1u8ixnyB5zun36Q@mail.gmail.com>

Hi,

Astropy have a interesting tutorials repo (
https://github.com/astropy/astropy-tutorials) we are planning on
implementing something similar using that for SunPy. There was some talk of
building this on a generic framework based on the Astropy repo, though I
don't think this has picked up much momentum.

If you are interested in something like this as well then we all could try
and work together on a IPython notebook gallery / tutorials framework?

Stuart


On 21 May 2014 08:14, St?fan van der Walt <stefan at sun.ac.za> wrote:

> Hey Juan
>
> On Wed, May 21, 2014 at 7:25 AM, Juan Nunez-Iglesias <jni.soma at gmail.com>
> wrote:
> > I'd like to have a repo for the tutorial Tony and I are doing at SciPy,
> and
> > all future scikit-image tutorials. I imagine it'll be a mix of markdown,
> > Python, and IPython notebooks. Do you think this is a good idea (say
> > github.com/scikit-image/skimage-tutorials), and if so, can you create
> it?
> > I'd suggest all core members should have write access to it.
>
> I think it's a great idea!
>
> https://github.com/scikit-image/skimage-tutorials
>
> With notebooks, I sometimes worry that the repository grows rapidly if
> you don't clear out the images before storing--what do you think is
> the best way to handle that?
>
> I could perhaps add a Travis config that runs all the notebooks (then
> one doesn't need to store the images because you are sure they can be
> generated). Also, another idea is to deploy to readthedocs upon merge.
>
> Thanks!
> St?fan
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From stuart at mumford.me.uk  Wed May 21 05:08:38 2014
From: stuart at mumford.me.uk (Stuart Mumford)
Date: Wed, 21 May 2014 10:08:38 +0100
Subject: Real-time interaction forum
In-Reply-To: <CAJ3G1Jq786fbv0C5SE_RApo6shHgC2O0NPCGsN6+W5us0DWCgA@mail.gmail.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
 <6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com> <CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>
 <47208ad9-da2e-4071-92de-d91581fe8bbd@googlegroups.com> <CAJ3G1Jp7GEiyOqNYonEBhprBcx35y0c4fPmwptqefp8afM4pOQ@mail.gmail.com>
 <6fd9151f-6be7-4450-8cd7-de2185425ceb@googlegroups.com> <39d3cb1c-ba2e-4cae-b2fb-9ebdb9e230e0@googlegroups.com>
 <CAJ3G1JpzqpmZe2m5raokJMvjyJwKXOxteRNpcWpvyOSsXaf7iA@mail.gmail.com>
 <CAD82iYp5MsP_HNaiYPcEdRf0U5Y5hzeffqCCpT3T7dmrWnP3mg@mail.gmail.com>
 <CAJ3G1Jp24icRykWQw4SHpH1D9eqN3L7i_MY-27A3PsYAPkFaGg@mail.gmail.com>
 <CAHJ7L49r+dbJZocUmnOfa28E19Z7NwBv3W6mS4OfttLaUS4VzQ@mail.gmail.com>
 <CAJ3G1JoP1mznUEiJGosCvRxx6tVsh3fsSfyO7e=kk9TU3vQtFw@mail.gmail.com>
 <CABDkGQ==6Q4J8em8uR=2T3HSsWPPXaMNWDA+fme83CeNok7tnQ@mail.gmail.com> <CAJ3G1Jq786fbv0C5SE_RApo6shHgC2O0NPCGsN6+W5us0DWCgA@mail.gmail.com>
Message-ID: <CAJ3G1JqimPR7g3qDDmMNyd9SY8W07Jdq681DPRE7B7AzWKEM2A@mail.gmail.com>

Hi,

You may also be interested in gitter (http://gitter.im) which integrates
well with GitHub, has a IRC beta module and generally looks quite cool.

Stuart


On 27 April 2014 11:04, Stuart Mumford <stuart at mumford.me.uk> wrote:

> Hello,
>
>  > https://github.com/Cadair/williemodules it is very basic but it works.
>>
>> That's really neat!
>>
>
> There are at least two quite major feature missing at the moment, the main
> one is rate limiting the notifications! The second is optionally turning
> off the notification when the user is online. Also from my limited testing
> I think that all the emails are being duplicated!
>
>
>> Thanks, that's very kind of you.  I think a lot of people would
>> appreciate having an IRC channel.  Does the logger update a page in
>> real-time so that a person could "watch" IRC via the web?
>>
>
> Yes, it has a js front end that updates in "real time" there is a variable
> delay, but it will update. Currently what the logger is missing is a decent
> way of scrolling through the history more than about 100-200 messages in
> the past (the js seems to go loopy). All the messages are in a MySQL
> database so I want to code up a better flask-based front end to it, but you
> know time is always a problem. (I also have a lovely little idea for
> integrating the logger and the notification module.)
>
> Stuart
>
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From stuart at mumford.me.uk  Wed May 21 05:27:06 2014
From: stuart at mumford.me.uk (Stuart Mumford)
Date: Wed, 21 May 2014 10:27:06 +0100
Subject: Tutorials
In-Reply-To: <CA+JHcKRFjsymt5rjHuxGLOg3SAZSK-=yo=F=jrWx7kFBFnKTow@mail.gmail.com>
References: <CA+JHcKT=u18Y1ggA7ZNv87g-50BBLAwx_-e6fsynJQOYVYtq0g@mail.gmail.com>
 <CABDkGQkZWU9-pDtpHGfdnEmwVuer_7zR0c=6=_Sn56OjvJo0rA@mail.gmail.com>
 <CAJ3G1JrmNKVhLPieY0KxZW2JudyTLjwfoWv1u8ixnyB5zun36Q@mail.gmail.com> <CA+JHcKRFjsymt5rjHuxGLOg3SAZSK-=yo=F=jrWx7kFBFnKTow@mail.gmail.com>
Message-ID: <CAJ3G1JriaD3GOGsTKN7xUuYeHZY3cDWMbcBHhsO48VYSMAmc-Q@mail.gmail.com>

Hi,

The other thing that the astropy repo does to manage the size of the
gh-pages branch is make it an orphan branch on every build, so there is no
history of the built notebooks only the empty ones.

Stuart


On 21 May 2014 10:23, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:

> Hi Stuart!
>
> This looks like a very good idea on first inspection ? iirc git will not
> clone/fork a gh-pages branch by default, so having the run notebooks (with
> a lot of images built-in as St?fan was concerned about) on that branch
> should not matter?
>
> I'm not sure I have time to get something like this working in time for
> SciPy... Perhaps I can use my own repo for drafting the tutorial, then move
> it into the tutorials repo as time allows?
>
>
> On Wed, May 21, 2014 at 7:06 PM, Stuart Mumford <stuart at mumford.me.uk>wrote:
>
>> Hi,
>>
>> Astropy have a interesting tutorials repo (
>> https://github.com/astropy/astropy-tutorials) we are planning on
>> implementing something similar using that for SunPy. There was some talk of
>> building this on a generic framework based on the Astropy repo, though I
>> don't think this has picked up much momentum.
>>
>> If you are interested in something like this as well then we all could
>> try and work together on a IPython notebook gallery / tutorials framework?
>>
>> Stuart
>>
>>
>> On 21 May 2014 08:14, St?fan van der Walt <stefan at sun.ac.za> wrote:
>>
>>> Hey Juan
>>>
>>> On Wed, May 21, 2014 at 7:25 AM, Juan Nunez-Iglesias <jni.soma at gmail.com>
>>> wrote:
>>> > I'd like to have a repo for the tutorial Tony and I are doing at
>>> SciPy, and
>>> > all future scikit-image tutorials. I imagine it'll be a mix of
>>> markdown,
>>> > Python, and IPython notebooks. Do you think this is a good idea (say
>>> > github.com/scikit-image/skimage-tutorials), and if so, can you create
>>> it?
>>> > I'd suggest all core members should have write access to it.
>>>
>>> I think it's a great idea!
>>>
>>> https://github.com/scikit-image/skimage-tutorials
>>>
>>> With notebooks, I sometimes worry that the repository grows rapidly if
>>> you don't clear out the images before storing--what do you think is
>>> the best way to handle that?
>>>
>>> I could perhaps add a Travis config that runs all the notebooks (then
>>> one doesn't need to store the images because you are sure they can be
>>> generated). Also, another idea is to deploy to readthedocs upon merge.
>>>
>>> Thanks!
>>> St?fan
>>>
>>> --
>>> You received this message because you are subscribed to the Google
>>> Groups "scikit-image" group.
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>>> an email to scikit-image+unsubscribe at googlegroups.com.
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>>
>>  --
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From jni.soma at gmail.com  Wed May 21 01:25:34 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Wed, 21 May 2014 15:25:34 +1000
Subject: Tutorials
Message-ID: <CA+JHcKT=u18Y1ggA7ZNv87g-50BBLAwx_-e6fsynJQOYVYtq0g@mail.gmail.com>

Hey St?fan,

I'd like to have a repo for the tutorial Tony and I are doing at SciPy, and
all future scikit-image tutorials. I imagine it'll be a mix of markdown,
Python, and IPython notebooks. Do you think this is a good idea (say
github.com/scikit-image/skimage-tutorials), and if so, can you create it?
I'd suggest all core members should have write access to it.

Thanks!

Juan.
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From jni.soma at gmail.com  Wed May 21 05:23:55 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Wed, 21 May 2014 19:23:55 +1000
Subject: Tutorials
In-Reply-To: <CAJ3G1JrmNKVhLPieY0KxZW2JudyTLjwfoWv1u8ixnyB5zun36Q@mail.gmail.com>
References: <CA+JHcKT=u18Y1ggA7ZNv87g-50BBLAwx_-e6fsynJQOYVYtq0g@mail.gmail.com>
 <CABDkGQkZWU9-pDtpHGfdnEmwVuer_7zR0c=6=_Sn56OjvJo0rA@mail.gmail.com> <CAJ3G1JrmNKVhLPieY0KxZW2JudyTLjwfoWv1u8ixnyB5zun36Q@mail.gmail.com>
Message-ID: <CA+JHcKRFjsymt5rjHuxGLOg3SAZSK-=yo=F=jrWx7kFBFnKTow@mail.gmail.com>

Hi Stuart!

This looks like a very good idea on first inspection -- iirc git will not
clone/fork a gh-pages branch by default, so having the run notebooks (with
a lot of images built-in as St?fan was concerned about) on that branch
should not matter?

