From erpayal2010 at gmail.com  Tue Oct  1 02:42:05 2013
From: erpayal2010 at gmail.com (Payal Gupta)
Date: Mon, 30 Sep 2013 23:42:05 -0700 (PDT)
Subject: import error on linux
In-Reply-To: <CAE5Ny9t1UMbvDOO+zrTR0NMasvP41QsjoG2gnsat5KPTHuMi_A@mail.gmail.com>
References: <CAE5Ny9t1UMbvDOO+zrTR0NMasvP41QsjoG2gnsat5KPTHuMi_A@mail.gmail.com>
Message-ID: <df835b83-2438-4b71-8f07-86303885af16@googlegroups.com>


hello everyone...

my problem solved... 
thanks to all.... :) :)


On Friday, September 27, 2013 12:52:35 PM UTC+5:30, Payal Gupta wrote:
>
> hello....
>
> i am using skimage library on raspberry pi which have  linux platform but 
> i cant import skimage module on this.
>  
> what do i do?
> anybody know this prob.
> reply
>
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From stefan at sun.ac.za  Wed Oct  2 08:14:48 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 2 Oct 2013 14:14:48 +0200
Subject: Release time
Message-ID: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com>

Hi everyone

I think we are just about ready for 0.9.  Please have a look at
outstanding PRs, and see if there is anything that can be included in
the next release.  If all goes well, we can tag the release this
Sunday.

St?fan


From jsch at demuc.de  Wed Oct  2 08:22:12 2013
From: jsch at demuc.de (=?windows-1252?Q?Johannes_Sch=F6nberger?=)
Date: Wed, 2 Oct 2013 14:22:12 +0200
Subject: Release time
In-Reply-To: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com>
Message-ID: <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de>

Hi St?fan,

I must say that I would not feel comfortable if we'd release 0.9 before the GSoC code is not cleaned up. There are some parts which definitely need an overhaul before we release it to the public in the form of a stable release. I can only speak for the feature detection and description part here? and I am not able to accomplish this until Sunday. Especially, I also need Ankit to polish some things first.

Is there a way to hold Ankit's changes back in 0.9 and defer them to 0.10?

Johannes

Am 02.10.2013 um 14:14 schrieb St?fan van der Walt <stefan at sun.ac.za>:

> Hi everyone
> 
> I think we are just about ready for 0.9.  Please have a look at
> outstanding PRs, and see if there is anything that can be included in
> the next release.  If all goes well, we can tag the release this
> Sunday.
> 
> St?fan
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
> 



From stefan at sun.ac.za  Wed Oct  2 08:29:07 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 2 Oct 2013 14:29:07 +0200
Subject: Release time
In-Reply-To: <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com>
 <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de>
Message-ID: <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com>

Hi Johannes

On Wed, Oct 2, 2013 at 2:22 PM, Johannes Sch?nberger <jsch at demuc.de> wrote:
> I must say that I would not feel comfortable if we'd release 0.9 before the GSoC code is not cleaned up. There are some parts which definitely need an overhaul before we release it to the public in the form of a stable release. I can only speak for the feature detection and description part here? and I am not able to accomplish this until Sunday. Especially, I also need Ankit to polish some things first.
>
> Is there a way to hold Ankit's changes back in 0.9 and defer them to 0.10?

How long would it take to fix things up, do you think?  If it
introduces a two week delay, we can do it, otherwise it's probably
best to forge ahead without it.

St?fan


From jsch at demuc.de  Wed Oct  2 08:36:16 2013
From: jsch at demuc.de (=?windows-1252?Q?Johannes_Sch=F6nberger?=)
Date: Wed, 2 Oct 2013 14:36:16 +0200
Subject: Release time
In-Reply-To: <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com> <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com>
Message-ID: <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de>

> How long would it take to fix things up, do you think?  If it
> introduces a two week delay, we can do it, otherwise it's probably
> best to forge ahead without it.

To finish everything (ORB and FREAK), I guess it needs more time - at least at the current pace.

I recommend to exclude the changes. How would you do that?


From stefan at sun.ac.za  Wed Oct  2 08:39:27 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 2 Oct 2013 14:39:27 +0200
Subject: Release time
In-Reply-To: <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com>
 <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com>
 <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de>
Message-ID: <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com>

On Wed, Oct 2, 2013 at 2:36 PM, Johannes Sch?nberger <jsch at demuc.de> wrote:
> To finish everything (ORB and FREAK), I guess it needs more time - at least at the current pace.
>
> I recommend to exclude the changes. How would you do that?

Those PRs haven't been merged, right?  So we only need to round off
the ones that are already in.

St?fan


From jsch at demuc.de  Wed Oct  2 08:48:32 2013
From: jsch at demuc.de (=?windows-1252?Q?Johannes_Sch=F6nberger?=)
Date: Wed, 2 Oct 2013 14:48:32 +0200
Subject: Release time
In-Reply-To: <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com> <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com> <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de> <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com>
Message-ID: <583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de>

Unfortunately I have merged 2 (+1):

https://github.com/scikit-image/scikit-image/pull/591
https://github.com/scikit-image/scikit-image/pull/668
(https://github.com/scikit-image/scikit-image/pull/669)

Back then I thought they were perfect. But during GSoC I changed my mind on some of the design decisions. I also discussed this with Ankit already?

Couldn't we just simply remove those functions from __all__ in the feature/__init__.py in the mean time?

Am 02.10.2013 um 14:39 schrieb St?fan van der Walt <stefan at sun.ac.za>:

> On Wed, Oct 2, 2013 at 2:36 PM, Johannes Sch?nberger <jsch at demuc.de> wrote:
>> To finish everything (ORB and FREAK), I guess it needs more time - at least at the current pace.
>> 
>> I recommend to exclude the changes. How would you do that?
> 
> Those PRs haven't been merged, right?  So we only need to round off
> the ones that are already in.
> 
> St?fan
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
> 



From stefan at sun.ac.za  Wed Oct  2 08:55:03 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 2 Oct 2013 14:55:03 +0200
Subject: Release time
In-Reply-To: <583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com>
 <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com>
 <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de> <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com>
 <583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de>
Message-ID: <CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com>

On Wed, Oct 2, 2013 at 2:48 PM, Johannes Sch?nberger <jsch at demuc.de> wrote:
> Couldn't we just simply remove those functions from __all__ in the feature/__init__.py in the mean time?

Good suggestion--can you update the docstrings to label them as experimental?

St?fan


From jsch at demuc.de  Wed Oct  2 09:05:56 2013
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Wed, 2 Oct 2013 15:05:56 +0200
Subject: Release time
In-Reply-To: <CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com> <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com> <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de> <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com> <583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de> <CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com>
Message-ID: <9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de>

I'll do that tonight. Is there as special syntax for marking a function as "experimental"?

Am 02.10.2013 um 14:55 schrieb St?fan van der Walt <stefan at sun.ac.za>:

> On Wed, Oct 2, 2013 at 2:48 PM, Johannes Sch?nberger <jsch at demuc.de> wrote:
>> Couldn't we just simply remove those functions from __all__ in the feature/__init__.py in the mean time?
> 
> Good suggestion--can you update the docstrings to label them as experimental?
> 
> St?fan
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
> 



From jsch at demuc.de  Wed Oct  2 10:49:24 2013
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Wed, 2 Oct 2013 16:49:24 +0200
Subject: Release time
In-Reply-To: <9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com> <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com> <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de> <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com> <583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de> <CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com> <9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de>
Message-ID: <3370D65E-B530-4B57-B71D-AC8549A7791B@demuc.de>

Stefan: https://github.com/scikit-image/scikit-image/pull/749

Am 02.10.2013 um 15:05 schrieb Johannes Sch?nberger <jsch at demuc.de>:

> I'll do that tonight. Is there as special syntax for marking a function as "experimental"?
> 
> Am 02.10.2013 um 14:55 schrieb St?fan van der Walt <stefan at sun.ac.za>:
> 
>> On Wed, Oct 2, 2013 at 2:48 PM, Johannes Sch?nberger <jsch at demuc.de> wrote:
>>> Couldn't we just simply remove those functions from __all__ in the feature/__init__.py in the mean time?
>> 
>> Good suggestion--can you update the docstrings to label them as experimental?
>> 
>> St?fan
>> 
>> -- 
>> You received this message because you are subscribed to the Google Groups "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/groups/opt_out.
>> 
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
> 



From jostein.floystad at gmail.com  Wed Oct  2 11:35:08 2013
From: jostein.floystad at gmail.com (=?ISO-8859-1?Q?Jostein_B=F8_Fl=F8ystad?=)
Date: Wed, 2 Oct 2013 17:35:08 +0200
Subject: Release time
In-Reply-To: <3370D65E-B530-4B57-B71D-AC8549A7791B@demuc.de>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com>
	<178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de>
	<CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com>
	<C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de>
	<CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com>
	<583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de>
	<CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com>
	<9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de>
	<3370D65E-B530-4B57-B71D-AC8549A7791B@demuc.de>
Message-ID: <CAF+hgui_p38G0duCHNCez85xa0ThkP9modmnESqEerxfyhy88A@mail.gmail.com>

The changes suggested here would require raising deprecation warnings in
0.9:

https://github.com/scikit-image/scikit-image/issues/744

It would be nice to discuss these before the new release.

Jostein


2013/10/2 Johannes Sch?nberger <jsch at demuc.de>

> Stefan: https://github.com/scikit-image/scikit-image/pull/749
>
> Am 02.10.2013 um 15:05 schrieb Johannes Sch?nberger <jsch at demuc.de>:
>
> > I'll do that tonight. Is there as special syntax for marking a function
> as "experimental"?
> >
> > Am 02.10.2013 um 14:55 schrieb St?fan van der Walt <stefan at sun.ac.za>:
> >
> >> On Wed, Oct 2, 2013 at 2:48 PM, Johannes Sch?nberger <jsch at demuc.de>
> wrote:
> >>> Couldn't we just simply remove those functions from __all__ in the
> feature/__init__.py in the mean time?
> >>
> >> Good suggestion--can you update the docstrings to label them as
> experimental?
> >>
> >> St?fan
> >>
> >> --
> >> You received this message because you are subscribed to the Google
> Groups "scikit-image" group.
> >> To unsubscribe from this group and stop receiving emails from it, send
> an email to scikit-image+unsubscribe at googlegroups.com.
> >> For more options, visit https://groups.google.com/groups/opt_out.
> >>
> >
> > --
> > You received this message because you are subscribed to the Google
> Groups "scikit-image" group.
> > To unsubscribe from this group and stop receiving emails from it, send
> an email to scikit-image+unsubscribe at googlegroups.com.
> > For more options, visit https://groups.google.com/groups/opt_out.
> >
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
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>
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From stefan at sun.ac.za  Wed Oct  2 11:54:41 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 2 Oct 2013 17:54:41 +0200
Subject: Release time
In-Reply-To: <CAF+hgui_p38G0duCHNCez85xa0ThkP9modmnESqEerxfyhy88A@mail.gmail.com>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com>
 <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com>
 <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de> <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com>
 <583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de> <CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com>
 <9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de> <3370D65E-B530-4B57-B71D-AC8549A7791B@demuc.de>
 <CAF+hgui_p38G0duCHNCez85xa0ThkP9modmnESqEerxfyhy88A@mail.gmail.com>
Message-ID: <CABDkGQkQNHUB=UVZzMsssanpqDqmMURNbSZ-iaW8vFKboQK_oA@mail.gmail.com>

On Wed, Oct 2, 2013 at 5:35 PM, Jostein B? Fl?ystad
<jostein.floystad at gmail.com> wrote:
> The changes suggested here would require raising deprecation warnings in
> 0.9:
>
> https://github.com/scikit-image/scikit-image/issues/744
>
> It would be nice to discuss these before the new release.

Good, let's get these discussions started, then we can tag in about a
week from now.