I'm not sure I have time to get something like this working in time for
SciPy... Perhaps I can use my own repo for drafting the tutorial, then move
it into the tutorials repo as time allows?


On Wed, May 21, 2014 at 7:06 PM, Stuart Mumford <stuart at mumford.me.uk>wrote:

> Hi,
>
> Astropy have a interesting tutorials repo (
> https://github.com/astropy/astropy-tutorials) we are planning on
> implementing something similar using that for SunPy. There was some talk of
> building this on a generic framework based on the Astropy repo, though I
> don't think this has picked up much momentum.
>
> If you are interested in something like this as well then we all could try
> and work together on a IPython notebook gallery / tutorials framework?
>
> Stuart
>
>
> On 21 May 2014 08:14, St?fan van der Walt <stefan at sun.ac.za> wrote:
>
>> Hey Juan
>>
>> On Wed, May 21, 2014 at 7:25 AM, Juan Nunez-Iglesias <jni.soma at gmail.com>
>> wrote:
>> > I'd like to have a repo for the tutorial Tony and I are doing at SciPy,
>> and
>> > all future scikit-image tutorials. I imagine it'll be a mix of markdown,
>> > Python, and IPython notebooks. Do you think this is a good idea (say
>> > github.com/scikit-image/skimage-tutorials), and if so, can you create
>> it?
>> > I'd suggest all core members should have write access to it.
>>
>> I think it's a great idea!
>>
>> https://github.com/scikit-image/skimage-tutorials
>>
>> With notebooks, I sometimes worry that the repository grows rapidly if
>> you don't clear out the images before storing--what do you think is
>> the best way to handle that?
>>
>> I could perhaps add a Travis config that runs all the notebooks (then
>> one doesn't need to store the images because you are sure they can be
>> generated). Also, another idea is to deploy to readthedocs upon merge.
>>
>> Thanks!
>> St?fan
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>  --
> 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  Fri May 23 10:20:45 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Fri, 23 May 2014 16:20:45 +0200
Subject: Real-time interaction forum
In-Reply-To: <CAJ3G1Jq786fbv0C5SE_RApo6shHgC2O0NPCGsN6+W5us0DWCgA@mail.gmail.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
 <6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com> <CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>
 <47208ad9-da2e-4071-92de-d91581fe8bbd@googlegroups.com> <CAJ3G1Jp7GEiyOqNYonEBhprBcx35y0c4fPmwptqefp8afM4pOQ@mail.gmail.com>
 <6fd9151f-6be7-4450-8cd7-de2185425ceb@googlegroups.com> <39d3cb1c-ba2e-4cae-b2fb-9ebdb9e230e0@googlegroups.com>
 <CAJ3G1JpzqpmZe2m5raokJMvjyJwKXOxteRNpcWpvyOSsXaf7iA@mail.gmail.com>
 <CAD82iYp5MsP_HNaiYPcEdRf0U5Y5hzeffqCCpT3T7dmrWnP3mg@mail.gmail.com>
 <CAJ3G1Jp24icRykWQw4SHpH1D9eqN3L7i_MY-27A3PsYAPkFaGg@mail.gmail.com>
 <CAHJ7L49r+dbJZocUmnOfa28E19Z7NwBv3W6mS4OfttLaUS4VzQ@mail.gmail.com>
 <CAJ3G1JoP1mznUEiJGosCvRxx6tVsh3fsSfyO7e=kk9TU3vQtFw@mail.gmail.com>
 <CABDkGQ==6Q4J8em8uR=2T3HSsWPPXaMNWDA+fme83CeNok7tnQ@mail.gmail.com> <CAJ3G1Jq786fbv0C5SE_RApo6shHgC2O0NPCGsN6+W5us0DWCgA@mail.gmail.com>
Message-ID: <CABDkGQnCyn6F61onLKAZcBW8gYzBBxfZjQZEDppEVxkxWOO-Lg@mail.gmail.com>

Hi Stuart

On Sun, Apr 27, 2014 at 12:04 PM, Stuart Mumford <stuart at mumford.me.uk> wrote:
>> Thanks, that's very kind of you.  I think a lot of people would
>> appreciate having an IRC channel.  Does the logger update a page in
>> real-time so that a person could "watch" IRC via the web?

I was wondering if you'd still be willing to set this IRC +
notification for us?  With GSoC, it would come in really handy.

Regards
St?fan


From stuart at mumford.me.uk  Fri May 23 16:04:46 2014
From: stuart at mumford.me.uk (Stuart Mumford)
Date: Fri, 23 May 2014 21:04:46 +0100
Subject: Real-time interaction forum
In-Reply-To: <CABDkGQnCyn6F61onLKAZcBW8gYzBBxfZjQZEDppEVxkxWOO-Lg@mail.gmail.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
	<6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com>
	<CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>
	<47208ad9-da2e-4071-92de-d91581fe8bbd@googlegroups.com>
	<CAJ3G1Jp7GEiyOqNYonEBhprBcx35y0c4fPmwptqefp8afM4pOQ@mail.gmail.com>
	<6fd9151f-6be7-4450-8cd7-de2185425ceb@googlegroups.com>
	<39d3cb1c-ba2e-4cae-b2fb-9ebdb9e230e0@googlegroups.com>
	<CAJ3G1JpzqpmZe2m5raokJMvjyJwKXOxteRNpcWpvyOSsXaf7iA@mail.gmail.com>
	<CAD82iYp5MsP_HNaiYPcEdRf0U5Y5hzeffqCCpT3T7dmrWnP3mg@mail.gmail.com>
	<CAJ3G1Jp24icRykWQw4SHpH1D9eqN3L7i_MY-27A3PsYAPkFaGg@mail.gmail.com>
	<CAHJ7L49r+dbJZocUmnOfa28E19Z7NwBv3W6mS4OfttLaUS4VzQ@mail.gmail.com>
	<CAJ3G1JoP1mznUEiJGosCvRxx6tVsh3fsSfyO7e=kk9TU3vQtFw@mail.gmail.com>
	<CABDkGQ==6Q4J8em8uR=2T3HSsWPPXaMNWDA+fme83CeNok7tnQ@mail.gmail.com>
	<CAJ3G1Jq786fbv0C5SE_RApo6shHgC2O0NPCGsN6+W5us0DWCgA@mail.gmail.com>
	<CABDkGQnCyn6F61onLKAZcBW8gYzBBxfZjQZEDppEVxkxWOO-Lg@mail.gmail.com>
Message-ID: <CAJ3G1JpVE=0ke0Z7+fVzZTonZ+Q-Gx5u0sa5K3dGth1abdCb_Q@mail.gmail.com>

Yeah no problem, what channel do you want to use. I think I am already
sitting in #scikit-image on freenode.

Stuart
On 23 May 2014 15:21, "St?fan van der Walt" <stefan at sun.ac.za> wrote:

> Hi Stuart
>
> On Sun, Apr 27, 2014 at 12:04 PM, Stuart Mumford <stuart at mumford.me.uk>
> wrote:
> >> Thanks, that's very kind of you.  I think a lot of people would
> >> appreciate having an IRC channel.  Does the logger update a page in
> >> real-time so that a person could "watch" IRC via the web?
>
> I was wondering if you'd still be willing to set this IRC +
> notification for us?  With GSoC, it would come in really handy.
>
> Regards
> St?fan
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From jni.soma at gmail.com  Fri May 23 22:19:46 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Sat, 24 May 2014 12:19:46 +1000
Subject: Real-time interaction forum
In-Reply-To: <CAJ3G1JqimPR7g3qDDmMNyd9SY8W07Jdq681DPRE7B7AzWKEM2A@mail.gmail.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
 <6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com> <CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>
 <47208ad9-da2e-4071-92de-d91581fe8bbd@googlegroups.com> <CAJ3G1Jp7GEiyOqNYonEBhprBcx35y0c4fPmwptqefp8afM4pOQ@mail.gmail.com>
 <6fd9151f-6be7-4450-8cd7-de2185425ceb@googlegroups.com> <39d3cb1c-ba2e-4cae-b2fb-9ebdb9e230e0@googlegroups.com>
 <CAJ3G1JpzqpmZe2m5raokJMvjyJwKXOxteRNpcWpvyOSsXaf7iA@mail.gmail.com>
 <CAD82iYp5MsP_HNaiYPcEdRf0U5Y5hzeffqCCpT3T7dmrWnP3mg@mail.gmail.com>
 <CAJ3G1Jp24icRykWQw4SHpH1D9eqN3L7i_MY-27A3PsYAPkFaGg@mail.gmail.com>
 <CAHJ7L49r+dbJZocUmnOfa28E19Z7NwBv3W6mS4OfttLaUS4VzQ@mail.gmail.com>
 <CAJ3G1JoP1mznUEiJGosCvRxx6tVsh3fsSfyO7e=kk9TU3vQtFw@mail.gmail.com>
 <CABDkGQ==6Q4J8em8uR=2T3HSsWPPXaMNWDA+fme83CeNok7tnQ@mail.gmail.com>
 <CAJ3G1Jq786fbv0C5SE_RApo6shHgC2O0NPCGsN6+W5us0DWCgA@mail.gmail.com> <CAJ3G1JqimPR7g3qDDmMNyd9SY8W07Jdq681DPRE7B7AzWKEM2A@mail.gmail.com>
Message-ID: <CA+JHcKRieKPRg4B-OpPj446KWF-6R-TDq3GHmxgr8Tq89gEf+w@mail.gmail.com>

Stuart, St?fan, I think gitter looks fantastic! How about we go with that?


On Wed, May 21, 2014 at 7:08 PM, Stuart Mumford <stuart at mumford.me.uk>wrote:

> Hi,
>
> You may also be interested in gitter (http://gitter.im) which integrates
> well with GitHub, has a IRC beta module and generally looks quite cool.
>
> Stuart
>
>
> On 27 April 2014 11:04, Stuart Mumford <stuart at mumford.me.uk> wrote:
>
>> Hello,
>>
>>  > https://github.com/Cadair/williemodules it is very basic but it works.
>>>
>>> That's really neat!
>>>
>>
>> There are at least two quite major feature missing at the moment, the
>> main one is rate limiting the notifications! The second is optionally
>> turning off the notification when the user is online. Also from my limited
>> testing I think that all the emails are being duplicated!
>>
>>
>>> Thanks, that's very kind of you.  I think a lot of people would
>>> appreciate having an IRC channel.  Does the logger update a page in
>>> real-time so that a person could "watch" IRC via the web?
>>>
>>
>> Yes, it has a js front end that updates in "real time" there is a
>> variable delay, but it will update. Currently what the logger is missing is
>> a decent way of scrolling through the history more than about 100-200
>> messages in the past (the js seems to go loopy). All the messages are in a
>> MySQL database so I want to code up a better flask-based front end to it,
>> but you know time is always a problem. (I also have a lovely little idea
>> for integrating the logger and the notification module.)
>>
>> Stuart
>>
>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From silvertrumpet999 at gmail.com  Sat May 24 20:34:00 2014
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Sat, 24 May 2014 17:34:00 -0700 (PDT)
Subject: Real-time interaction forum
In-Reply-To: <CA+JHcKRieKPRg4B-OpPj446KWF-6R-TDq3GHmxgr8Tq89gEf+w@mail.gmail.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
 <6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com> <CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>
 <47208ad9-da2e-4071-92de-d91581fe8bbd@googlegroups.com> <CAJ3G1Jp7GEiyOqNYonEBhprBcx35y0c4fPmwptqefp8afM4pOQ@mail.gmail.com>
 <6fd9151f-6be7-4450-8cd7-de2185425ceb@googlegroups.com> <39d3cb1c-ba2e-4cae-b2fb-9ebdb9e230e0@googlegroups.com>
 <CAJ3G1JpzqpmZe2m5raokJMvjyJwKXOxteRNpcWpvyOSsXaf7iA@mail.gmail.com>
 <CAD82iYp5MsP_HNaiYPcEdRf0U5Y5hzeffqCCpT3T7dmrWnP3mg@mail.gmail.com>
 <CAJ3G1Jp24icRykWQw4SHpH1D9eqN3L7i_MY-27A3PsYAPkFaGg@mail.gmail.com>
 <CAHJ7L49r+dbJZocUmnOfa28E19Z7NwBv3W6mS4OfttLaUS4VzQ@mail.gmail.com>
 <CAJ3G1JoP1mznUEiJGosCvRxx6tVsh3fsSfyO7e=kk9TU3vQtFw@mail.gmail.com>
 <CABDkGQ==6Q4J8em8uR=2T3HSsWPPXaMNWDA+fme83CeNok7tnQ@mail.gmail.com>
 <CAJ3G1Jq786fbv0C5SE_RApo6shHgC2O0NPCGsN6+W5us0DWCgA@mail.gmail.com> <CAJ3G1JqimPR7g3qDDmMNyd9SY8W07Jdq681DPRE7B7AzWKEM2A@mail.gmail.com>
 <CA+JHcKRieKPRg4B-OpPj446KWF-6R-TDq3GHmxgr8Tq89gEf+w@mail.gmail.com>
Message-ID: <42ea90a3-b333-495b-a0e3-4dd67f0ddbb7@googlegroups.com>

Two thumbs way, way up for trialing Gutter, looks nearly perfect for our purposes.

Josh

From stefan at sun.ac.za  Sat May 24 11:59:08 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Sat, 24 May 2014 17:59:08 +0200
Subject: Real-time interaction forum
In-Reply-To: <CA+JHcKRieKPRg4B-OpPj446KWF-6R-TDq3GHmxgr8Tq89gEf+w@mail.gmail.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
 <6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com> <CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>
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 <CAJ3G1JpzqpmZe2m5raokJMvjyJwKXOxteRNpcWpvyOSsXaf7iA@mail.gmail.com>
 <CAD82iYp5MsP_HNaiYPcEdRf0U5Y5hzeffqCCpT3T7dmrWnP3mg@mail.gmail.com>
 <CAJ3G1Jp24icRykWQw4SHpH1D9eqN3L7i_MY-27A3PsYAPkFaGg@mail.gmail.com>
 <CAHJ7L49r+dbJZocUmnOfa28E19Z7NwBv3W6mS4OfttLaUS4VzQ@mail.gmail.com>
 <CAJ3G1JoP1mznUEiJGosCvRxx6tVsh3fsSfyO7e=kk9TU3vQtFw@mail.gmail.com>
 <CABDkGQ==6Q4J8em8uR=2T3HSsWPPXaMNWDA+fme83CeNok7tnQ@mail.gmail.com>
 <CAJ3G1Jq786fbv0C5SE_RApo6shHgC2O0NPCGsN6+W5us0DWCgA@mail.gmail.com>
 <CAJ3G1JqimPR7g3qDDmMNyd9SY8W07Jdq681DPRE7B7AzWKEM2A@mail.gmail.com> <CA+JHcKRieKPRg4B-OpPj446KWF-6R-TDq3GHmxgr8Tq89gEf+w@mail.gmail.com>
Message-ID: <CABDkGQnto=noOxTyDNFXNKcawmz3L_qa6Dv3ZUkH-kHxiaoqTQ@mail.gmail.com>

On Sat, May 24, 2014 at 4:19 AM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> Stuart, St?fan, I think gitter looks fantastic! How about we go with that?

Thanks for the suggestion, Stuart!

I've signed in to

https://gitter.im/scikit-image

Let's give this a go and see whether it does what we need.

St?fan


From silvertrumpet999 at gmail.com  Sun May 25 01:25:14 2014
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Sat, 24 May 2014 22:25:14 -0700 (PDT)
Subject: Real-time interaction forum
In-Reply-To: <CA+JHcKTsD33QqWR3Ks1qMUJHEZPHxcoDn8sY9HmHJ-dZtQ+=4A@mail.gmail.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
 <6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com> <CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>
 <47208ad9-da2e-4071-92de-d91581fe8bbd@googlegroups.com> <CAJ3G1Jp7GEiyOqNYonEBhprBcx35y0c4fPmwptqefp8afM4pOQ@mail.gmail.com>
 <6fd9151f-6be7-4450-8cd7-de2185425ceb@googlegroups.com> <39d3cb1c-ba2e-4cae-b2fb-9ebdb9e230e0@googlegroups.com>
 <CAJ3G1JpzqpmZe2m5raokJMvjyJwKXOxteRNpcWpvyOSsXaf7iA@mail.gmail.com>
 <CAD82iYp5MsP_HNaiYPcEdRf0U5Y5hzeffqCCpT3T7dmrWnP3mg@mail.gmail.com>
 <CAJ3G1Jp24icRykWQw4SHpH1D9eqN3L7i_MY-27A3PsYAPkFaGg@mail.gmail.com>
 <CAHJ7L49r+dbJZocUmnOfa28E19Z7NwBv3W6mS4OfttLaUS4VzQ@mail.gmail.com>
 <CAJ3G1JoP1mznUEiJGosCvRxx6tVsh3fsSfyO7e=kk9TU3vQtFw@mail.gmail.com>
 <CABDkGQ==6Q4J8em8uR=2T3HSsWPPXaMNWDA+fme83CeNok7tnQ@mail.gmail.com>
 <CAJ3G1Jq786fbv0C5SE_RApo6shHgC2O0NPCGsN6+W5us0DWCgA@mail.gmail.com>
 <CAJ3G1JqimPR7g3qDDmMNyd9SY8W07Jdq681DPRE7B7AzWKEM2A@mail.gmail.com>
 <CA+JHcKRieKPRg4B-OpPj446KWF-6R-TDq3GHmxgr8Tq89gEf+w@mail.gmail.com> <42ea90a3-b333-495b-a0e3-4dd67f0ddbb7@googlegroups.com>
 <CA+JHcKTsD33QqWR3Ks1qMUJHEZPHxcoDn8sY9HmHJ-dZtQ+=4A@mail.gmail.com>
Message-ID: <faf3284d-478e-455e-881d-8e92d0a96ce0@googlegroups.com>

This is why I generally don't compose messages on my phone...


On Saturday, May 24, 2014 10:07:21 PM UTC-5, Juan Nunez-Iglesias wrote:
>
> Josh, that was a funny typo... =D
>
>
> On Sun, May 25, 2014 at 10:34 AM, Josh Warner <silvertrumpet999 at gmail.com>wrote:
>
>> Two thumbs way, way up for trialing Gutter, looks nearly perfect for our 
>> purposes.
>>
>> Josh
>>
>> --
>> You received this message because you are subscribed to the Google Groups 
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an 
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>
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From stefan at sun.ac.za  Sat May 24 20:36:12 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Sun, 25 May 2014 02:36:12 +0200
Subject: Real-time interaction forum
In-Reply-To: <42ea90a3-b333-495b-a0e3-4dd67f0ddbb7@googlegroups.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
 <6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com> <CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>
 <47208ad9-da2e-4071-92de-d91581fe8bbd@googlegroups.com> <CAJ3G1Jp7GEiyOqNYonEBhprBcx35y0c4fPmwptqefp8afM4pOQ@mail.gmail.com>
 <6fd9151f-6be7-4450-8cd7-de2185425ceb@googlegroups.com> <39d3cb1c-ba2e-4cae-b2fb-9ebdb9e230e0@googlegroups.com>
 <CAJ3G1JpzqpmZe2m5raokJMvjyJwKXOxteRNpcWpvyOSsXaf7iA@mail.gmail.com>
 <CAD82iYp5MsP_HNaiYPcEdRf0U5Y5hzeffqCCpT3T7dmrWnP3mg@mail.gmail.com>
 <CAJ3G1Jp24icRykWQw4SHpH1D9eqN3L7i_MY-27A3PsYAPkFaGg@mail.gmail.com>
 <CAHJ7L49r+dbJZocUmnOfa28E19Z7NwBv3W6mS4OfttLaUS4VzQ@mail.gmail.com>
 <CAJ3G1JoP1mznUEiJGosCvRxx6tVsh3fsSfyO7e=kk9TU3vQtFw@mail.gmail.com>
 <CABDkGQ==6Q4J8em8uR=2T3HSsWPPXaMNWDA+fme83CeNok7tnQ@mail.gmail.com>
 <CAJ3G1Jq786fbv0C5SE_RApo6shHgC2O0NPCGsN6+W5us0DWCgA@mail.gmail.com>
 <CAJ3G1JqimPR7g3qDDmMNyd9SY8W07Jdq681DPRE7B7AzWKEM2A@mail.gmail.com>
 <CA+JHcKRieKPRg4B-OpPj446KWF-6R-TDq3GHmxgr8Tq89gEf+w@mail.gmail.com> <42ea90a3-b333-495b-a0e3-4dd67f0ddbb7@googlegroups.com>
Message-ID: <CABDkGQn8WRHk52N7fZBYKVodtFAS_zqdz+NNmW7BKe572wcQUg@mail.gmail.com>

On Sun, May 25, 2014 at 2:34 AM, Josh Warner <silvertrumpet999 at gmail.com> wrote:
> Two thumbs way, way up for trialing Gutter, looks nearly perfect for our purposes.