St?fan


From stefan at sun.ac.za  Wed Oct  2 12:21:21 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 2 Oct 2013 18:21:21 +0200
Subject: Screenshots for PyCon
Message-ID: <CABDkGQn=nYWFvNu9r7doVJOCGpxw0ZoJ58ZK4YuvwNwvEbH-gA@mail.gmail.com>

Hi folks,

I'm giving a talk on skimage at PyCon ZA tomorrow. I still have room for a
few screenshots or for one demo. If anyone has a particularly nice example,
please send it my way.

Thanks!
St?fan
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From fboulogne at sciunto.org  Wed Oct  2 12:47:01 2013
From: fboulogne at sciunto.org (=?ISO-8859-1?Q?Fran=E7ois_Boulogne?=)
Date: Wed, 02 Oct 2013 18:47:01 +0200
Subject: Release time
In-Reply-To: <CABDkGQkQNHUB=UVZzMsssanpqDqmMURNbSZ-iaW8vFKboQK_oA@mail.gmail.com>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com> <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com> <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de> <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com> <583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de> <CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com> <9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de> <3370D65E-B530-4B57-B71D-AC8549A7791B@demuc.de> <CAF+hgui_p38G0duCHNCez85xa0ThkP9modmnESqEerxfyhy88A@mail.gmail.com> <CABDkGQkQNHUB=UVZzMsssanpqDqmMURNbSZ-iaW8vFKboQK_oA@mail.gmail.com>
Message-ID: <524C4E05.4030408@sciunto.org>

Hi,

I saw this ticket: https://github.com/scikit-image/scikit-image/issues/745
possible issue with numpy 1.8.0.

Cheers,

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



From erpayal2010 at gmail.com  Thu Oct  3 04:14:22 2013
From: erpayal2010 at gmail.com (Payal Gupta)
Date: Thu, 3 Oct 2013 01:14:22 -0700 (PDT)
Subject: Screenshots for PyCon
In-Reply-To: <CABDkGQn=nYWFvNu9r7doVJOCGpxw0ZoJ58ZK4YuvwNwvEbH-gA@mail.gmail.com>
References: <CABDkGQn=nYWFvNu9r7doVJOCGpxw0ZoJ58ZK4YuvwNwvEbH-gA@mail.gmail.com>
Message-ID: <fa617b53-fd21-4928-b0d1-d9ac97d3f3ee@googlegroups.com>



On Wednesday, October 2, 2013 9:51:21 PM UTC+5:30, Stefan van der Walt 
wrote:
>
> Hi folks, 
>
> I'm giving a talk on skimage at PyCon ZA tomorrow. I still have room for a 
> few screenshots or for one demo. If anyone has a particularly nice example, 
> please send it my way. 
>
> Thanks! 
> St?fan 
>
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From erpayal2010 at gmail.com  Thu Oct  3 04:14:42 2013
From: erpayal2010 at gmail.com (Payal Gupta)
Date: Thu, 3 Oct 2013 01:14:42 -0700 (PDT)
Subject: Screenshots for PyCon
In-Reply-To: <CA+JHcKSdqe6++Lk9mttnRj7B4EYygRtH8n_BTm-L7eYB+WWGjg@mail.gmail.com>
References: <CABDkGQn=nYWFvNu9r7doVJOCGpxw0ZoJ58ZK4YuvwNwvEbH-gA@mail.gmail.com>
 <CA+JHcKSdqe6++Lk9mttnRj7B4EYygRtH8n_BTm-L7eYB+WWGjg@mail.gmail.com>
Message-ID: <1e26ff82-a58f-493c-a83b-a3830daa1040@googlegroups.com>

hey juan,

i am using threshold_otsu for thresholding  but  i am not getting 
appropriate result. And how to use threshold_adapt?
i want to convert gray image to binary image.
how can i do?
anybody help in this problem.

thanks  

On Thursday, October 3, 2013 7:28:44 AM UTC+5:30, Juan Nunez-Iglesias wrote:
>
> Hi Stefan,
>
> I hope this isn't too late. I recently had to segment out the chromosomes 
> in this picture:
>
> [image: Inline image 1]
>
> You can see the illumination is really uneven, so `threshold_otsu` does 
> really poorly. `threshold_adapt` works as advertised but you get some 
> artifacts:
>
> [image: Inline image 2]
>
> The key to getting around this was seeing the "grain" in the outside 
> regions compared to the chromosomes themselves. So after a `binary_opening` 
> with the right parameters (don't have them off the top of my head), 
> followed by a `remove_small_objects`:
>
> [image: Inline image 3]
>
> Hope that helps!
>
> Juan.
>
> PS: I also made this notebook<http://nbviewer.ipython.org/urls/github.com/jni/notebooks/raw/master/potholes.ipynb>to help Mehmet Kunt, a civil engineering professor Emmanuelle and I met at 
> EuroSciPy, measure potholes in images.
>
>
>
> On Thu, Oct 3, 2013 at 2:21 AM, St?fan van der Walt <ste... at sun.ac.za<javascript:>
> > wrote:
>
>> Hi folks, 
>>
>> I'm giving a talk on skimage at PyCon ZA tomorrow. I still have room for 
>> a few screenshots or for one demo. If anyone has a particularly nice 
>> example, please send it my way. 
>>
>> Thanks! 
>> St?fan 
>>
>> -- 
>> You received this message because you are subscribed to the Google Groups 
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an 
>> email to scikit-image... at googlegroups.com <javascript:>.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>
>
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From stefan at sun.ac.za  Thu Oct  3 00:45:05 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 3 Oct 2013 06:45:05 +0200
Subject: Screenshots for PyCon
In-Reply-To: <CA+JHcKSdqe6++Lk9mttnRj7B4EYygRtH8n_BTm-L7eYB+WWGjg@mail.gmail.com>
References: <CABDkGQn=nYWFvNu9r7doVJOCGpxw0ZoJ58ZK4YuvwNwvEbH-gA@mail.gmail.com>
 <CA+JHcKSdqe6++Lk9mttnRj7B4EYygRtH8n_BTm-L7eYB+WWGjg@mail.gmail.com>
Message-ID: <CABDkGQno-fmZqQz6QUF0NzXqD065kDwZ9b8-AoyYvc46U7kXpA@mail.gmail.com>

On Thu, Oct 3, 2013 at 3:58 AM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> I hope this isn't too late. I recently had to segment out the chromosomes in this picture:

Very nicely done, thank you!

St?fan


From jni.soma at gmail.com  Wed Oct  2 21:58:44 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Thu, 3 Oct 2013 11:58:44 +1000
Subject: Screenshots for PyCon
In-Reply-To: <CABDkGQn=nYWFvNu9r7doVJOCGpxw0ZoJ58ZK4YuvwNwvEbH-gA@mail.gmail.com>
References: <CABDkGQn=nYWFvNu9r7doVJOCGpxw0ZoJ58ZK4YuvwNwvEbH-gA@mail.gmail.com>
Message-ID: <CA+JHcKSdqe6++Lk9mttnRj7B4EYygRtH8n_BTm-L7eYB+WWGjg@mail.gmail.com>

Hi Stefan,

I hope this isn't too late. I recently had to segment out the chromosomes
in this picture:

[image: Inline image 1]

You can see the illumination is really uneven, so `threshold_otsu` does
really poorly. `threshold_adapt` works as advertised but you get some
artifacts:

[image: Inline image 2]

The key to getting around this was seeing the "grain" in the outside
regions compared to the chromosomes themselves. So after a `binary_opening`
with the right parameters (don't have them off the top of my head),
followed by a `remove_small_objects`:

[image: Inline image 3]

Hope that helps!

Juan.

PS: I also made this
notebook<http://nbviewer.ipython.org/urls/github.com/jni/notebooks/raw/master/potholes.ipynb>to
help Mehmet Kunt, a civil engineering professor Emmanuelle and I met
at
EuroSciPy, measure potholes in images.



On Thu, Oct 3, 2013 at 2:21 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> Hi folks,
>
> I'm giving a talk on skimage at PyCon ZA tomorrow. I still have room for a
> few screenshots or for one demo. If anyone has a particularly nice example,
> please send it my way.
>
> Thanks!
> St?fan
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>
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From silvertrumpet999 at gmail.com  Thu Oct  3 19:10:45 2013
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Thu, 3 Oct 2013 16:10:45 -0700 (PDT)
Subject: umfpack error
In-Reply-To: <CA+JHcKSZZKrP5y_3R+CQh5UartSuJdJf_Z86u6e9V-P+0kRD9A@mail.gmail.com>
References: <CA+JHcKSZZKrP5y_3R+CQh5UartSuJdJf_Z86u6e9V-P+0kRD9A@mail.gmail.com>
Message-ID: <95be83e4-743f-4ed7-938f-d1a88868ee16@googlegroups.com>

SciPy has a number of optional dependencies, which `pip` doesn't attempt to 
install. Largely because several of them are not directly Python based, and 
`pip` isn't a true package manager. Without them SciPy builds and runs, but 
certain pieces either run slower (in this case, parts of `scipy.sparse`) or 
don't exist at all.

Near the top of the very lengthy build and compile log for SciPy there is a 
brief report on which optional dependencies are present at time of build.

Presumably you don't have umfpack. It's also possible you do, but lack the 
development headers - but for the purposes of this argument, let's assume 
you don't. 


   1. The first step is to get umfpack. Doing this varies across platforms, 
   but if you're on linux check repos first. If not, look online for the best 
   method; I've always gotten it this way.
   2. Next step is to get the development headers for umfpack. Usually in 
   Linux package managers (yum, apt, etc.) these have the same name with 
   `'-dev'` appended. They're what SciPy needs to find and use umfpack.
   3. Finally, you'll need to remove and rebuild SciPy with `$ pip 
   uninstall scipy` followed by `$pip install scipy`. The new build should 
   auto-detect umfpack and build appropriately.

Hopefully that helps. God help you if you're on Windows; I sure can't.

Josh

On Thursday, October 3, 2013 1:21:43 AM UTC-5, Juan Nunez-Iglesias wrote:
>
> Hi guys,
>
> How do I build scipy with umfpack to silence this error:
>
> Exception AttributeError: "'UmfpackContext' object has no attribute '_symbolic'" in <bound method UmfpackContext.__del__ of <scipy.sparse.linalg.dsolve.umfpack.umfpack.UmfpackContext object at 0x101b62050>> ignored
>
> and speed up random_walker? I've just been doing a pip install scipy till 
> now.
>
> Juan.
>
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From silvertrumpet999 at gmail.com  Thu Oct  3 19:17:07 2013
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Thu, 3 Oct 2013 16:17:07 -0700 (PDT)
Subject: umfpack error
In-Reply-To: <CA+JHcKSZZKrP5y_3R+CQh5UartSuJdJf_Z86u6e9V-P+0kRD9A@mail.gmail.com>
References: <CA+JHcKSZZKrP5y_3R+CQh5UartSuJdJf_Z86u6e9V-P+0kRD9A@mail.gmail.com>
Message-ID: <762baf0e-52c2-488b-ac8b-9e5e7caa4dc9@googlegroups.com>



Final note - umfpack enables mode='cg' in random_walker, which is better 
than brute force but not the fastest or most efficient mode. The multi-grid 
preconditioned conjugate gradient method is: mode='cg_mg'. This is enabled 
by pyamg, which is independent of umfpack and is considerably easier to 
install and use than the method I just described.

Come to think of it, we probably should suppress that warning if import 
pyamg works. It incorrectly implies the user doesn't have the fastest mode 
available.

On Thursday, October 3, 2013 1:21:43 AM UTC-5, Juan Nunez-Iglesias wrote:

Hi guys,
>
> How do I build scipy with umfpack to silence this error:
>
> Exception AttributeError: "'UmfpackContext' object has no attribute '_symbolic'" in <bound method UmfpackContext.__del__ of <scipy.sparse.linalg.dsolve.umfpack.umfpack.UmfpackContext object at 0x101b62050>> ignored
>
> and speed up random_walker? I've just been doing a pip install scipy till 
> now.
>
> Juan.
>
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From jni.soma at gmail.com  Thu Oct  3 02:21:43 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Thu, 3 Oct 2013 16:21:43 +1000
Subject: umfpack error
Message-ID: <CA+JHcKSZZKrP5y_3R+CQh5UartSuJdJf_Z86u6e9V-P+0kRD9A@mail.gmail.com>

Hi guys,

How do I build scipy with umfpack to silence this error:

Exception AttributeError: "'UmfpackContext' object has no attribute
'_symbolic'" in <bound method UmfpackContext.__del__ of
<scipy.sparse.linalg.dsolve.umfpack.umfpack.UmfpackContext object at
0x101b62050>> ignored

and speed up random_walker? I've just been doing a pip install scipy till
now.

Juan.
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From fboulogne at sciunto.org  Fri Oct  4 04:15:13 2013
From: fboulogne at sciunto.org (=?ISO-8859-1?Q?Fran=E7ois_Boulogne?=)
Date: Fri, 04 Oct 2013 10:15:13 +0200
Subject: Fwd: large PyWavelets update, please test
In-Reply-To: <CABL7CQgNmOqkhytubRh1E84AwnCjxK1RsZpu6J2bh54ndmPAWA@mail.gmail.com>
References: <CABL7CQgNmOqkhytubRh1E84AwnCjxK1RsZpu6J2bh54ndmPAWA@mail.gmail.com>
Message-ID: <524E7911.2020307@sciunto.org>

Dear skimagers,


With Ralf, we initiated a "friendly" fork of pywavelet for a future
inclusion in scipy and David joined us in this work. We improved the
doc, removed old-fashioned codes and we are trying now to add tests.
We started this because I was considering this ticket:
https://github.com/scikit-image/scikit-image/issues/602
Indeed, I believe wavelets may be useful for scikit-image. Instead of
requiring a new dependency, I thought it is much more valuable to
integrate the code in scipy and this is now in the workplan for scipy1.0.

If some of you used pywavelet before, we would be grateful to you if you
can check your code against the fork. It must be fully compatible with
pywavelets.

Thanks!
Cheers.
Fran?ois.


-------- Message original --------
Sujet: 	large PyWavelets update, please test
Date : 	Tue, 1 Oct 2013 17:56:36 +0200
De : 	Ralf Gommers <ralf.gommers at gmail.com>
Pour : 	pywavelets at googlegroups.com
Copie ? : 	Fran?ois Boulogne <fboulogne at sciunto.org>,
david.menendez.hurtado at scilifelab.se



Hi all,

https://github.com/nigma/pywt/pull/7 contains a large refactoring of
PyWavelets, with contributions from Francois Boulogne, David Menendez
Hurtado and myself. Main feature is support for Python 3 (single code
base). Other changes are:

- Numpy style docstrings for all public functions
- A unit test suite with reasonable coverage (see
https://coveralls.io/r/rgommers/pywt)
- PEP8 and Numpy C code standard compliance
- Changes to source tree layout, build setup, Numpy interfaces and C and
Cython templating to more standard styles.

This set of changes is supposed to be fully backwards compatible. They
were quite invasive though (~150 commits), so there's a decent chance
that some things not covered by the test suite were broken in the
process. To catch those now, it would be very helpful if people could
test their own code against either use the PR or the master branch of
https://github.com/rgommers/pywt.

While we've kept full backwards compatibility so far, we've also
compiled a list of things that could be improved in the current API:
https://github.com/rgommers/pywt/issues/38. Please add suggestions there
if you have them.

Cheers,
Ralf





From stuart at mumford.me.uk  Fri Oct  4 06:32:34 2013
From: stuart at mumford.me.uk (Stuart Mumford)
Date: Fri, 4 Oct 2013 11:32:34 +0100
Subject: large PyWavelets update, please test
In-Reply-To: <524E7911.2020307@sciunto.org>
References: <CABL7CQgNmOqkhytubRh1E84AwnCjxK1RsZpu6J2bh54ndmPAWA@mail.gmail.com>
 <524E7911.2020307@sciunto.org>
Message-ID: <CAJ3G1JqLhRO918F66jxfe9Q-b0nLtkDXqR_M=5caxyNevbKSUg@mail.gmail.com>

Hello,

On the topic of wavelet's I am involved in a very small scale effort to
tidy up this continuous wavelet package, with (if we can contact the
original author) the eventual aim of making it useful and potentially a
part of some larger package (scipy?).

https://github.com/nabobalis/kPyWavelet

Stuart


On 4 October 2013 09:15, Fran?ois Boulogne <fboulogne at sciunto.org> wrote:

> Dear skimagers,
>
>
> With Ralf, we initiated a "friendly" fork of pywavelet for a future
> inclusion in scipy and David joined us in this work. We improved the
> doc, removed old-fashioned codes and we are trying now to add tests.
> We started this because I was considering this ticket:
> https://github.com/scikit-image/scikit-image/issues/602
> Indeed, I believe wavelets may be useful for scikit-image. Instead of
> requiring a new dependency, I thought it is much more valuable to
> integrate the code in scipy and this is now in the workplan for scipy1.0.
>
> If some of you used pywavelet before, we would be grateful to you if you
> can check your code against the fork. It must be fully compatible with
> pywavelets.
>
> Thanks!
> Cheers.
> Fran?ois.
>
>
> -------- Message original --------
> Sujet:  large PyWavelets update, please test
> Date :  Tue, 1 Oct 2013 17:56:36 +0200
> De :    Ralf Gommers <ralf.gommers at gmail.com>
> Pour :  pywavelets at googlegroups.com
> Copie ? :       Fran?ois Boulogne <fboulogne at sciunto.org>,
> david.menendez.hurtado at scilifelab.se
>
>
>
> Hi all,
>
> https://github.com/nigma/pywt/pull/7 contains a large refactoring of
> PyWavelets, with contributions from Francois Boulogne, David Menendez
> Hurtado and myself. Main feature is support for Python 3 (single code
> base). Other changes are:
>
> - Numpy style docstrings for all public functions
> - A unit test suite with reasonable coverage (see
> https://coveralls.io/r/rgommers/pywt)
> - PEP8 and Numpy C code standard compliance
> - Changes to source tree layout, build setup, Numpy interfaces and C and
> Cython templating to more standard styles.
>
> This set of changes is supposed to be fully backwards compatible. They
> were quite invasive though (~150 commits), so there's a decent chance
> that some things not covered by the test suite were broken in the
> process. To catch those now, it would be very helpful if people could
> test their own code against either use the PR or the master branch of
> https://github.com/rgommers/pywt.
>
> While we've kept full backwards compatibility so far, we've also
> compiled a list of things that could be improved in the current API:
> https://github.com/rgommers/pywt/issues/38. Please add suggestions there
> if you have them.
>
> Cheers,
> Ralf
>
>
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>
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From stuart at mumford.me.uk  Fri Oct  4 06:46:09 2013
From: stuart at mumford.me.uk (Stuart Mumford)
Date: Fri, 4 Oct 2013 11:46:09 +0100
Subject: large PyWavelets update, please test
In-Reply-To: <CABL7CQjY5V2iNydoQbGpqk8XB_dMRa4dsbAvtR_ET3-PZBNNRA@mail.gmail.com>
References: <CABL7CQgNmOqkhytubRh1E84AwnCjxK1RsZpu6J2bh54ndmPAWA@mail.gmail.com>
 <524E7911.2020307@sciunto.org> <CAJ3G1JqLhRO918F66jxfe9Q-b0nLtkDXqR_M=5caxyNevbKSUg@mail.gmail.com>
 <CABL7CQjY5V2iNydoQbGpqk8XB_dMRa4dsbAvtR_ET3-PZBNNRA@mail.gmail.com>
Message-ID: <CAJ3G1Jp4ArX330XtFZ4Y_Rcgu9aaBd0tBUsFNd2N8QMS8dLfnA@mail.gmail.com>

Hi Ralf,

I realise the license is pants! We are making efforts to contact the author
and persuade him to change it! ;)

The reason we are looking at this is it has all the features my friend
needed, so it seemed easier (at least from a getting work done perspective)
to start with this code, which also happened to be a (far to direct)
implementation of the IDL code he was having to use before.

While it would be nice to build some or all of this into a bigger package,
at the end of the day just having a decent Python implementation of the C.
Torrence and G. P. Compo wavelet code will be yet another thing people
don't need IDL for.

Stuart

P.S. I am a solar physicist and IDL is everywhere *shudders*


On 4 October 2013 11:41, Ralf Gommers <ralf.gommers at gmail.com> wrote:

>
>
>
> On Fri, Oct 4, 2013 at 12:32 PM, Stuart Mumford <stuart at mumford.me.uk>wrote:
>
>> Hello,
>>
>> On the topic of wavelet's I am involved in a very small scale effort to
>> tidy up this continuous wavelet package, with (if we can contact the
>> original author) the eventual aim of making it useful and potentially a
>> part of some larger package (scipy?).
>>
>> https://github.com/nabobalis/kPyWavelet
>>
>
> Hi Stuart, that code has a license that's incompatible with both BSD and
> GPL licenses so it's pretty much useless. The amount of code there is not
> much more than what's already in scipy.signal.wavelets, so improving the
> scipy cwt code would probably be a better idea.
>
> Ralf
>
>
>
>>
>>  Stuart
>>
>>
>> On 4 October 2013 09:15, Fran?ois Boulogne <fboulogne at sciunto.org> wrote:
>>
>>> Dear skimagers,
>>>
>>>
>>> With Ralf, we initiated a "friendly" fork of pywavelet for a future
>>> inclusion in scipy and David joined us in this work. We improved the
>>> doc, removed old-fashioned codes and we are trying now to add tests.
>>> We started this because I was considering this ticket:
>>> https://github.com/scikit-image/scikit-image/issues/602
>>> Indeed, I believe wavelets may be useful for scikit-image. Instead of
>>> requiring a new dependency, I thought it is much more valuable to
>>> integrate the code in scipy and this is now in the workplan for scipy1.0.
>>>
>>> If some of you used pywavelet before, we would be grateful to you if you
>>> can check your code against the fork. It must be fully compatible with
>>> pywavelets.
>>>
>>> Thanks!
>>> Cheers.
>>> Fran?ois.
>>>
>>>
>>> -------- Message original --------
>>> Sujet:  large PyWavelets update, please test
>>> Date :  Tue, 1 Oct 2013 17:56:36 +0200
>>> De :    Ralf Gommers <ralf.gommers at gmail.com>
>>> Pour :  pywavelets at googlegroups.com
>>> Copie ? :       Fran?ois Boulogne <fboulogne at sciunto.org>,
>>> david.menendez.hurtado at scilifelab.se
>>>
>>>
>>>
>>> Hi all,
>>>
>>> https://github.com/nigma/pywt/pull/7 contains a large refactoring of
>>> PyWavelets, with contributions from Francois Boulogne, David Menendez
>>> Hurtado and myself. Main feature is support for Python 3 (single code
>>> base). Other changes are:
>>>
>>> - Numpy style docstrings for all public functions
>>> - A unit test suite with reasonable coverage (see
>>> https://coveralls.io/r/rgommers/pywt)
>>> - PEP8 and Numpy C code standard compliance
>>> - Changes to source tree layout, build setup, Numpy interfaces and C and
>>> Cython templating to more standard styles.
>>>
>>> This set of changes is supposed to be fully backwards compatible. They
>>> were quite invasive though (~150 commits), so there's a decent chance
>>> that some things not covered by the test suite were broken in the
>>> process. To catch those now, it would be very helpful if people could
>>> test their own code against either use the PR or the master branch of
>>> https://github.com/rgommers/pywt.
>>>
>>> While we've kept full backwards compatibility so far, we've also
>>> compiled a list of things that could be improved in the current API:
>>> https://github.com/rgommers/pywt/issues/38. Please add suggestions there
>>> if you have them.
>>>
>>> Cheers,
>>> Ralf
>>>
>>>
>>>
>>> --
>>> You received this message because you are subscribed to the Google
>>> Groups "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>> For more options, visit https://groups.google.com/groups/opt_out.
>>>
>>
>>  --
>> You received this message because you are subscribed to the Google Groups
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>> To unsubscribe from this group and stop receiving emails from it, send an
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>
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From ralf.gommers at gmail.com  Fri Oct  4 06:41:20 2013
From: ralf.gommers at gmail.com (Ralf Gommers)
Date: Fri, 4 Oct 2013 12:41:20 +0200
Subject: large PyWavelets update, please test
In-Reply-To: <CAJ3G1JqLhRO918F66jxfe9Q-b0nLtkDXqR_M=5caxyNevbKSUg@mail.gmail.com>
References: <CABL7CQgNmOqkhytubRh1E84AwnCjxK1RsZpu6J2bh54ndmPAWA@mail.gmail.com>
	<524E7911.2020307@sciunto.org>
	<CAJ3G1JqLhRO918F66jxfe9Q-b0nLtkDXqR_M=5caxyNevbKSUg@mail.gmail.com>
Message-ID: <CABL7CQjY5V2iNydoQbGpqk8XB_dMRa4dsbAvtR_ET3-PZBNNRA@mail.gmail.com>