I've set up a Hubot for us in the channel (called "Nestor", even
though he is invisible and responds as if he's me :-).  I'm now
working on a PushOver notification hook for it.

It looks like Gitter will soon integrate irc support, judging from irc.gitter.im

St?fan


From stuart at mumford.me.uk  Sun May 25 07:42:57 2014
From: stuart at mumford.me.uk (Stuart Mumford)
Date: Sun, 25 May 2014 12:42:57 +0100
Subject: Real-time interaction forum
In-Reply-To: <CABDkGQkBEwNGeHv+_K4r93sowbRo4K4du7K4aAJ503uMXv+HPw@mail.gmail.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
 <6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com> <CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>
 <47208ad9-da2e-4071-92de-d91581fe8bbd@googlegroups.com> <CAJ3G1Jp7GEiyOqNYonEBhprBcx35y0c4fPmwptqefp8afM4pOQ@mail.gmail.com>
 <6fd9151f-6be7-4450-8cd7-de2185425ceb@googlegroups.com> <39d3cb1c-ba2e-4cae-b2fb-9ebdb9e230e0@googlegroups.com>
 <CAJ3G1JpzqpmZe2m5raokJMvjyJwKXOxteRNpcWpvyOSsXaf7iA@mail.gmail.com>
 <CAD82iYp5MsP_HNaiYPcEdRf0U5Y5hzeffqCCpT3T7dmrWnP3mg@mail.gmail.com>
 <CAJ3G1Jp24icRykWQw4SHpH1D9eqN3L7i_MY-27A3PsYAPkFaGg@mail.gmail.com>
 <CAHJ7L49r+dbJZocUmnOfa28E19Z7NwBv3W6mS4OfttLaUS4VzQ@mail.gmail.com>
 <CAJ3G1JoP1mznUEiJGosCvRxx6tVsh3fsSfyO7e=kk9TU3vQtFw@mail.gmail.com>
 <CABDkGQ==6Q4J8em8uR=2T3HSsWPPXaMNWDA+fme83CeNok7tnQ@mail.gmail.com>
 <CAJ3G1Jq786fbv0C5SE_RApo6shHgC2O0NPCGsN6+W5us0DWCgA@mail.gmail.com>
 <CAJ3G1JqimPR7g3qDDmMNyd9SY8W07Jdq681DPRE7B7AzWKEM2A@mail.gmail.com>
 <CA+JHcKRieKPRg4B-OpPj446KWF-6R-TDq3GHmxgr8Tq89gEf+w@mail.gmail.com>
 <42ea90a3-b333-495b-a0e3-4dd67f0ddbb7@googlegroups.com> <CA+JHcKTsD33QqWR3Ks1qMUJHEZPHxcoDn8sY9HmHJ-dZtQ+=4A@mail.gmail.com>
 <faf3284d-478e-455e-881d-8e92d0a96ce0@googlegroups.com> <CABDkGQkBEwNGeHv+_K4r93sowbRo4K4du7K4aAJ503uMXv+HPw@mail.gmail.com>
Message-ID: <CAJ3G1JoxBBisPZsM8x8eWsmzDd_xWuaZcBFUCAgMwdb6URdtrA@mail.gmail.com>

Hello,

I added your channell to my log bot, you can now get logs here:
http://sunpy.cadair.com/irc-logs/ (you have to select scikit-image from the
dropdown at the top).

Stuart


On 25 May 2014 11:59, St?fan van der Walt <stefan at sun.ac.za> wrote:

> After (too much) experimentation, I've come to the conclusion that
> Gitter may, after all, not be ready for prime time yet.
>
> I suggest that we use #scikit-image on Freenode for now.  I'll deploy
> a Hubot for us there, and add logging ASAP. If that doesn't work, I'm
> going to have to ask Stuart to help us out some more.
>
> St?fan
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From stefan at sun.ac.za  Sun May 25 06:59:11 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Sun, 25 May 2014 12:59:11 +0200
Subject: Real-time interaction forum
In-Reply-To: <faf3284d-478e-455e-881d-8e92d0a96ce0@googlegroups.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
 <6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com> <CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>
 <47208ad9-da2e-4071-92de-d91581fe8bbd@googlegroups.com> <CAJ3G1Jp7GEiyOqNYonEBhprBcx35y0c4fPmwptqefp8afM4pOQ@mail.gmail.com>
 <6fd9151f-6be7-4450-8cd7-de2185425ceb@googlegroups.com> <39d3cb1c-ba2e-4cae-b2fb-9ebdb9e230e0@googlegroups.com>
 <CAJ3G1JpzqpmZe2m5raokJMvjyJwKXOxteRNpcWpvyOSsXaf7iA@mail.gmail.com>
 <CAD82iYp5MsP_HNaiYPcEdRf0U5Y5hzeffqCCpT3T7dmrWnP3mg@mail.gmail.com>
 <CAJ3G1Jp24icRykWQw4SHpH1D9eqN3L7i_MY-27A3PsYAPkFaGg@mail.gmail.com>
 <CAHJ7L49r+dbJZocUmnOfa28E19Z7NwBv3W6mS4OfttLaUS4VzQ@mail.gmail.com>
 <CAJ3G1JoP1mznUEiJGosCvRxx6tVsh3fsSfyO7e=kk9TU3vQtFw@mail.gmail.com>
 <CABDkGQ==6Q4J8em8uR=2T3HSsWPPXaMNWDA+fme83CeNok7tnQ@mail.gmail.com>
 <CAJ3G1Jq786fbv0C5SE_RApo6shHgC2O0NPCGsN6+W5us0DWCgA@mail.gmail.com>
 <CAJ3G1JqimPR7g3qDDmMNyd9SY8W07Jdq681DPRE7B7AzWKEM2A@mail.gmail.com>
 <CA+JHcKRieKPRg4B-OpPj446KWF-6R-TDq3GHmxgr8Tq89gEf+w@mail.gmail.com>
 <42ea90a3-b333-495b-a0e3-4dd67f0ddbb7@googlegroups.com> <CA+JHcKTsD33QqWR3Ks1qMUJHEZPHxcoDn8sY9HmHJ-dZtQ+=4A@mail.gmail.com>
 <faf3284d-478e-455e-881d-8e92d0a96ce0@googlegroups.com>
Message-ID: <CABDkGQkBEwNGeHv+_K4r93sowbRo4K4du7K4aAJ503uMXv+HPw@mail.gmail.com>

After (too much) experimentation, I've come to the conclusion that
Gitter may, after all, not be ready for prime time yet.

I suggest that we use #scikit-image on Freenode for now.  I'll deploy
a Hubot for us there, and add logging ASAP. If that doesn't work, I'm
going to have to ask Stuart to help us out some more.

St?fan


From jni.soma at gmail.com  Sat May 24 23:07:00 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Sun, 25 May 2014 13:07:00 +1000
Subject: Real-time interaction forum
In-Reply-To: <42ea90a3-b333-495b-a0e3-4dd67f0ddbb7@googlegroups.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
 <6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com> <CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>
 <47208ad9-da2e-4071-92de-d91581fe8bbd@googlegroups.com> <CAJ3G1Jp7GEiyOqNYonEBhprBcx35y0c4fPmwptqefp8afM4pOQ@mail.gmail.com>
 <6fd9151f-6be7-4450-8cd7-de2185425ceb@googlegroups.com> <39d3cb1c-ba2e-4cae-b2fb-9ebdb9e230e0@googlegroups.com>
 <CAJ3G1JpzqpmZe2m5raokJMvjyJwKXOxteRNpcWpvyOSsXaf7iA@mail.gmail.com>
 <CAD82iYp5MsP_HNaiYPcEdRf0U5Y5hzeffqCCpT3T7dmrWnP3mg@mail.gmail.com>
 <CAJ3G1Jp24icRykWQw4SHpH1D9eqN3L7i_MY-27A3PsYAPkFaGg@mail.gmail.com>
 <CAHJ7L49r+dbJZocUmnOfa28E19Z7NwBv3W6mS4OfttLaUS4VzQ@mail.gmail.com>
 <CAJ3G1JoP1mznUEiJGosCvRxx6tVsh3fsSfyO7e=kk9TU3vQtFw@mail.gmail.com>
 <CABDkGQ==6Q4J8em8uR=2T3HSsWPPXaMNWDA+fme83CeNok7tnQ@mail.gmail.com>
 <CAJ3G1Jq786fbv0C5SE_RApo6shHgC2O0NPCGsN6+W5us0DWCgA@mail.gmail.com>
 <CAJ3G1JqimPR7g3qDDmMNyd9SY8W07Jdq681DPRE7B7AzWKEM2A@mail.gmail.com>
 <CA+JHcKRieKPRg4B-OpPj446KWF-6R-TDq3GHmxgr8Tq89gEf+w@mail.gmail.com> <42ea90a3-b333-495b-a0e3-4dd67f0ddbb7@googlegroups.com>
Message-ID: <CA+JHcKTsD33QqWR3Ks1qMUJHEZPHxcoDn8sY9HmHJ-dZtQ+=4A@mail.gmail.com>

Josh, that was a funny typo... =D


On Sun, May 25, 2014 at 10:34 AM, Josh Warner <silvertrumpet999 at gmail.com>wrote:

> Two thumbs way, way up for trialing Gutter, looks nearly perfect for our
> purposes.
>
> Josh
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From qianchencan at gmail.com  Mon May 26 02:50:10 2014
From: qianchencan at gmail.com (Chencan QIAN)
Date: Sun, 25 May 2014 23:50:10 -0700 (PDT)
Subject: generic non-linear filtering that support selem and boundary
 handling
Message-ID: <92352f83-537a-4d42-947f-fdcf6945043c@googlegroups.com>

Essentially, this is something similar 
to scipy.ndimage.filters.generic_filter (which is too slow because of its 
internal python for-loop), but implemented in cython as with 
skimage.filter.rank family.