On Fri, Oct 4, 2013 at 12:32 PM, Stuart Mumford <stuart at mumford.me.uk>wrote:

> Hello,
>
> On the topic of wavelet's I am involved in a very small scale effort to
> tidy up this continuous wavelet package, with (if we can contact the
> original author) the eventual aim of making it useful and potentially a
> part of some larger package (scipy?).
>
> https://github.com/nabobalis/kPyWavelet
>

Hi Stuart, that code has a license that's incompatible with both BSD and
GPL licenses so it's pretty much useless. The amount of code there is not
much more than what's already in scipy.signal.wavelets, so improving the
scipy cwt code would probably be a better idea.

Ralf



>
> Stuart
>
>
> On 4 October 2013 09:15, Fran?ois Boulogne <fboulogne at sciunto.org> wrote:
>
>> Dear skimagers,
>>
>>
>> With Ralf, we initiated a "friendly" fork of pywavelet for a future
>> inclusion in scipy and David joined us in this work. We improved the
>> doc, removed old-fashioned codes and we are trying now to add tests.
>> We started this because I was considering this ticket:
>> https://github.com/scikit-image/scikit-image/issues/602
>> Indeed, I believe wavelets may be useful for scikit-image. Instead of
>> requiring a new dependency, I thought it is much more valuable to
>> integrate the code in scipy and this is now in the workplan for scipy1.0.
>>
>> If some of you used pywavelet before, we would be grateful to you if you
>> can check your code against the fork. It must be fully compatible with
>> pywavelets.
>>
>> Thanks!
>> Cheers.
>> Fran?ois.
>>
>>
>> -------- Message original --------
>> Sujet:  large PyWavelets update, please test
>> Date :  Tue, 1 Oct 2013 17:56:36 +0200
>> De :    Ralf Gommers <ralf.gommers at gmail.com>
>> Pour :  pywavelets at googlegroups.com
>> Copie ? :       Fran?ois Boulogne <fboulogne at sciunto.org>,
>> david.menendez.hurtado at scilifelab.se
>>
>>
>>
>> Hi all,
>>
>> https://github.com/nigma/pywt/pull/7 contains a large refactoring of
>> PyWavelets, with contributions from Francois Boulogne, David Menendez
>> Hurtado and myself. Main feature is support for Python 3 (single code
>> base). Other changes are:
>>
>> - Numpy style docstrings for all public functions
>> - A unit test suite with reasonable coverage (see
>> https://coveralls.io/r/rgommers/pywt)
>> - PEP8 and Numpy C code standard compliance
>> - Changes to source tree layout, build setup, Numpy interfaces and C and
>> Cython templating to more standard styles.
>>
>> This set of changes is supposed to be fully backwards compatible. They
>> were quite invasive though (~150 commits), so there's a decent chance
>> that some things not covered by the test suite were broken in the
>> process. To catch those now, it would be very helpful if people could
>> test their own code against either use the PR or the master branch of
>> https://github.com/rgommers/pywt.
>>
>> While we've kept full backwards compatibility so far, we've also
>> compiled a list of things that could be improved in the current API:
>> https://github.com/rgommers/pywt/issues/38. Please add suggestions there
>> if you have them.
>>
>> Cheers,
>> Ralf
>>
>>
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
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From stuart at mumford.me.uk  Fri Oct  4 07:56:43 2013
From: stuart at mumford.me.uk (Stuart Mumford)
Date: Fri, 4 Oct 2013 12:56:43 +0100
Subject: large PyWavelets update, please test
In-Reply-To: <CABL7CQjZqWjONf7Hzc4g29foYtj4rHYx+UT_DhBNmMWYcd0TFg@mail.gmail.com>
References: <CABL7CQgNmOqkhytubRh1E84AwnCjxK1RsZpu6J2bh54ndmPAWA@mail.gmail.com>
 <524E7911.2020307@sciunto.org> <CAJ3G1JqLhRO918F66jxfe9Q-b0nLtkDXqR_M=5caxyNevbKSUg@mail.gmail.com>
 <CABL7CQjY5V2iNydoQbGpqk8XB_dMRa4dsbAvtR_ET3-PZBNNRA@mail.gmail.com>
 <CAJ3G1Jp4ArX330XtFZ4Y_Rcgu9aaBd0tBUsFNd2N8QMS8dLfnA@mail.gmail.com>
 <CABL7CQg3qB961EChtpvvAH1VZTHzr8w9hsuCVSHZuNToLDwN=A@mail.gmail.com> <CABL7CQjZqWjONf7Hzc4g29foYtj4rHYx+UT_DhBNmMWYcd0TFg@mail.gmail.com>
Message-ID: <CAJ3G1JqLhffu+njUb+pjzOZfQc56kh-=iPEUXsJiE1x9tzo=DQ@mail.gmail.com>

Hi,

Thanks for your help. Would this be worthwhile doing? i.e. is this code
something that scipy would appreciate if we could re-licence it?

Stuart


On 4 October 2013 12:09, Ralf Gommers <ralf.gommers at gmail.com> wrote:

>
>
>
> On Fri, Oct 4, 2013 at 1:04 PM, Ralf Gommers <ralf.gommers at gmail.com>wrote:
>
>>
>>
>>
>> On Fri, Oct 4, 2013 at 12:46 PM, Stuart Mumford <stuart at mumford.me.uk>wrote:
>>
>>> Hi Ralf,
>>>
>>> I realise the license is pants! We are making efforts to contact the
>>> author and persuade him to change it! ;)
>>>
>>
>> The original author can't do this, you also need at least permission from
>> Torrence/Compo as well as from these guys:
>> http://noc.ac.uk/using-science/crosswavelet-wavelet-coherence. And maybe
>> also from A. Brazhe; can't check because the link to his site is dead. So
>> the odds you can get the license changed seem on the low side.
>>
>
> Found the Brazhe code, it's (now?) GPL licensed:
> https://pypi.python.org/pypi/swan
>
> Ralf
>
>
>>
>> The reason we are looking at this is it has all the features my friend
>>> needed, so it seemed easier (at least from a getting work done perspective)
>>> to start with this code, which also happened to be a (far to direct)
>>> implementation of the IDL code he was having to use before.
>>>
>>> While it would be nice to build some or all of this into a bigger
>>> package, at the end of the day just having a decent Python implementation
>>> of the C. Torrence and G. P. Compo wavelet code will be yet another thing
>>> people don't need IDL for.
>>>
>>
>> I just checked the Matlab code from
>> http://paos.colorado.edu/research/wavelets/ (I don't speak IDL) and it's
>> not a lot of code nor is it very complicated. What I would suggest is to
>> contact Torrence and Compo directly to see if they're willing to change to
>> a BSD license, and otherwise just reimplement the algorithm based on their
>> paper.
>>
>>
>>>
>>> Stuart
>>>
>>> P.S. I am a solar physicist and IDL is everywhere *shudders*
>>>
>>
>> :)
>>
>> Cheers,
>> Ralf
>>
>>
>>>
>>>
>>> On 4 October 2013 11:41, Ralf Gommers <ralf.gommers at gmail.com> wrote:
>>>
>>>>
>>>>
>>>>
>>>> On Fri, Oct 4, 2013 at 12:32 PM, Stuart Mumford <stuart at mumford.me.uk>wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> On the topic of wavelet's I am involved in a very small scale effort
>>>>> to tidy up this continuous wavelet package, with (if we can contact the
>>>>> original author) the eventual aim of making it useful and potentially a
>>>>> part of some larger package (scipy?).
>>>>>
>>>>> https://github.com/nabobalis/kPyWavelet
>>>>>
>>>>
>>>> Hi Stuart, that code has a license that's incompatible with both BSD
>>>> and GPL licenses so it's pretty much useless. The amount of code there is
>>>> not much more than what's already in scipy.signal.wavelets, so improving
>>>> the scipy cwt code would probably be a better idea.
>>>>
>>>> Ralf
>>>>
>>>>
>>>>
>>>>>
>>>>>  Stuart
>>>>>
>>>>>
>>>>> On 4 October 2013 09:15, Fran?ois Boulogne <fboulogne at sciunto.org>wrote:
>>>>>
>>>>>> Dear skimagers,
>>>>>>
>>>>>>
>>>>>> With Ralf, we initiated a "friendly" fork of pywavelet for a future
>>>>>> inclusion in scipy and David joined us in this work. We improved the
>>>>>> doc, removed old-fashioned codes and we are trying now to add tests.
>>>>>> We started this because I was considering this ticket:
>>>>>> https://github.com/scikit-image/scikit-image/issues/602
>>>>>> Indeed, I believe wavelets may be useful for scikit-image. Instead of
>>>>>> requiring a new dependency, I thought it is much more valuable to
>>>>>> integrate the code in scipy and this is now in the workplan for
>>>>>> scipy1.0.
>>>>>>
>>>>>> If some of you used pywavelet before, we would be grateful to you if
>>>>>> you
>>>>>> can check your code against the fork. It must be fully compatible with
>>>>>> pywavelets.
>>>>>>
>>>>>> Thanks!
>>>>>> Cheers.
>>>>>> Fran?ois.
>>>>>>
>>>>>>
>>>>>> -------- Message original --------
>>>>>> Sujet:  large PyWavelets update, please test
>>>>>> Date :  Tue, 1 Oct 2013 17:56:36 +0200
>>>>>> De :    Ralf Gommers <ralf.gommers at gmail.com>
>>>>>> Pour :  pywavelets at googlegroups.com
>>>>>> Copie ? :       Fran?ois Boulogne <fboulogne at sciunto.org>,
>>>>>> david.menendez.hurtado at scilifelab.se
>>>>>>
>>>>>>
>>>>>>
>>>>>> Hi all,
>>>>>>
>>>>>> https://github.com/nigma/pywt/pull/7 contains a large refactoring of
>>>>>> PyWavelets, with contributions from Francois Boulogne, David Menendez
>>>>>> Hurtado and myself. Main feature is support for Python 3 (single code
>>>>>> base). Other changes are:
>>>>>>
>>>>>> - Numpy style docstrings for all public functions
>>>>>> - A unit test suite with reasonable coverage (see
>>>>>> https://coveralls.io/r/rgommers/pywt)
>>>>>> - PEP8 and Numpy C code standard compliance
>>>>>> - Changes to source tree layout, build setup, Numpy interfaces and C
>>>>>> and
>>>>>> Cython templating to more standard styles.
>>>>>>
>>>>>> This set of changes is supposed to be fully backwards compatible. They
>>>>>> were quite invasive though (~150 commits), so there's a decent chance
>>>>>> that some things not covered by the test suite were broken in the
>>>>>> process. To catch those now, it would be very helpful if people could
>>>>>> test their own code against either use the PR or the master branch of
>>>>>> https://github.com/rgommers/pywt.
>>>>>>
>>>>>> While we've kept full backwards compatibility so far, we've also
>>>>>> compiled a list of things that could be improved in the current API:
>>>>>> https://github.com/rgommers/pywt/issues/38. Please add suggestions
>>>>>> there
>>>>>> if you have them.
>>>>>>
>>>>>> Cheers,
>>>>>> Ralf
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> You received this message because you are subscribed to the Google
>>>>>> Groups "scikit-image" group.
>>>>>> To unsubscribe from this group and stop receiving emails from it,
>>>>>> send an email to scikit-image+unsubscribe at googlegroups.com.
>>>>>> For more options, visit https://groups.google.com/groups/opt_out.
>>>>>>
>>>>>
>>>>>  --
>>>>> You received this message because you are subscribed to the Google
>>>>> Groups "scikit-image" group.
>>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>>>> For more options, visit https://groups.google.com/groups/opt_out.
>>>>>
>>>>
>>>>  --
>>>> You received this message because you are subscribed to the Google
>>>> Groups "scikit-image" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>>> For more options, visit https://groups.google.com/groups/opt_out.
>>>>
>>>
>>>  --
>>> You received this message because you are subscribed to the Google
>>> Groups "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to scikit-image+unsubscribe at googlegroups.com.
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>>>
>>
>>
>  --
> You received this message because you are subscribed to the Google Groups
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From jsch at demuc.de  Fri Oct  4 06:59:58 2013
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Fri, 4 Oct 2013 12:59:58 +0200
Subject: umfpack error
In-Reply-To: <CA+JHcKTtp5ZOjZi6dbTsMJ4mTFbBkvMeyAS3qVF60aj8xz9fbg@mail.gmail.com>
References: <CA+JHcKSZZKrP5y_3R+CQh5UartSuJdJf_Z86u6e9V-P+0kRD9A@mail.gmail.com> <762baf0e-52c2-488b-ac8b-9e5e7caa4dc9@googlegroups.com> <CA+JHcKT88aF2yDOYO5=mkLd1CUzs01QOjhv3fS_wABv1CZ+SBQ@mail.gmail.com> <CA+JHcKTtp5ZOjZi6dbTsMJ4mTFbBkvMeyAS3qVF60aj8xz9fbg@mail.gmail.com>
Message-ID: <1EDEEF3D-F300-4D8B-B463-65C69896B567@demuc.de>