Given the diversity within skimage.filter.rank, a generic function would be 
very useful. For example, I'd like to calculate local variance, which is 
conceptually similar to skimage.filter.rank.mean, but not supported 
currently.

I guess the absence of such a function must be due to some unresolved 
technical obstacle?

Thanks~

Chencan
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From jni.soma at gmail.com  Mon May 26 03:12:39 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Mon, 26 May 2014 17:12:39 +1000
Subject: Real-time interaction forum
In-Reply-To: <CABDkGQn8WRHk52N7fZBYKVodtFAS_zqdz+NNmW7BKe572wcQUg@mail.gmail.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
 <6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com> <CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>
 <47208ad9-da2e-4071-92de-d91581fe8bbd@googlegroups.com> <CAJ3G1Jp7GEiyOqNYonEBhprBcx35y0c4fPmwptqefp8afM4pOQ@mail.gmail.com>
 <6fd9151f-6be7-4450-8cd7-de2185425ceb@googlegroups.com> <39d3cb1c-ba2e-4cae-b2fb-9ebdb9e230e0@googlegroups.com>
 <CAJ3G1JpzqpmZe2m5raokJMvjyJwKXOxteRNpcWpvyOSsXaf7iA@mail.gmail.com>
 <CAD82iYp5MsP_HNaiYPcEdRf0U5Y5hzeffqCCpT3T7dmrWnP3mg@mail.gmail.com>
 <CAJ3G1Jp24icRykWQw4SHpH1D9eqN3L7i_MY-27A3PsYAPkFaGg@mail.gmail.com>
 <CAHJ7L49r+dbJZocUmnOfa28E19Z7NwBv3W6mS4OfttLaUS4VzQ@mail.gmail.com>
 <CAJ3G1JoP1mznUEiJGosCvRxx6tVsh3fsSfyO7e=kk9TU3vQtFw@mail.gmail.com>
 <CABDkGQ==6Q4J8em8uR=2T3HSsWPPXaMNWDA+fme83CeNok7tnQ@mail.gmail.com>
 <CAJ3G1Jq786fbv0C5SE_RApo6shHgC2O0NPCGsN6+W5us0DWCgA@mail.gmail.com>
 <CAJ3G1JqimPR7g3qDDmMNyd9SY8W07Jdq681DPRE7B7AzWKEM2A@mail.gmail.com>
 <CA+JHcKRieKPRg4B-OpPj446KWF-6R-TDq3GHmxgr8Tq89gEf+w@mail.gmail.com>
 <42ea90a3-b333-495b-a0e3-4dd67f0ddbb7@googlegroups.com> <CABDkGQn8WRHk52N7fZBYKVodtFAS_zqdz+NNmW7BKe572wcQUg@mail.gmail.com>
Message-ID: <CA+JHcKQPYBcbELTr1OgMLGc2T1M09fLEwgm8sr7azuuYMJ4hVg@mail.gmail.com>

LOL, I just saw all your testing, St?fan, it is hilarious. You sound
completely demented. =D


On Sun, May 25, 2014 at 10:36 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> On Sun, May 25, 2014 at 2:34 AM, Josh Warner <silvertrumpet999 at gmail.com>
> wrote:
> > Two thumbs way, way up for trialing Gutter, looks nearly perfect for our
> purposes.
>
> I've set up a Hubot for us in the channel (called "Nestor", even
> though he is invisible and responds as if he's me :-).  I'm now
> working on a PushOver notification hook for it.
>
> It looks like Gitter will soon integrate irc support, judging from
> irc.gitter.im
>
> St?fan
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From stefan at sun.ac.za  Mon May 26 11:12:58 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Mon, 26 May 2014 17:12:58 +0200
Subject: generic non-linear filtering that support selem and boundary handling
In-Reply-To: <92352f83-537a-4d42-947f-fdcf6945043c@googlegroups.com>
References: <92352f83-537a-4d42-947f-fdcf6945043c@googlegroups.com>
Message-ID: <CABDkGQk5natY-SPqpQ6TVfpXzCjNR3Pk+RDJ-rJpwMFE5WPdvg@mail.gmail.com>

Hi Chencan,

On Mon, May 26, 2014 at 8:50 AM, Chencan QIAN <qianchencan at gmail.com> wrote:
> I guess the absence of such a function must be due to some unresolved
> technical obstacle?

The main obstacle is: how would you specify such a filter?  If you
provide it as a function call, then we have to go through Python (not
Cython), which slows things down back to the speed that ndimage's
generic filter would give you.

Regards
St?fan


From qianchencan at gmail.com  Mon May 26 20:52:59 2014
From: qianchencan at gmail.com (Chencan QIAN)
Date: Mon, 26 May 2014 17:52:59 -0700 (PDT)
Subject: generic non-linear filtering that support selem and boundary
 handling
In-Reply-To: <CABDkGQk5natY-SPqpQ6TVfpXzCjNR3Pk+RDJ-rJpwMFE5WPdvg@mail.gmail.com>
References: <92352f83-537a-4d42-947f-fdcf6945043c@googlegroups.com>
 <CABDkGQk5natY-SPqpQ6TVfpXzCjNR3Pk+RDJ-rJpwMFE5WPdvg@mail.gmail.com>
Message-ID: <46ecb39b-946e-47b2-92e1-48b7aea12298@googlegroups.com>

Thanks for your reply, St?fan.

This is also what I was thinking. But I'm not sure whether it will still 
provide some performance gain by eliminating the outmost python for-loop 
through pixels. And if the filter is something as simple as np.std (or 
other well vectorized function), will it work OK? Will just calling back to 
python slow things down back?

Thanks again!

Regards
Chencan

On Monday, May 26, 2014 11:13:20 PM UTC+8, Stefan van der Walt wrote:
>
> Hi Chencan, 
>
> On Mon, May 26, 2014 at 8:50 AM, Chencan QIAN <qianc... at gmail.com<javascript:>> 
> wrote: 
> > I guess the absence of such a function must be due to some unresolved 
> > technical obstacle? 
>
> The main obstacle is: how would you specify such a filter?  If you 
> provide it as a function call, then we have to go through Python (not 
> Cython), which slows things down back to the speed that ndimage's 
> generic filter would give you. 
>
> Regards 
> St?fan 
>
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From silvertrumpet999 at gmail.com  Mon May 26 23:07:43 2014
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Mon, 26 May 2014 20:07:43 -0700 (PDT)
Subject: generic non-linear filtering that support selem and boundary
 handling
In-Reply-To: <92352f83-537a-4d42-947f-fdcf6945043c@googlegroups.com>
References: <92352f83-537a-4d42-947f-fdcf6945043c@googlegroups.com>
Message-ID: <6358a1c1-e101-471c-8e52-067f52e0f584@googlegroups.com>

Funny you should request this. I built a Cython framework do exactly what 
you want (arbitrary selem, boundary handling [padding], and even arbitrary 
weighting of the selem in 2D and 3D) for local *weighted *variance.

The framework is about as useful as the actual calculation. Replace the 
innermost loop, change the name, and you get an entirely different 
non-linear weighted local feature. This requires a somewhat skilled user, 
but the framework is already done so it isn't as hard as it sounds.

Trouble is, I used some features from cython.parallel so those would have 
to be stripped out, losing over an order of magnitude in speed. I've been 
kicking around submitting them, but going back and ripping out the parallel 
features is painful.

If interested I can clean up and put them in a Gist or two.

Josh

On Monday, May 26, 2014 1:50:10 AM UTC-5, Chencan QIAN wrote:
>
> Essentially, this is something similar 
> to scipy.ndimage.filters.generic_filter (which is too slow because of its 
> internal python for-loop), but implemented in cython as with 
> skimage.filter.rank family.
>
> Given the diversity within skimage.filter.rank, a generic function would 
> be very useful. For example, I'd like to calculate local variance, which is 
> conceptually similar to skimage.filter.rank.mean, but not supported 
> currently.
>
> I guess the absence of such a function must be due to some unresolved 
> technical obstacle?
>
> Thanks~
>
> Chencan
>
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From silvertrumpet999 at gmail.com  Tue May 27 00:49:55 2014
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Mon, 26 May 2014 21:49:55 -0700 (PDT)
Subject: generic non-linear filtering that support selem and boundary
 handling
In-Reply-To: <CA+JHcKR+L=-tY8jCSoiMRgeXpdnpAyC3GpazAA9EBP2id=4C3Q@mail.gmail.com>
References: <92352f83-537a-4d42-947f-fdcf6945043c@googlegroups.com> <6358a1c1-e101-471c-8e52-067f52e0f584@googlegroups.com>
 <CA+JHcKR+L=-tY8jCSoiMRgeXpdnpAyC3GpazAA9EBP2id=4C3Q@mail.gmail.com>
Message-ID: <e5de8a65-9435-4f17-9deb-8b6a6eb6f2d1@googlegroups.com>

Basically OSX uses Clang, and Clang doesn't (yet) support OpenMP. Some 
people are working toward this, but it's not in there yet. OSX is the only 
architecture for which this is a problem.

There are a lot of places in skimage where relatively simple optimizations 
(release the GIL, use prange) would reap very large performance benefits. 
I'd asked about this before, and it was viewed as not feasible due to 
Clang's limitations.

However, I looked at this again just now and it *might *be that Cython 
simply ignores OpenMP features under Clang, compiling as if they didn't 
exist (i.e. basically substitution range for prange). If that is true, I 
could submit these without much issue... and we could expose pretty 
dramatic improvements to some existing Cython loops. Sadly, I don't have a 
Clang platform to test this behavior.

Josh


On Monday, May 26, 2014 10:48:15 PM UTC-5, Juan Nunez-Iglesias wrote:
>
> Josh, why the parallel stripping out? Is it a Cython version requirement? 
> We can always have this as a "dormant" PR for 1.0, for which we might bump 
> up the version required. It might also be possible to wrap the import 
> around a try-catch clause so that it fails gracefully on an earlier Cython 
> version.
>
> Juan.
>
>
> On Tue, May 27, 2014 at 1:07 PM, Josh Warner <silvertrumpet999 at gmail.com>wrote:
>
>> Funny you should request this. I built a Cython framework do exactly what 
>> you want (arbitrary selem, boundary handling [padding], and even arbitrary 
>> weighting of the selem in 2D and 3D) for local *weighted *variance.
>>
>> The framework is about as useful as the actual calculation. Replace the 
>> innermost loop, change the name, and you get an entirely different 
>> non-linear weighted local feature. This requires a somewhat skilled user, 
>> but the framework is already done so it isn't as hard as it sounds.
>>
>> Trouble is, I used some features from cython.parallel so those would have 
>> to be stripped out, losing over an order of magnitude in speed. I've been 
>> kicking around submitting them, but going back and ripping out the parallel 
>> features is painful.
>>
>> If interested I can clean up and put them in a Gist or two.
>>
>> Josh
>>
>>
>> On Monday, May 26, 2014 1:50:10 AM UTC-5, Chencan QIAN wrote:
>>>
>>> Essentially, this is something similar to scipy.ndimage.filters.generic_filter 
>>> (which is too slow because of its internal python for-loop), but 
>>> implemented in cython as with skimage.filter.rank family.
>>>
>>> Given the diversity within skimage.filter.rank, a generic function would 
>>> be very useful. For example, I'd like to calculate local variance, which is 
>>> conceptually similar to skimage.filter.rank.mean, but not supported 
>>> currently.
>>>
>>> I guess the absence of such a function must be due to some unresolved 
>>> technical obstacle?
>>>
>>> Thanks~
>>>
>>> Chencan
>>>
>>  -- 
>> You received this message because you are subscribed to the Google Groups 
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an 
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>
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From qianchencan at gmail.com  Tue May 27 01:17:44 2014
From: qianchencan at gmail.com (Chencan QIAN)
Date: Mon, 26 May 2014 22:17:44 -0700 (PDT)
Subject: generic non-linear filtering that support selem and boundary
 handling
In-Reply-To: <6358a1c1-e101-471c-8e52-067f52e0f584@googlegroups.com>
References: <92352f83-537a-4d42-947f-fdcf6945043c@googlegroups.com>
 <6358a1c1-e101-471c-8e52-067f52e0f584@googlegroups.com>
Message-ID: <84cbf3d0-4aa5-4fe8-80d4-76da63b89ea5@googlegroups.com>

Hi Josh,

Your framework sounds really interesting!

In my opinion, it would be great to keep the current implementation (with 
cython.parallel) for the routine that calculates local weighted variance, 
while at the same time, expose a general purpose interface that accepts 
arbitrary python function (provided it still offers some performance gain 
compared with ndimage.filters.generic_filter. Will this be the case?).

On Tuesday, May 27, 2014 11:07:43 AM UTC+8, Josh Warner wrote:
>
> Funny you should request this. I built a Cython framework do exactly what 
> you want (arbitrary selem, boundary handling [padding], and even arbitrary 
> weighting of the selem in 2D and 3D) for local *weighted *variance.
>
> The framework is about as useful as the actual calculation. Replace the 
> innermost loop, change the name, and you get an entirely different 
> non-linear weighted local feature. This requires a somewhat skilled user, 
> but the framework is already done so it isn't as hard as it sounds.
>
> Trouble is, I used some features from cython.parallel so those would have 
> to be stripped out, losing over an order of magnitude in speed. I've been 
> kicking around submitting them, but going back and ripping out the parallel 
> features is painful.
>
> If interested I can clean up and put them in a Gist or two.
>
> Josh
>
> On Monday, May 26, 2014 1:50:10 AM UTC-5, Chencan QIAN wrote:
>>
>> Essentially, this is something similar 
>> to scipy.ndimage.filters.generic_filter (which is too slow because of its 
>> internal python for-loop), but implemented in cython as with 
>> skimage.filter.rank family.
>>
>> Given the diversity within skimage.filter.rank, a generic function would 
>> be very useful. For example, I'd like to calculate local variance, which is 
>> conceptually similar to skimage.filter.rank.mean, but not supported 
>> currently.
>>
>> I guess the absence of such a function must be due to some unresolved 
>> technical obstacle?
>>
>> Thanks~
>>
>> Chencan
>>
>
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From stefan at sun.ac.za  Tue May 27 01:40:45 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Tue, 27 May 2014 07:40:45 +0200
Subject: generic non-linear filtering that support selem and boundary handling
In-Reply-To: <CA+JHcKSZvr+gA10opUu6UtJ5kAPPRsiTwZFSPDOAp0Ss+pJCqg@mail.gmail.com>
References: <92352f83-537a-4d42-947f-fdcf6945043c@googlegroups.com>
 <6358a1c1-e101-471c-8e52-067f52e0f584@googlegroups.com> <CA+JHcKR+L=-tY8jCSoiMRgeXpdnpAyC3GpazAA9EBP2id=4C3Q@mail.gmail.com>
 <e5de8a65-9435-4f17-9deb-8b6a6eb6f2d1@googlegroups.com> <CA+JHcKSZvr+gA10opUu6UtJ5kAPPRsiTwZFSPDOAp0Ss+pJCqg@mail.gmail.com>
Message-ID: <CABDkGQmB9jVO3WFUKv_UJ6fVUcpe5Apnx6d9u3no=+dDjs=w_A@mail.gmail.com>

On Tue, May 27, 2014 at 7:27 AM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> St?fan, I thought I saw some message recently about access to some OSX
> machines for scikit-image testing?

Yes, Christoph Deil made available a machine for us to test on, so if
you'd like access please get in touch off-list.

Regards
St?fan


From jim at rybarski.com  Tue May 27 13:33:55 2014
From: jim at rybarski.com (jim at rybarski.com)
Date: Tue, 27 May 2014 10:33:55 -0700 (PDT)
Subject: Consistent equalization on set of images
Message-ID: <77538a38-b152-4585-95b1-fe507dbb7c0a@googlegroups.com>

I want to use exposure.equalize_adapthist() on a set of images, but a 
defined part of each image occasionally will have a very bright object in 
it, which I would like to ignore when calculating the equalization. 
Currently, the images with the very bright object are much darker than the 
images without it.

Really, one of two solutions would work, but I don't know how to do either 
with scikit-image:
1) Calculate a histogram equalization for the entire set of images and 
apply the same equalization to each one
2) Mask the area with the bright object, calculate the equalization of the 
rest of the image, and apply that equalization to the original image.

Are either possible? Thanks!
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From jsch at demuc.de  Tue May 27 06:55:45 2014
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Tue, 27 May 2014 10:55:45 +0000
Subject: generic non-linear filtering that support selem and boundary
 handling
In-Reply-To: <CABDkGQmB9jVO3WFUKv_UJ6fVUcpe5Apnx6d9u3no=+dDjs=w_A@mail.gmail.com>
References: <92352f83-537a-4d42-947f-fdcf6945043c@googlegroups.com>
 <6358a1c1-e101-471c-8e52-067f52e0f584@googlegroups.com>
 <CA+JHcKR+L=-tY8jCSoiMRgeXpdnpAyC3GpazAA9EBP2id=4C3Q@mail.gmail.com>
 <e5de8a65-9435-4f17-9deb-8b6a6eb6f2d1@googlegroups.com>
 <CA+JHcKSZvr+gA10opUu6UtJ5kAPPRsiTwZFSPDOAp0Ss+pJCqg@mail.gmail.com>,<CABDkGQmB9jVO3WFUKv_UJ6fVUcpe5Apnx6d9u3no=+dDjs=w_A@mail.gmail.com>
Message-ID: <71CD212A-BE9E-425D-8CBF-BD7E40B7E693@demuc.de>

Since this is a feature for 1.0 and my main system is OSX, I am happy to look into it when I'm back...

> On May 27, 2014, at 1:41 AM, "St?fan van der Walt" <stefan at sun.ac.za> wrote:
> 
>> On Tue, May 27, 2014 at 7:27 AM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
>> St?fan, I thought I saw some message recently about access to some OSX
>> machines for scikit-image testing?
> 
> Yes, Christoph Deil made available a machine for us to test on, so if
> you'd like access please get in touch off-list.
> 
> Regards
> St?fan
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.


From nadavh.horesh at gmail.com  Tue May 27 04:47:46 2014
From: nadavh.horesh at gmail.com (Nadav Horesh)
Date: Tue, 27 May 2014 11:47:46 +0300
Subject: Updating LinePorofile on image changed
Message-ID: <CA+oBP_s54qzPVRmeETGTbzTYEJgNCnoCovNtSa2Z8w_r3=X3Jg@mail.gmail.com>

Hi,

 I built an application based on skimage viewer some image filter plugins
and a LineProfile. In this application I want to investigate the influence
of the filters (tuned by some attached sliders) via the LineProfile tool.
My problem is that the tool sees only the original image, and not those
generated (and displayed in viewer window) by the filters.

 How can I make the LineProfile tool relate to the modified image?

  Thanks,

    Nadav.
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From jni.soma at gmail.com  Mon May 26 23:47:54 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Tue, 27 May 2014 13:47:54 +1000
Subject: generic non-linear filtering that support selem and boundary handling
In-Reply-To: <6358a1c1-e101-471c-8e52-067f52e0f584@googlegroups.com>
References: <92352f83-537a-4d42-947f-fdcf6945043c@googlegroups.com> <6358a1c1-e101-471c-8e52-067f52e0f584@googlegroups.com>
Message-ID: <CA+JHcKR+L=-tY8jCSoiMRgeXpdnpAyC3GpazAA9EBP2id=4C3Q@mail.gmail.com>

Josh, why the parallel stripping out? Is it a Cython version requirement?
We can always have this as a "dormant" PR for 1.0, for which we might bump
up the version required. It might also be possible to wrap the import
around a try-catch clause so that it fails gracefully on an earlier Cython
version.

Juan.