Are you sure you have SWIG installed?

Am 04.10.2013 um 12:49 schrieb Juan Nunez-Iglesias <jni.soma at gmail.com>:

> Just for future reference, and because it wasn't immediately obvious from googling: the umfpack headers in Ubuntu 13.04 are in the package libsuitesparse-dev.
> 
> But now the scipy build fails with some weird error. Hmmm.
> 
> building extension "scipy.sparse.linalg.dsolve.umfpack.__umfpack" sources
> 
> creating build/src.linux-x86_64-2.7/scipy/sparse/linalg/dsolve
> 
> creating build/src.linux-x86_64-2.7/scipy/sparse/linalg/dsolve/umfpack
> 
>   adding 'scipy/sparse/linalg/dsolve/umfpack/umfpack.i' to sources.
> 
> swig: scipy/sparse/linalg/dsolve/umfpack/umfpack.i
> 
> swig -python -I/usr/include/suitesparse -I/usr/include/suitesparse -I/usr/include/suitesparse -o build/src.linux-x86_64-2.7/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c -outdir build/src.linux-x86_64-2.7/scipy/sparse/linalg/dsolve/umfpack scipy/sparse/linalg/dsolve/umfpack/umfpack.i
> 
> unable to execute swig: No such file or directory
> 
> error: command 'swig' failed with exit status 1
> 
> 
> 
> 
> On Fri, Oct 4, 2013 at 2:39 PM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> Thanks Josh for the detailed response and discussion! I think you're absolutely right that it should be suppressed if pyamg is available. And it's probably worth getting that in before the release. Happy to tackle this.
> 
> Juan.
> 
> PS: I'm mostly on OSX, with some Linux on the side. =)
> 
> 
> On Fri, Oct 4, 2013 at 9:17 AM, Josh Warner <silvertrumpet999 at gmail.com> wrote:
> Final note - umfpack enables mode='cg' in random_walker, which is better than brute force but not the fastest or most efficient mode. The multi-grid preconditioned conjugate gradient method is: mode='cg_mg'. This is enabled by pyamg, which is independent of umfpack and is considerably easier to install and use than the method I just described.
> 
> Come to think of it, we probably should suppress that warning if import pyamg works. It incorrectly implies the user doesn't have the fastest mode available.
> 
> On Thursday, October 3, 2013 1:21:43 AM UTC-5, Juan Nunez-Iglesias wrote:
> 
> 
> 
> Hi guys,
> 
> How do I build scipy with umfpack to silence this error:
> 
> Exception AttributeError: "'UmfpackContext' object has no attribute '_symbolic'" in <bound method UmfpackContext.__del__ of <scipy.sparse.linalg.dsolve.umfpack.umfpack.UmfpackContext object at 0x101b62050>> ignored
> and speed up random_walker? I've just been doing a pip install scipy till now.
> 
> Juan.
> 
> 
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
> 
> 
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
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From ralf.gommers at gmail.com  Fri Oct  4 07:04:23 2013
From: ralf.gommers at gmail.com (Ralf Gommers)
Date: Fri, 4 Oct 2013 13:04:23 +0200
Subject: large PyWavelets update, please test
In-Reply-To: <CAJ3G1Jp4ArX330XtFZ4Y_Rcgu9aaBd0tBUsFNd2N8QMS8dLfnA@mail.gmail.com>
References: <CABL7CQgNmOqkhytubRh1E84AwnCjxK1RsZpu6J2bh54ndmPAWA@mail.gmail.com>
	<524E7911.2020307@sciunto.org>
	<CAJ3G1JqLhRO918F66jxfe9Q-b0nLtkDXqR_M=5caxyNevbKSUg@mail.gmail.com>
	<CABL7CQjY5V2iNydoQbGpqk8XB_dMRa4dsbAvtR_ET3-PZBNNRA@mail.gmail.com>
	<CAJ3G1Jp4ArX330XtFZ4Y_Rcgu9aaBd0tBUsFNd2N8QMS8dLfnA@mail.gmail.com>
Message-ID: <CABL7CQg3qB961EChtpvvAH1VZTHzr8w9hsuCVSHZuNToLDwN=A@mail.gmail.com>

On Fri, Oct 4, 2013 at 12:46 PM, Stuart Mumford <stuart at mumford.me.uk>wrote:

> Hi Ralf,
>
> I realise the license is pants! We are making efforts to contact the
> author and persuade him to change it! ;)
>

The original author can't do this, you also need at least permission from
Torrence/Compo as well as from these guys:
http://noc.ac.uk/using-science/crosswavelet-wavelet-coherence. And maybe
also from A. Brazhe; can't check because the link to his site is dead. So
the odds you can get the license changed seem on the low side.

The reason we are looking at this is it has all the features my friend
> needed, so it seemed easier (at least from a getting work done perspective)
> to start with this code, which also happened to be a (far to direct)
> implementation of the IDL code he was having to use before.
>
> While it would be nice to build some or all of this into a bigger package,
> at the end of the day just having a decent Python implementation of the C.
> Torrence and G. P. Compo wavelet code will be yet another thing people
> don't need IDL for.
>

I just checked the Matlab code from
http://paos.colorado.edu/research/wavelets/ (I don't speak IDL) and it's
not a lot of code nor is it very complicated. What I would suggest is to
contact Torrence and Compo directly to see if they're willing to change to
a BSD license, and otherwise just reimplement the algorithm based on their
paper.


>
> Stuart
>
> P.S. I am a solar physicist and IDL is everywhere *shudders*
>

:)

Cheers,
Ralf


>
>
> On 4 October 2013 11:41, Ralf Gommers <ralf.gommers at gmail.com> wrote:
>
>>
>>
>>
>> On Fri, Oct 4, 2013 at 12:32 PM, Stuart Mumford <stuart at mumford.me.uk>wrote:
>>
>>> Hello,
>>>
>>> On the topic of wavelet's I am involved in a very small scale effort to
>>> tidy up this continuous wavelet package, with (if we can contact the
>>> original author) the eventual aim of making it useful and potentially a
>>> part of some larger package (scipy?).
>>>
>>> https://github.com/nabobalis/kPyWavelet
>>>
>>
>> Hi Stuart, that code has a license that's incompatible with both BSD and
>> GPL licenses so it's pretty much useless. The amount of code there is not
>> much more than what's already in scipy.signal.wavelets, so improving the
>> scipy cwt code would probably be a better idea.
>>
>> Ralf
>>
>>
>>
>>>
>>>  Stuart
>>>
>>>
>>> On 4 October 2013 09:15, Fran?ois Boulogne <fboulogne at sciunto.org>wrote:
>>>
>>>> Dear skimagers,
>>>>
>>>>
>>>> With Ralf, we initiated a "friendly" fork of pywavelet for a future
>>>> inclusion in scipy and David joined us in this work. We improved the
>>>> doc, removed old-fashioned codes and we are trying now to add tests.
>>>> We started this because I was considering this ticket:
>>>> https://github.com/scikit-image/scikit-image/issues/602
>>>> Indeed, I believe wavelets may be useful for scikit-image. Instead of
>>>> requiring a new dependency, I thought it is much more valuable to
>>>> integrate the code in scipy and this is now in the workplan for
>>>> scipy1.0.
>>>>
>>>> If some of you used pywavelet before, we would be grateful to you if you
>>>> can check your code against the fork. It must be fully compatible with
>>>> pywavelets.
>>>>
>>>> Thanks!
>>>> Cheers.
>>>> Fran?ois.
>>>>
>>>>
>>>> -------- Message original --------
>>>> Sujet:  large PyWavelets update, please test
>>>> Date :  Tue, 1 Oct 2013 17:56:36 +0200
>>>> De :    Ralf Gommers <ralf.gommers at gmail.com>
>>>> Pour :  pywavelets at googlegroups.com
>>>> Copie ? :       Fran?ois Boulogne <fboulogne at sciunto.org>,
>>>> david.menendez.hurtado at scilifelab.se
>>>>
>>>>
>>>>
>>>> Hi all,
>>>>
>>>> https://github.com/nigma/pywt/pull/7 contains a large refactoring of
>>>> PyWavelets, with contributions from Francois Boulogne, David Menendez
>>>> Hurtado and myself. Main feature is support for Python 3 (single code
>>>> base). Other changes are:
>>>>
>>>> - Numpy style docstrings for all public functions
>>>> - A unit test suite with reasonable coverage (see
>>>> https://coveralls.io/r/rgommers/pywt)
>>>> - PEP8 and Numpy C code standard compliance
>>>> - Changes to source tree layout, build setup, Numpy interfaces and C and
>>>> Cython templating to more standard styles.
>>>>
>>>> This set of changes is supposed to be fully backwards compatible. They
>>>> were quite invasive though (~150 commits), so there's a decent chance
>>>> that some things not covered by the test suite were broken in the
>>>> process. To catch those now, it would be very helpful if people could
>>>> test their own code against either use the PR or the master branch of
>>>> https://github.com/rgommers/pywt.
>>>>
>>>> While we've kept full backwards compatibility so far, we've also
>>>> compiled a list of things that could be improved in the current API:
>>>> https://github.com/rgommers/pywt/issues/38. Please add suggestions
>>>> there
>>>> if you have them.
>>>>
>>>> Cheers,
>>>> Ralf
>>>>
>>>>
>>>>
>>>> --
>>>> You received this message because you are subscribed to the Google
>>>> Groups "scikit-image" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>>> For more options, visit https://groups.google.com/groups/opt_out.
>>>>
>>>
>>>  --
>>> You received this message because you are subscribed to the Google
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>>> an email to scikit-image+unsubscribe at googlegroups.com.
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>>
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From ralf.gommers at gmail.com  Fri Oct  4 07:09:53 2013
From: ralf.gommers at gmail.com (Ralf Gommers)
Date: Fri, 4 Oct 2013 13:09:53 +0200
Subject: large PyWavelets update, please test
In-Reply-To: <CABL7CQg3qB961EChtpvvAH1VZTHzr8w9hsuCVSHZuNToLDwN=A@mail.gmail.com>
References: <CABL7CQgNmOqkhytubRh1E84AwnCjxK1RsZpu6J2bh54ndmPAWA@mail.gmail.com>
	<524E7911.2020307@sciunto.org>
	<CAJ3G1JqLhRO918F66jxfe9Q-b0nLtkDXqR_M=5caxyNevbKSUg@mail.gmail.com>
	<CABL7CQjY5V2iNydoQbGpqk8XB_dMRa4dsbAvtR_ET3-PZBNNRA@mail.gmail.com>
	<CAJ3G1Jp4ArX330XtFZ4Y_Rcgu9aaBd0tBUsFNd2N8QMS8dLfnA@mail.gmail.com>
	<CABL7CQg3qB961EChtpvvAH1VZTHzr8w9hsuCVSHZuNToLDwN=A@mail.gmail.com>
Message-ID: <CABL7CQjZqWjONf7Hzc4g29foYtj4rHYx+UT_DhBNmMWYcd0TFg@mail.gmail.com>