On Tue, May 27, 2014 at 1:07 PM, Josh Warner <silvertrumpet999 at gmail.com>wrote:

> Funny you should request this. I built a Cython framework do exactly what
> you want (arbitrary selem, boundary handling [padding], and even arbitrary
> weighting of the selem in 2D and 3D) for local *weighted *variance.
>
> The framework is about as useful as the actual calculation. Replace the
> innermost loop, change the name, and you get an entirely different
> non-linear weighted local feature. This requires a somewhat skilled user,
> but the framework is already done so it isn't as hard as it sounds.
>
> Trouble is, I used some features from cython.parallel so those would have
> to be stripped out, losing over an order of magnitude in speed. I've been
> kicking around submitting them, but going back and ripping out the parallel
> features is painful.
>
> If interested I can clean up and put them in a Gist or two.
>
> Josh
>
>
> On Monday, May 26, 2014 1:50:10 AM UTC-5, Chencan QIAN wrote:
>>
>> Essentially, this is something similar to scipy.ndimage.filters.generic_filter
>> (which is too slow because of its internal python for-loop), but
>> implemented in cython as with skimage.filter.rank family.
>>
>> Given the diversity within skimage.filter.rank, a generic function would
>> be very useful. For example, I'd like to calculate local variance, which is
>> conceptually similar to skimage.filter.rank.mean, but not supported
>> currently.
>>
>> I guess the absence of such a function must be due to some unresolved
>> technical obstacle?
>>
>> Thanks~
>>
>> Chencan
>>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From jni.soma at gmail.com  Tue May 27 01:27:39 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Tue, 27 May 2014 15:27:39 +1000
Subject: generic non-linear filtering that support selem and boundary handling
In-Reply-To: <e5de8a65-9435-4f17-9deb-8b6a6eb6f2d1@googlegroups.com>
References: <92352f83-537a-4d42-947f-fdcf6945043c@googlegroups.com>
 <6358a1c1-e101-471c-8e52-067f52e0f584@googlegroups.com> <CA+JHcKR+L=-tY8jCSoiMRgeXpdnpAyC3GpazAA9EBP2id=4C3Q@mail.gmail.com>
 <e5de8a65-9435-4f17-9deb-8b6a6eb6f2d1@googlegroups.com>
Message-ID: <CA+JHcKSZvr+gA10opUu6UtJ5kAPPRsiTwZFSPDOAp0Ss+pJCqg@mail.gmail.com>

St?fan, I thought I saw some message recently about access to some OSX
machines for scikit-image testing?

I have one (my laptop) but zero bandwidth for anything but the simplest
tests for now...

Juan.


On Tue, May 27, 2014 at 2:49 PM, Josh Warner <silvertrumpet999 at gmail.com>wrote:

> Basically OSX uses Clang, and Clang doesn't (yet) support OpenMP. Some
> people are working toward this, but it's not in there yet. OSX is the only
> architecture for which this is a problem.
>
> There are a lot of places in skimage where relatively simple optimizations
> (release the GIL, use prange) would reap very large performance benefits.
> I'd asked about this before, and it was viewed as not feasible due to
> Clang's limitations.
>
> However, I looked at this again just now and it *might *be that Cython
> simply ignores OpenMP features under Clang, compiling as if they didn't
> exist (i.e. basically substitution range for prange). If that is true, I
> could submit these without much issue... and we could expose pretty
> dramatic improvements to some existing Cython loops. Sadly, I don't have a
> Clang platform to test this behavior.
>
> Josh
>
>
> On Monday, May 26, 2014 10:48:15 PM UTC-5, Juan Nunez-Iglesias wrote:
>>
>> Josh, why the parallel stripping out? Is it a Cython version requirement?
>> We can always have this as a "dormant" PR for 1.0, for which we might bump
>> up the version required. It might also be possible to wrap the import
>> around a try-catch clause so that it fails gracefully on an earlier Cython
>> version.
>>
>> Juan.
>>
>>
>> On Tue, May 27, 2014 at 1:07 PM, Josh Warner <silvertrumpet999 at gmail.com>wrote:
>>
>>> Funny you should request this. I built a Cython framework do exactly
>>> what you want (arbitrary selem, boundary handling [padding], and even
>>> arbitrary weighting of the selem in 2D and 3D) for local *weighted *
>>> variance.
>>>
>>> The framework is about as useful as the actual calculation. Replace the
>>> innermost loop, change the name, and you get an entirely different
>>> non-linear weighted local feature. This requires a somewhat skilled user,
>>> but the framework is already done so it isn't as hard as it sounds.
>>>
>>> Trouble is, I used some features from cython.parallel so those would
>>> have to be stripped out, losing over an order of magnitude in speed. I've
>>> been kicking around submitting them, but going back and ripping out the
>>> parallel features is painful.
>>>
>>> If interested I can clean up and put them in a Gist or two.
>>>
>>> Josh
>>>
>>>
>>> On Monday, May 26, 2014 1:50:10 AM UTC-5, Chencan QIAN wrote:
>>>>
>>>> Essentially, this is something similar to scipy.ndimage.filters.generic_filter
>>>> (which is too slow because of its internal python for-loop), but
>>>> implemented in cython as with skimage.filter.rank family.
>>>>
>>>> Given the diversity within skimage.filter.rank, a generic function
>>>> would be very useful. For example, I'd like to calculate local variance,
>>>> which is conceptually similar to skimage.filter.rank.mean, but not
>>>> supported currently.
>>>>
>>>> I guess the absence of such a function must be due to some unresolved
>>>> technical obstacle?
>>>>
>>>> Thanks~
>>>>
>>>> Chencan
>>>>
>>>  --
>>> You received this message because you are subscribed to the Google
>>> Groups "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>
>>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From hannesschoenberger at gmail.com  Tue May 27 22:58:35 2014
From: hannesschoenberger at gmail.com (=?UTF-8?Q?Johannes_Sch=C3=B6nberger?=)
Date: Tue, 27 May 2014 19:58:35 -0700 (PDT)
Subject: ANN: scikit-image 0.10.0
In-Reply-To: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de>
References: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de>
Message-ID: <cd681a5b-ca64-42c6-8183-e079a2b16c92@googlegroups.com>

I'd wait for the Debian release until we push out 0.10.1 or 0.10.2...

On Tuesday, May 27, 2014 10:56:59 PM UTC-4, Johannes Sch?nberger wrote:
>
> Announcement: scikit-image 0.10.0 
> ================================= 
>
> We're happy to announce the release of scikit-image v0.10.0! 
>
> scikit-image is an image processing toolbox for SciPy that includes 
> algorithms 
> for segmentation, geometric transformations, color space manipulation, 
> analysis, filtering, morphology, feature detection, and more. 
>
> For more information, examples, and documentation, please visit our 
> website: 
>
>    http://scikit-image.org 
>
>
> New Features 
> ------------ 
>
> In addition to many bug fixes, (speed) improvements and new examples, the 
> 118 pull 
> requests (1112 commits) merged for this release include the following new 
> features (PR number in brackets): 
>
> - Viewer returns overlays (#810) 
> - Luv colorspace conversion (#798) 
> - Phase unwrapping (#644) 
> - Add Wiener deconvolution (#800) 
> - Sum filter to rank filters (#844) 
> - Updates to MCP algorithm. (#854) 
> - Add ISODATA thresholding (#859) 
> - Add `imread_collection` automatically if plugin provides `imread` (#862) 
> - Enforce SLIC superpixels connectivity (#857) 
> - Estimator class parameters now public (#840) 
> - BRIEF, ORB and CENSURE features (#834) 
> - SLIC-zero capabilities for SLIC segmentation. (#864) 
> - Shaded Polygon for LineProfile Plugin Output (#875) 
> - Add string inputs for range parameters of `rescale_intensity` (#897) 
> - Blob Detection (#903) 
> - `peak_local_max` support for N-d images (#906) 
> - Add loading from URL in novice module (#916) 
> - Correct mesh orientation in marching cubes algorithm (#882) 
> - Added alpha channel support to novice (#946) 
> - Equality for regionprops (#956) 
> - IPython notebook export for examples (#1000) 
>
>
> API changes 
> ----------- 
>
> The following backward-incompatible API changes were made between 0.9 and 
> 0.10: 
>
> - Removed deprecated functions in `skimage.filter.rank.*` 
> - Removed deprecated parameter `epsilon` of `skimage.viewer.LineProfile` 
> - Removed backwards-compatability of `skimage.measure.regionprops` 
> - Removed {`ratio`, `sigma`} deprecation warnings of 
> `skimage.segmentation.slic` 
>   and also remove explicit `sigma` parameter from doc-string example 
> - Changed default mode of random_walker segmentation to 'cg_mg' > 'cg' > 
> 'bf', 
>   depending on which optional dependencies are available. 
> - Removed deprecated `out` parameter of `skimage.morphology.binary_*` 
> - Removed deprecated parameter `depth` in 
> `skimage.segmentation.random_walker` 
> - Removed deprecated logger function in `skimage/__init__.py` 
> - Removed deprecated function `filter.median_filter` 
> - Removed deprecated `skimage.color.is_gray` and `skimage.color.is_rgb` 
>   functions 
> - Removed deprecated `skimage.segmentation.visualize_boundaries` 
> - Removed deprecated `skimage.morphology.greyscale_*` 
> - Removed deprecated `skimage.exposure.equalize` 
>
>
>
> Contributors to this release 
> ---------------------------- 
>
> This release was made possible by the collaborative efforts of many 
> contributors, both new and old.  They are listed in alphabetical order by 
> surname: 
>
> - Raphael Ackermann 
> - Ankit Agrawal 
> - Maximilian Albert 
> - Pietro Berkes 
> - Vighnesh Birodkar 
> - Fran?ois Boulogne 
> - Olivier Debeir 
> - Christoph Deil 
> - Jaidev Deshpande 
> - Jostein B? Fl?ystad 
> - Neeraj Gangwar 
> - Michael Hansen 
> - Almar Klein 
> - Jeremy Metz 
> - Juan Nunez-Iglesias 
> - Fran?ois Orieux 
> - Guillem Palou 
> - Rishabh Raj 
> - Thomas Robitaille 
> - Michal Romaniuk 
> - Johannes L. Sch?nberger 
> - Julian Taylor 
> - Gregor Thalhammer 
> - Matthew Trentacoste 
> - Siva Prasad Varma 
> - Guillem Palou Visa 
> - Stefan van der Walt 
> - Josh Warner 
> - Tony S Yu 
> - blink1073 
> - cgohlke 
> - jaimefrio 
> - radioxoma 
> - sharky93 
>
>
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From jsch at demuc.de  Tue May 27 22:42:19 2014
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=0F=F6nberger?=)
Date: Tue, 27 May 2014 22:42:19 -0400
Subject: ANN: scikit-image 0.10.0
Message-ID: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de>

Announcement: scikit-image 0.10.0
=================================

We're happy to announce the release of scikit-image v0.10.0!