On Fri, Oct 4, 2013 at 1:04 PM, Ralf Gommers <ralf.gommers at gmail.com> wrote:

>
>
>
> On Fri, Oct 4, 2013 at 12:46 PM, Stuart Mumford <stuart at mumford.me.uk>wrote:
>
>> Hi Ralf,
>>
>> I realise the license is pants! We are making efforts to contact the
>> author and persuade him to change it! ;)
>>
>
> The original author can't do this, you also need at least permission from
> Torrence/Compo as well as from these guys:
> http://noc.ac.uk/using-science/crosswavelet-wavelet-coherence. And maybe
> also from A. Brazhe; can't check because the link to his site is dead. So
> the odds you can get the license changed seem on the low side.
>

Found the Brazhe code, it's (now?) GPL licensed:
https://pypi.python.org/pypi/swan

Ralf


>
> The reason we are looking at this is it has all the features my friend
>> needed, so it seemed easier (at least from a getting work done perspective)
>> to start with this code, which also happened to be a (far to direct)
>> implementation of the IDL code he was having to use before.
>>
>> While it would be nice to build some or all of this into a bigger
>> package, at the end of the day just having a decent Python implementation
>> of the C. Torrence and G. P. Compo wavelet code will be yet another thing
>> people don't need IDL for.
>>
>
> I just checked the Matlab code from
> http://paos.colorado.edu/research/wavelets/ (I don't speak IDL) and it's
> not a lot of code nor is it very complicated. What I would suggest is to
> contact Torrence and Compo directly to see if they're willing to change to
> a BSD license, and otherwise just reimplement the algorithm based on their
> paper.
>
>
>>
>> Stuart
>>
>> P.S. I am a solar physicist and IDL is everywhere *shudders*
>>
>
> :)
>
> Cheers,
> Ralf
>
>
>>
>>
>> On 4 October 2013 11:41, Ralf Gommers <ralf.gommers at gmail.com> wrote:
>>
>>>
>>>
>>>
>>> On Fri, Oct 4, 2013 at 12:32 PM, Stuart Mumford <stuart at mumford.me.uk>wrote:
>>>
>>>> Hello,
>>>>
>>>> On the topic of wavelet's I am involved in a very small scale effort to
>>>> tidy up this continuous wavelet package, with (if we can contact the
>>>> original author) the eventual aim of making it useful and potentially a
>>>> part of some larger package (scipy?).
>>>>
>>>> https://github.com/nabobalis/kPyWavelet
>>>>
>>>
>>> Hi Stuart, that code has a license that's incompatible with both BSD and
>>> GPL licenses so it's pretty much useless. The amount of code there is not
>>> much more than what's already in scipy.signal.wavelets, so improving the
>>> scipy cwt code would probably be a better idea.
>>>
>>> Ralf
>>>
>>>
>>>
>>>>
>>>>  Stuart
>>>>
>>>>
>>>> On 4 October 2013 09:15, Fran?ois Boulogne <fboulogne at sciunto.org>wrote:
>>>>
>>>>> Dear skimagers,
>>>>>
>>>>>
>>>>> With Ralf, we initiated a "friendly" fork of pywavelet for a future
>>>>> inclusion in scipy and David joined us in this work. We improved the
>>>>> doc, removed old-fashioned codes and we are trying now to add tests.
>>>>> We started this because I was considering this ticket:
>>>>> https://github.com/scikit-image/scikit-image/issues/602
>>>>> Indeed, I believe wavelets may be useful for scikit-image. Instead of
>>>>> requiring a new dependency, I thought it is much more valuable to
>>>>> integrate the code in scipy and this is now in the workplan for
>>>>> scipy1.0.
>>>>>
>>>>> If some of you used pywavelet before, we would be grateful to you if
>>>>> you
>>>>> can check your code against the fork. It must be fully compatible with
>>>>> pywavelets.
>>>>>
>>>>> Thanks!
>>>>> Cheers.
>>>>> Fran?ois.
>>>>>
>>>>>
>>>>> -------- Message original --------
>>>>> Sujet:  large PyWavelets update, please test
>>>>> Date :  Tue, 1 Oct 2013 17:56:36 +0200
>>>>> De :    Ralf Gommers <ralf.gommers at gmail.com>
>>>>> Pour :  pywavelets at googlegroups.com
>>>>> Copie ? :       Fran?ois Boulogne <fboulogne at sciunto.org>,
>>>>> david.menendez.hurtado at scilifelab.se
>>>>>
>>>>>
>>>>>
>>>>> Hi all,
>>>>>
>>>>> https://github.com/nigma/pywt/pull/7 contains a large refactoring of
>>>>> PyWavelets, with contributions from Francois Boulogne, David Menendez
>>>>> Hurtado and myself. Main feature is support for Python 3 (single code
>>>>> base). Other changes are:
>>>>>
>>>>> - Numpy style docstrings for all public functions
>>>>> - A unit test suite with reasonable coverage (see
>>>>> https://coveralls.io/r/rgommers/pywt)
>>>>> - PEP8 and Numpy C code standard compliance
>>>>> - Changes to source tree layout, build setup, Numpy interfaces and C
>>>>> and
>>>>> Cython templating to more standard styles.
>>>>>
>>>>> This set of changes is supposed to be fully backwards compatible. They
>>>>> were quite invasive though (~150 commits), so there's a decent chance
>>>>> that some things not covered by the test suite were broken in the
>>>>> process. To catch those now, it would be very helpful if people could
>>>>> test their own code against either use the PR or the master branch of
>>>>> https://github.com/rgommers/pywt.
>>>>>
>>>>> While we've kept full backwards compatibility so far, we've also
>>>>> compiled a list of things that could be improved in the current API:
>>>>> https://github.com/rgommers/pywt/issues/38. Please add suggestions
>>>>> there
>>>>> if you have them.
>>>>>
>>>>> Cheers,
>>>>> Ralf
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> You received this message because you are subscribed to the Google
>>>>> Groups "scikit-image" group.
>>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>>>> For more options, visit https://groups.google.com/groups/opt_out.
>>>>>
>>>>
>>>>  --
>>>> You received this message because you are subscribed to the Google
>>>> Groups "scikit-image" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>>> For more options, visit https://groups.google.com/groups/opt_out.
>>>>
>>>
>>>  --
>>> You received this message because you are subscribed to the Google
>>> Groups "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to scikit-image+unsubscribe at googlegroups.com.
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>>>
>>
>>  --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
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>
>
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From ralf.gommers at gmail.com  Fri Oct  4 08:22:48 2013
From: ralf.gommers at gmail.com (Ralf Gommers)
Date: Fri, 4 Oct 2013 14:22:48 +0200
Subject: large PyWavelets update, please test
In-Reply-To: <CAJ3G1JqLhffu+njUb+pjzOZfQc56kh-=iPEUXsJiE1x9tzo=DQ@mail.gmail.com>
References: <CABL7CQgNmOqkhytubRh1E84AwnCjxK1RsZpu6J2bh54ndmPAWA@mail.gmail.com>
	<524E7911.2020307@sciunto.org>
	<CAJ3G1JqLhRO918F66jxfe9Q-b0nLtkDXqR_M=5caxyNevbKSUg@mail.gmail.com>
	<CABL7CQjY5V2iNydoQbGpqk8XB_dMRa4dsbAvtR_ET3-PZBNNRA@mail.gmail.com>
	<CAJ3G1Jp4ArX330XtFZ4Y_Rcgu9aaBd0tBUsFNd2N8QMS8dLfnA@mail.gmail.com>
	<CABL7CQg3qB961EChtpvvAH1VZTHzr8w9hsuCVSHZuNToLDwN=A@mail.gmail.com>
	<CABL7CQjZqWjONf7Hzc4g29foYtj4rHYx+UT_DhBNmMWYcd0TFg@mail.gmail.com>
	<CAJ3G1JqLhffu+njUb+pjzOZfQc56kh-=iPEUXsJiE1x9tzo=DQ@mail.gmail.com>
Message-ID: <CABL7CQjm86DwK3Ge3THDY7mQtYyonyioCBDbEwmphQfC7JA=mg@mail.gmail.com>

On Fri, Oct 4, 2013 at 1:56 PM, Stuart Mumford <stuart at mumford.me.uk> wrote:

> Hi,
>
> Thanks for your help. Would this be worthwhile doing? i.e. is this code
> something that scipy would appreciate if we could re-licence it?
>

Adding the missing parts in scipy would definitely be worth doing imho. The
chisquare stuff and Morlet wavelet are already in scipy, DOG and Paul
wavelets can certainly be added. Then there's the FFT-based cwt function to
be added. The Torrence code comments aren't very clear, but it's the Matlab
cwtft function as far as I can tell:
http://www.mathworks.nl/help/wavelet/ref/cwtft.html. It could probably be
added with the same name.

Ralf



>
> Stuart
>
>
> On 4 October 2013 12:09, Ralf Gommers <ralf.gommers at gmail.com> wrote:
>
>>
>>
>>
>> On Fri, Oct 4, 2013 at 1:04 PM, Ralf Gommers <ralf.gommers at gmail.com>wrote:
>>
>>>
>>>
>>>
>>> On Fri, Oct 4, 2013 at 12:46 PM, Stuart Mumford <stuart at mumford.me.uk>wrote:
>>>
>>>> Hi Ralf,
>>>>
>>>> I realise the license is pants! We are making efforts to contact the
>>>> author and persuade him to change it! ;)
>>>>
>>>
>>> The original author can't do this, you also need at least permission
>>> from Torrence/Compo as well as from these guys:
>>> http://noc.ac.uk/using-science/crosswavelet-wavelet-coherence. And
>>> maybe also from A. Brazhe; can't check because the link to his site is
>>> dead. So the odds you can get the license changed seem on the low side.
>>>
>>
>> Found the Brazhe code, it's (now?) GPL licensed:
>> https://pypi.python.org/pypi/swan
>>
>> Ralf
>>
>>
>>>
>>> The reason we are looking at this is it has all the features my friend
>>>> needed, so it seemed easier (at least from a getting work done perspective)
>>>> to start with this code, which also happened to be a (far to direct)
>>>> implementation of the IDL code he was having to use before.
>>>>
>>>> While it would be nice to build some or all of this into a bigger
>>>> package, at the end of the day just having a decent Python implementation
>>>> of the C. Torrence and G. P. Compo wavelet code will be yet another thing
>>>> people don't need IDL for.
>>>>
>>>
>>> I just checked the Matlab code from
>>> http://paos.colorado.edu/research/wavelets/ (I don't speak IDL) and
>>> it's not a lot of code nor is it very complicated. What I would suggest is
>>> to contact Torrence and Compo directly to see if they're willing to change
>>> to a BSD license, and otherwise just reimplement the algorithm based on
>>> their paper.
>>>
>>>
>>>>
>>>> Stuart
>>>>
>>>> P.S. I am a solar physicist and IDL is everywhere *shudders*
>>>>
>>>
>>> :)
>>>
>>> Cheers,
>>> Ralf
>>>
>>>
>>>>
>>>>
>>>> On 4 October 2013 11:41, Ralf Gommers <ralf.gommers at gmail.com> wrote:
>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Fri, Oct 4, 2013 at 12:32 PM, Stuart Mumford <stuart at mumford.me.uk>wrote:
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> On the topic of wavelet's I am involved in a very small scale effort
>>>>>> to tidy up this continuous wavelet package, with (if we can contact the
>>>>>> original author) the eventual aim of making it useful and potentially a
>>>>>> part of some larger package (scipy?).
>>>>>>
>>>>>> https://github.com/nabobalis/kPyWavelet
>>>>>>
>>>>>
>>>>> Hi Stuart, that code has a license that's incompatible with both BSD
>>>>> and GPL licenses so it's pretty much useless. The amount of code there is
>>>>> not much more than what's already in scipy.signal.wavelets, so improving
>>>>> the scipy cwt code would probably be a better idea.
>>>>>
>>>>> Ralf
>>>>>
>>>>>
>>>>>
>>>>>>
>>>>>>  Stuart
>>>>>>
>>>>>>
>>>>>> On 4 October 2013 09:15, Fran?ois Boulogne <fboulogne at sciunto.org>wrote:
>>>>>>
>>>>>>> Dear skimagers,
>>>>>>>
>>>>>>>
>>>>>>> With Ralf, we initiated a "friendly" fork of pywavelet for a future
>>>>>>> inclusion in scipy and David joined us in this work. We improved the
>>>>>>> doc, removed old-fashioned codes and we are trying now to add tests.
>>>>>>> We started this because I was considering this ticket:
>>>>>>> https://github.com/scikit-image/scikit-image/issues/602
>>>>>>> Indeed, I believe wavelets may be useful for scikit-image. Instead of
>>>>>>> requiring a new dependency, I thought it is much more valuable to
>>>>>>> integrate the code in scipy and this is now in the workplan for
>>>>>>> scipy1.0.
>>>>>>>
>>>>>>> If some of you used pywavelet before, we would be grateful to you if
>>>>>>> you
>>>>>>> can check your code against the fork. It must be fully compatible
>>>>>>> with
>>>>>>> pywavelets.
>>>>>>>
>>>>>>> Thanks!
>>>>>>> Cheers.
>>>>>>> Fran?ois.
>>>>>>>
>>>>>>>
>>>>>>> -------- Message original --------
>>>>>>> Sujet:  large PyWavelets update, please test
>>>>>>> Date :  Tue, 1 Oct 2013 17:56:36 +0200
>>>>>>> De :    Ralf Gommers <ralf.gommers at gmail.com>
>>>>>>> Pour :  pywavelets at googlegroups.com
>>>>>>> Copie ? :       Fran?ois Boulogne <fboulogne at sciunto.org>,
>>>>>>> david.menendez.hurtado at scilifelab.se
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Hi all,
>>>>>>>
>>>>>>> https://github.com/nigma/pywt/pull/7 contains a large refactoring of
>>>>>>> PyWavelets, with contributions from Francois Boulogne, David Menendez
>>>>>>> Hurtado and myself. Main feature is support for Python 3 (single code
>>>>>>> base). Other changes are:
>>>>>>>
>>>>>>> - Numpy style docstrings for all public functions
>>>>>>> - A unit test suite with reasonable coverage (see
>>>>>>> https://coveralls.io/r/rgommers/pywt)
>>>>>>> - PEP8 and Numpy C code standard compliance
>>>>>>> - Changes to source tree layout, build setup, Numpy interfaces and C
>>>>>>> and
>>>>>>> Cython templating to more standard styles.
>>>>>>>
>>>>>>> This set of changes is supposed to be fully backwards compatible.
>>>>>>> They
>>>>>>> were quite invasive though (~150 commits), so there's a decent chance
>>>>>>> that some things not covered by the test suite were broken in the
>>>>>>> process. To catch those now, it would be very helpful if people could
>>>>>>> test their own code against either use the PR or the master branch of
>>>>>>> https://github.com/rgommers/pywt.
>>>>>>>
>>>>>>> While we've kept full backwards compatibility so far, we've also
>>>>>>> compiled a list of things that could be improved in the current API:
>>>>>>> https://github.com/rgommers/pywt/issues/38. Please add suggestions
>>>>>>> there
>>>>>>> if you have them.
>>>>>>>
>>>>>>> Cheers,
>>>>>>> Ralf
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> You received this message because you are subscribed to the Google
>>>>>>> Groups "scikit-image" group.
>>>>>>> To unsubscribe from this group and stop receiving emails from it,
>>>>>>> send an email to scikit-image+unsubscribe at googlegroups.com.
>>>>>>> For more options, visit https://groups.google.com/groups/opt_out.
>>>>>>>
>>>>>>
>>>>>>  --
>>>>>> You received this message because you are subscribed to the Google
>>>>>> Groups "scikit-image" group.
>>>>>> To unsubscribe from this group and stop receiving emails from it,
>>>>>> send an email to scikit-image+unsubscribe at googlegroups.com.
>>>>>> For more options, visit https://groups.google.com/groups/opt_out.
>>>>>>
>>>>>
>>>>>  --
>>>>> You received this message because you are subscribed to the Google
>>>>> Groups "scikit-image" group.
>>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>>>> For more options, visit https://groups.google.com/groups/opt_out.
>>>>>
>>>>
>>>>  --
>>>> You received this message because you are subscribed to the Google
>>>> Groups "scikit-image" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>>> For more options, visit https://groups.google.com/groups/opt_out.
>>>>
>>>
>>>
>>  --
>> You received this message because you are subscribed to the Google Groups
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>
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From ralf.gommers at gmail.com  Fri Oct  4 08:32:30 2013
From: ralf.gommers at gmail.com (Ralf Gommers)
Date: Fri, 4 Oct 2013 14:32:30 +0200
Subject: umfpack error
In-Reply-To: <CA+JHcKQ_GD-O2tzUWzUn6jAu2GxpNo4+5z_fHxO2r=e64-PZ1Q@mail.gmail.com>
References: <CA+JHcKSZZKrP5y_3R+CQh5UartSuJdJf_Z86u6e9V-P+0kRD9A@mail.gmail.com>
	<762baf0e-52c2-488b-ac8b-9e5e7caa4dc9@googlegroups.com>
	<CA+JHcKT88aF2yDOYO5=mkLd1CUzs01QOjhv3fS_wABv1CZ+SBQ@mail.gmail.com>
	<CA+JHcKTtp5ZOjZi6dbTsMJ4mTFbBkvMeyAS3qVF60aj8xz9fbg@mail.gmail.com>
	<1EDEEF3D-F300-4D8B-B463-65C69896B567@demuc.de>
	<CA+JHcKQ_GD-O2tzUWzUn6jAu2GxpNo4+5z_fHxO2r=e64-PZ1Q@mail.gmail.com>
Message-ID: <CABL7CQiw04+TcHpMF5CWym54RaDkHwiv9PvfZozOPt=U-AqyQA@mail.gmail.com>

On Fri, Oct 4, 2013 at 1:33 PM, Juan Nunez-Iglesias <jni.soma at gmail.com>wrote:

> On Fri, Oct 4, 2013 at 8:59 PM, Johannes Sch?nberger <jsch at demuc.de>wrote:
>
>> Are you sure you have SWIG installed?
>>
>
> I wasn't and I didn't. =)
>
> Bloody hell scipy takes a long time to build. =)
>

$ time python setup.py build_ext -i
real    12m6.843s
user    6m3.244s
sys     0m13.124s

$ time ../Bento/bentomaker build -i -j   # -j == parallel build (on 4 cores
here)
real    1m46.466s
user    2m54.628s
sys     0m10.900s

Blame distutils (and start using Bento) :)

Ralf




> Juan.
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
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From jni.soma at gmail.com  Fri Oct  4 00:39:06 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Fri, 4 Oct 2013 14:39:06 +1000
Subject: umfpack error
In-Reply-To: <762baf0e-52c2-488b-ac8b-9e5e7caa4dc9@googlegroups.com>
References: <CA+JHcKSZZKrP5y_3R+CQh5UartSuJdJf_Z86u6e9V-P+0kRD9A@mail.gmail.com>
 <762baf0e-52c2-488b-ac8b-9e5e7caa4dc9@googlegroups.com>
Message-ID: <CA+JHcKT88aF2yDOYO5=mkLd1CUzs01QOjhv3fS_wABv1CZ+SBQ@mail.gmail.com>

Thanks Josh for the detailed response and discussion! I think you're
absolutely right that it should be suppressed if pyamg is available. And
it's probably worth getting that in before the release. Happy to tackle
this.

Juan.

PS: I'm mostly on OSX, with some Linux on the side. =)


On Fri, Oct 4, 2013 at 9:17 AM, Josh Warner <silvertrumpet999 at gmail.com>wrote:

> Final note - umfpack enables mode='cg' in random_walker, which is better
> than brute force but not the fastest or most efficient mode. The multi-grid
> preconditioned conjugate gradient method is: mode='cg_mg'. This is
> enabled by pyamg, which is independent of umfpack and is considerably
> easier to install and use than the method I just described.
>
> Come to think of it, we probably should suppress that warning if import
> pyamg works. It incorrectly implies the user doesn't have the fastest
> mode available.
>
> On Thursday, October 3, 2013 1:21:43 AM UTC-5, Juan Nunez-Iglesias wrote:
>
> Hi guys,
>>
>> How do I build scipy with umfpack to silence this error:
>>
>> Exception AttributeError: "'UmfpackContext' object has no attribute '_symbolic'" in <bound method UmfpackContext.__del__ of <scipy.sparse.linalg.dsolve.**umfpack.umfpack.UmfpackContext object at 0x101b62050>> ignored
>>
>> and speed up random_walker? I've just been doing a pip install scipy till
>> now.
>>
>> Juan.
>>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
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From silvertrumpet999 at gmail.com  Fri Oct  4 19:41:39 2013
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Fri, 4 Oct 2013 16:41:39 -0700 (PDT)
Subject: umfpack error
In-Reply-To: <CA+JHcKQYxwU0xcML+-DcaXJtq3Cbsy1ZVS_swXk18K2eyGwFxg@mail.gmail.com>
References: <CA+JHcKSZZKrP5y_3R+CQh5UartSuJdJf_Z86u6e9V-P+0kRD9A@mail.gmail.com>
 <762baf0e-52c2-488b-ac8b-9e5e7caa4dc9@googlegroups.com> <CA+JHcKT88aF2yDOYO5=mkLd1CUzs01QOjhv3fS_wABv1CZ+SBQ@mail.gmail.com>
 <CA+JHcKTtp5ZOjZi6dbTsMJ4mTFbBkvMeyAS3qVF60aj8xz9fbg@mail.gmail.com>
 <1EDEEF3D-F300-4D8B-B463-65C69896B567@demuc.de> <CA+JHcKQ_GD-O2tzUWzUn6jAu2GxpNo4+5z_fHxO2r=e64-PZ1Q@mail.gmail.com>
 <CABL7CQiw04+TcHpMF5CWym54RaDkHwiv9PvfZozOPt=U-AqyQA@mail.gmail.com> <CA+JHcKRQExrnGo+kg1qaQWhi0GR-+G9VfQ4qMMxbnDZHm8HCMA@mail.gmail.com>
 <CA+JHcKQYxwU0xcML+-DcaXJtq3Cbsy1ZVS_swXk18K2eyGwFxg@mail.gmail.com>
Message-ID: <ead13bc1-12c5-46d3-8ae0-49452a2e4a51@googlegroups.com>

This would probably involve an API change, but instead of importing umfpack 
*at all* we could try `import pyamg` first. If pyamg is available, we 
wouldn't even attempt to import umfpack, instead using `'cg_mg'` instead of 
`'cg'`. This sidesteps stderr issues.