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

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

   http://scikit-image.org


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

In addition to many bug fixes, (speed) improvements and new examples, the 118 pull
requests (1112 commits) merged for this release include the following new
features (PR number in brackets):

- Viewer returns overlays (#810)
- Luv colorspace conversion (#798)
- Phase unwrapping (#644)
- Add Wiener deconvolution (#800)
- Sum filter to rank filters (#844)
- Updates to MCP algorithm. (#854)
- Add ISODATA thresholding (#859)
- Add `imread_collection` automatically if plugin provides `imread` (#862)
- Enforce SLIC superpixels connectivity (#857)
- Estimator class parameters now public (#840)
- BRIEF, ORB and CENSURE features (#834)
- SLIC-zero capabilities for SLIC segmentation. (#864)
- Shaded Polygon for LineProfile Plugin Output (#875)
- Add string inputs for range parameters of `rescale_intensity` (#897)
- Blob Detection (#903)
- `peak_local_max` support for N-d images (#906)
- Add loading from URL in novice module (#916)
- Correct mesh orientation in marching cubes algorithm (#882)
- Added alpha channel support to novice (#946)
- Equality for regionprops (#956)
- IPython notebook export for examples (#1000)


API changes
-----------

The following backward-incompatible API changes were made between 0.9 and 0.10:

- Removed deprecated functions in `skimage.filter.rank.*`
- Removed deprecated parameter `epsilon` of `skimage.viewer.LineProfile`
- Removed backwards-compatability of `skimage.measure.regionprops`
- Removed {`ratio`, `sigma`} deprecation warnings of `skimage.segmentation.slic`
  and also remove explicit `sigma` parameter from doc-string example
- Changed default mode of random_walker segmentation to 'cg_mg' > 'cg' > 'bf',
  depending on which optional dependencies are available.
- Removed deprecated `out` parameter of `skimage.morphology.binary_*`
- Removed deprecated parameter `depth` in `skimage.segmentation.random_walker`
- Removed deprecated logger function in `skimage/__init__.py`
- Removed deprecated function `filter.median_filter`
- Removed deprecated `skimage.color.is_gray` and `skimage.color.is_rgb`
  functions
- Removed deprecated `skimage.segmentation.visualize_boundaries`
- Removed deprecated `skimage.morphology.greyscale_*`
- Removed deprecated `skimage.exposure.equalize`



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

This release was made possible by the collaborative efforts of many
contributors, both new and old.  They are listed in alphabetical order by
surname:

- Raphael Ackermann
- Ankit Agrawal
- Maximilian Albert
- Pietro Berkes
- Vighnesh Birodkar
- Fran?ois Boulogne
- Olivier Debeir
- Christoph Deil
- Jaidev Deshpande
- Jostein B? Fl?ystad
- Neeraj Gangwar
- Michael Hansen
- Almar Klein
- Jeremy Metz
- Juan Nunez-Iglesias
- Fran?ois Orieux
- Guillem Palou
- Rishabh Raj
- Thomas Robitaille
- Michal Romaniuk
- Johannes L. Sch?nberger
- Julian Taylor
- Gregor Thalhammer
- Matthew Trentacoste
- Siva Prasad Varma
- Guillem Palou Visa
- Stefan van der Walt
- Josh Warner
- Tony S Yu
- blink1073
- cgohlke
- jaimefrio
- radioxoma
- sharky93



From steven.silvester at gmail.com  Wed May 28 19:44:42 2014
From: steven.silvester at gmail.com (Steven Silvester)
Date: Wed, 28 May 2014 16:44:42 -0700 (PDT)
Subject: Consistent equalization on set of images
In-Reply-To: <77538a38-b152-4585-95b1-fe507dbb7c0a@googlegroups.com>
References: <77538a38-b152-4585-95b1-fe507dbb7c0a@googlegroups.com>
Message-ID: <8fb1d9cd-abec-444b-93e0-9c5e79e3935f@googlegroups.com>

There is no way to do either directly, however:

1.  You could take the mean of all images and apply the equalization to that image.
2.  If you know the affected region you could just set the pixels in that region to the mean count in the image or take the pixels directly from an image that does not have the bright spot.  Then run the equalization on that image.

From stefan at sun.ac.za  Wed May 28 19:50:55 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Thu, 29 May 2014 01:50:55 +0200
Subject: Consistent equalization on set of images
In-Reply-To: <77538a38-b152-4585-95b1-fe507dbb7c0a@googlegroups.com>
References: <77538a38-b152-4585-95b1-fe507dbb7c0a@googlegroups.com>
Message-ID: <CABDkGQ=82PZnbDntLPc320=7dH0pb2Nh+x8PSo3yJ_7i7yQeTQ@mail.gmail.com>

Hi Jim

On Tue, May 27, 2014 at 7:33 PM,  <jim at rybarski.com> wrote:
> I want to use exposure.equalize_adapthist() on a set of images, but a
> defined part of each image occasionally will have a very bright object in
> it, which I would like to ignore when calculating the equalization.
> Currently, the images with the very bright object are much darker than the
> images without it.

It sounds like histogram matching might be a good first step.  See, e.g.,

https://github.com/stefanv/supreme/blob/master/supreme/photometry/register.py#L30

That function hasn't been battle tested, so you may want to use it as
inspiration only.

St?fan


From matthew.brett at gmail.com  Thu May 29 20:26:26 2014
From: matthew.brett at gmail.com (Matthew Brett)
Date: Thu, 29 May 2014 17:26:26 -0700 (PDT)
Subject: ANN: scikit-image 0.10.0
In-Reply-To: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de>
References: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de>
Message-ID: <e398fadf-c73f-4320-8b4e-1d46dc4828a1@googlegroups.com>

Hi guys,

On Tuesday, May 27, 2014 7:56:59 PM UTC-7, Johannes Sch?nberger wrote:
>
> Announcement: scikit-image 0.10.0 
> ================================= 
>
> We're happy to announce the release of scikit-image v0.10.0! 
>
> scikit-image is an image processing toolbox for SciPy that includes 
> algorithms 
> for segmentation, geometric transformations, color space manipulation, 
> analysis, filtering, morphology, feature detection, and more. 
>
> For more information, examples, and documentation, please visit our 
> website: 
>
>    http://scikit-image.org 
>
>
> New Features 
> ------------ 
>
> In addition to many bug fixes, (speed) improvements and new examples, the 
> 118 pull 
> requests (1112 commits) merged for this release include the following new 
> features (PR number in brackets): 
>
> - Viewer returns overlays (#810) 
> - Luv colorspace conversion (#798) 
> - Phase unwrapping (#644) 
> - Add Wiener deconvolution (#800) 
> - Sum filter to rank filters (#844) 
> - Updates to MCP algorithm. (#854) 
> - Add ISODATA thresholding (#859) 
> - Add `imread_collection` automatically if plugin provides `imread` (#862) 
> - Enforce SLIC superpixels connectivity (#857) 
> - Estimator class parameters now public (#840) 
> - BRIEF, ORB and CENSURE features (#834) 
> - SLIC-zero capabilities for SLIC segmentation. (#864) 
> - Shaded Polygon for LineProfile Plugin Output (#875) 
> - Add string inputs for range parameters of `rescale_intensity` (#897) 
> - Blob Detection (#903) 
> - `peak_local_max` support for N-d images (#906) 
> - Add loading from URL in novice module (#916) 
> - Correct mesh orientation in marching cubes algorithm (#882) 
> - Added alpha channel support to novice (#946) 
> - Equality for regionprops (#956) 
> - IPython notebook export for examples (#1000) 
>
>
> API changes 
> ----------- 
>
> The following backward-incompatible API changes were made between 0.9 and 
> 0.10: 
>
> - Removed deprecated functions in `skimage.filter.rank.*` 
> - Removed deprecated parameter `epsilon` of `skimage.viewer.LineProfile` 
> - Removed backwards-compatability of `skimage.measure.regionprops` 
> - Removed {`ratio`, `sigma`} deprecation warnings of 
> `skimage.segmentation.slic` 
>   and also remove explicit `sigma` parameter from doc-string example 
> - Changed default mode of random_walker segmentation to 'cg_mg' > 'cg' > 
> 'bf', 
>   depending on which optional dependencies are available. 
> - Removed deprecated `out` parameter of `skimage.morphology.binary_*` 
> - Removed deprecated parameter `depth` in 
> `skimage.segmentation.random_walker` 
> - Removed deprecated logger function in `skimage/__init__.py` 
> - Removed deprecated function `filter.median_filter` 
> - Removed deprecated `skimage.color.is_gray` and `skimage.color.is_rgb` 
>   functions 
> - Removed deprecated `skimage.segmentation.visualize_boundaries` 
> - Removed deprecated `skimage.morphology.greyscale_*` 
> - Removed deprecated `skimage.exposure.equalize` 
>
>
>
> Contributors to this release 
> ---------------------------- 
>
> This release was made possible by the collaborative efforts of many 
> contributors, both new and old.  They are listed in alphabetical order by 
> surname: 
>
> - Raphael Ackermann 
> - Ankit Agrawal 
> - Maximilian Albert 
> - Pietro Berkes 
> - Vighnesh Birodkar 
> - Fran?ois Boulogne 
> - Olivier Debeir 
> - Christoph Deil 
> - Jaidev Deshpande 
> - Jostein B? Fl?ystad 
> - Neeraj Gangwar 
> - Michael Hansen 
> - Almar Klein 
> - Jeremy Metz 
> - Juan Nunez-Iglesias 
> - Fran?ois Orieux 
> - Guillem Palou 
> - Rishabh Raj 
> - Thomas Robitaille 
> - Michal Romaniuk 
> - Johannes L. Sch?nberger 
> - Julian Taylor 
> - Gregor Thalhammer 
> - Matthew Trentacoste 
> - Siva Prasad Varma 
> - Guillem Palou Visa 
> - Stefan van der Walt 
> - Josh Warner 
> - Tony S Yu 
> - blink1073 
> - cgohlke 
> - jaimefrio 
> - radioxoma 
> - sharky93
>


Congratulations?  Any chance of putting up some OSX wheels on pypi?

I've built some here if you'd like to use those:

https://nipy.bic.berkeley.edu/scipy_installers/scikit_image-0.10.0-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.whl
https://nipy.bic.berkeley.edu/scipy_installers/scikit_image-0.10.0-cp33-cp33m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.whl
https://nipy.bic.berkeley.edu/scipy_installers/scikit_image-0.10.0-cp34-cp34m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.whl

General build recipe for OSX wheels here:

https://github.com/MacPython/wiki/wiki/Spinning-wheels#practical-example-of-building-wheels-for-a-project

Cheers,

Matthew
 
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