The approach only works because the results are equivalent, differing only 
in speed/memory. I don't know why we default to the worst brute force 
option, either. Seems like we could default to `None` and attempt a 
fallback scheme of pyamg -> umfpack -> brute force in order, with a 
different warning structure.

On Friday, October 4, 2013 8:07:39 AM UTC-5, Juan Nunez-Iglesias wrote:
>
> Ok so I'm having trouble actually suppressing this thing. The problem is 
> that to detect whether umfpack is present we try to build the 
> UmfpackContect() object:
>
> try:
>     from scipy.sparse.linalg.dsolve import umfpack
>     UmfpackContext = umfpack.UmfpackContext()except:
>     UmfpackContext = None
>
>
> The constructor raises an ImportError, which we duly catch (although that 
> line should really specify the error type, but whatever). Unfortunately, 
> the UmfpackContext class has a destructor (__del__) which then tries to 
> delete some objects that were never created and raises an AttributeError ? 
> which, since we are already in a try: except: clause, gets ignored, hence 
> the message to stderr.
>
> Basically this is a bug in scipy I think?
>
> The standard approach is to temporarily redirect stderr to /dev/null, and 
> this works interactively:
>
> In [1]: from scipy.sparse.linalg.dsolve import umfpack
>
> In [2]: try:
>     UC = umfpack.UmfpackContext()except ImportError:
>     print 'hello'
>    ...:
> hello
> Exception AttributeError: "'UmfpackContext' object has no attribute '_symbolic'" in <bound method UmfpackContext.__del__ of <scipy.sparse.linalg.dsolve.umfpack.umfpack.UmfpackContext object at 0x103938250>> ignored
>
> In [3]: import sys, os
>
> In [4]: null = open(os.devnull, 'w')
>
> In [5]: null.write('hello!')
>
> In [6]: sys.stdout.write('hello!')
> hello!
> In [7]: sys.stderr.write('hello')
> hello
> In [8]: sys.stderr = null
>
> In [9]: sys.stderr.write('hello')
>
> In [10]: try:
>     UC = umfpack.UmfpackContext()except ImportError:
>     print 'hello'
>    ....:
> hello
>
> In [11]: sys.stderr = sys.__stderr__
>
> In [12]: sys.stderr.write('hello')
> hello
>
>
> However, doing this in the code doesn't work, even when I try to flush the 
> redirected stderr! (I'm not even sure that makes sense!)
>
> sys.stderr = open(os.devnull, 'w')try:
>     from scipy.sparse.linalg.dsolve import umfpack
>     UmfpackContext = umfpack.UmfpackContext()except:
>     UmfpackContext = Nonefinally:
>     sys.stderr.flush()
>     sys.stderr = sys.__stderr__
>
>
> Thoughts/ideas?
>
>
>
> On Fri, Oct 4, 2013 at 10:54 PM, Juan Nunez-Iglesias <jni.... at gmail.com<javascript:>
> > wrote:
>
>> Thanks! Although in this case I was using pip install *and* it was on an 
>> EC2 micro instance so I only have 1 CPU. =)
>>
>> But it is noted and very useful going forward. =)
>>
>>
>>
>> On Fri, Oct 4, 2013 at 10:32 PM, Ralf Gommers <ralf.g... at gmail.com<javascript:>
>> > wrote:
>>
>>>
>>>
>>>
>>> On Fri, Oct 4, 2013 at 1:33 PM, Juan Nunez-Iglesias <jni.... at gmail.com<javascript:>
>>> > wrote:
>>>
>>>> On Fri, Oct 4, 2013 at 8:59 PM, Johannes Sch?nberger <js... at demuc.de<javascript:>
>>>> > wrote:
>>>>  
>>>>> Are you sure you have SWIG installed?
>>>>>
>>>>
>>>> I wasn't and I didn't. =)
>>>>
>>>> Bloody hell scipy takes a long time to build. =)
>>>>
>>>
>>> $ time python setup.py build_ext -i
>>> real    12m6.843s
>>> user    6m3.244s
>>> sys     0m13.124s
>>>
>>> $ time ../Bento/bentomaker build -i -j   # -j == parallel build (on 4 
>>> cores here)
>>> real    1m46.466s
>>> user    2m54.628s
>>> sys     0m10.900s
>>>
>>> Blame distutils (and start using Bento) :)
>>>
>>> Ralf
>>>
>>>
>>>  
>>>
>>>>  Juan.
>>>>
>>>> -- 
>>>> You received this message because you are subscribed to the Google 
>>>> Groups "scikit-image" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send 
>>>> an email to scikit-image... at googlegroups.com <javascript:>.
>>>> For more options, visit https://groups.google.com/groups/opt_out.
>>>>
>>>
>>>  -- 
>>> You received this message because you are subscribed to the Google 
>>> Groups "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send 
>>> an email to scikit-image... at googlegroups.com <javascript:>.
>>> For more options, visit https://groups.google.com/groups/opt_out.
>>>
>>
>>
>
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From jni.soma at gmail.com  Fri Oct  4 06:49:46 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Fri, 4 Oct 2013 20:49:46 +1000
Subject: umfpack error
In-Reply-To: <CA+JHcKT88aF2yDOYO5=mkLd1CUzs01QOjhv3fS_wABv1CZ+SBQ@mail.gmail.com>
References: <CA+JHcKSZZKrP5y_3R+CQh5UartSuJdJf_Z86u6e9V-P+0kRD9A@mail.gmail.com>
 <762baf0e-52c2-488b-ac8b-9e5e7caa4dc9@googlegroups.com> <CA+JHcKT88aF2yDOYO5=mkLd1CUzs01QOjhv3fS_wABv1CZ+SBQ@mail.gmail.com>
Message-ID: <CA+JHcKTtp5ZOjZi6dbTsMJ4mTFbBkvMeyAS3qVF60aj8xz9fbg@mail.gmail.com>

Just for future reference, and because it wasn't immediately obvious from
googling: the umfpack headers in Ubuntu 13.04 are in the package
libsuitesparse-dev.

But now the scipy build fails with some weird error. Hmmm.

building extension "scipy.sparse.linalg.dsolve.umfpack.__umfpack" sources

creating build/src.linux-x86_64-2.7/scipy/sparse/linalg/dsolve

creating build/src.linux-x86_64-2.7/scipy/sparse/linalg/dsolve/umfpack

  adding 'scipy/sparse/linalg/dsolve/umfpack/umfpack.i' to sources.

swig: scipy/sparse/linalg/dsolve/umfpack/umfpack.i

swig -python -I/usr/include/suitesparse -I/usr/include/suitesparse
-I/usr/include/suitesparse -o
build/src.linux-x86_64-2.7/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c
-outdir build/src.linux-x86_64-2.7/scipy/sparse/linalg/dsolve/umfpack
scipy/sparse/linalg/dsolve/umfpack/umfpack.i

unable to execute swig: No such file or directory

error: command 'swig' failed with exit status 1




On Fri, Oct 4, 2013 at 2:39 PM, Juan Nunez-Iglesias <jni.soma at gmail.com>wrote:

> Thanks Josh for the detailed response and discussion! I think you're
> absolutely right that it should be suppressed if pyamg is available. And
> it's probably worth getting that in before the release. Happy to tackle
> this.
>
> Juan.
>
> PS: I'm mostly on OSX, with some Linux on the side. =)
>
>
> On Fri, Oct 4, 2013 at 9:17 AM, Josh Warner <silvertrumpet999 at gmail.com>wrote:
>
>> Final note - umfpack enables mode='cg' in random_walker, which is better
>> than brute force but not the fastest or most efficient mode. The multi-grid
>> preconditioned conjugate gradient method is: mode='cg_mg'. This is
>> enabled by pyamg, which is independent of umfpack and is considerably
>> easier to install and use than the method I just described.
>>
>> Come to think of it, we probably should suppress that warning if import
>> pyamg works. It incorrectly implies the user doesn't have the fastest
>> mode available.
>>
>> On Thursday, October 3, 2013 1:21:43 AM UTC-5, Juan Nunez-Iglesias wrote:
>>
>> Hi guys,
>>>
>>> How do I build scipy with umfpack to silence this error:
>>>
>>> Exception AttributeError: "'UmfpackContext' object has no attribute '_symbolic'" in <bound method UmfpackContext.__del__ of <scipy.sparse.linalg.dsolve.**umfpack.umfpack.UmfpackContext object at 0x101b62050>> ignored
>>>
>>> and speed up random_walker? I've just been doing a pip install scipy
>>> till now.
>>>
>>> Juan.
>>>
>>  --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>
>
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From jni.soma at gmail.com  Fri Oct  4 07:33:04 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Fri, 4 Oct 2013 21:33:04 +1000
Subject: umfpack error
In-Reply-To: <1EDEEF3D-F300-4D8B-B463-65C69896B567@demuc.de>
References: <CA+JHcKSZZKrP5y_3R+CQh5UartSuJdJf_Z86u6e9V-P+0kRD9A@mail.gmail.com>
 <762baf0e-52c2-488b-ac8b-9e5e7caa4dc9@googlegroups.com> <CA+JHcKT88aF2yDOYO5=mkLd1CUzs01QOjhv3fS_wABv1CZ+SBQ@mail.gmail.com>
 <CA+JHcKTtp5ZOjZi6dbTsMJ4mTFbBkvMeyAS3qVF60aj8xz9fbg@mail.gmail.com> <1EDEEF3D-F300-4D8B-B463-65C69896B567@demuc.de>
Message-ID: <CA+JHcKQ_GD-O2tzUWzUn6jAu2GxpNo4+5z_fHxO2r=e64-PZ1Q@mail.gmail.com>

On Fri, Oct 4, 2013 at 8:59 PM, Johannes Sch?nberger <jsch at demuc.de> wrote:

> Are you sure you have SWIG installed?
>

I wasn't and I didn't. =)

Bloody hell scipy takes a long time to build. =)

Juan.
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From jni.soma at gmail.com  Fri Oct  4 08:54:23 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Fri, 4 Oct 2013 22:54:23 +1000
Subject: umfpack error
In-Reply-To: <CABL7CQiw04+TcHpMF5CWym54RaDkHwiv9PvfZozOPt=U-AqyQA@mail.gmail.com>
References: <CA+JHcKSZZKrP5y_3R+CQh5UartSuJdJf_Z86u6e9V-P+0kRD9A@mail.gmail.com>
 <762baf0e-52c2-488b-ac8b-9e5e7caa4dc9@googlegroups.com> <CA+JHcKT88aF2yDOYO5=mkLd1CUzs01QOjhv3fS_wABv1CZ+SBQ@mail.gmail.com>
 <CA+JHcKTtp5ZOjZi6dbTsMJ4mTFbBkvMeyAS3qVF60aj8xz9fbg@mail.gmail.com>
 <1EDEEF3D-F300-4D8B-B463-65C69896B567@demuc.de> <CA+JHcKQ_GD-O2tzUWzUn6jAu2GxpNo4+5z_fHxO2r=e64-PZ1Q@mail.gmail.com>
 <CABL7CQiw04+TcHpMF5CWym54RaDkHwiv9PvfZozOPt=U-AqyQA@mail.gmail.com>
Message-ID: <CA+JHcKRQExrnGo+kg1qaQWhi0GR-+G9VfQ4qMMxbnDZHm8HCMA@mail.gmail.com>

Thanks! Although in this case I was using pip install *and* it was on an
EC2 micro instance so I only have 1 CPU. =)

But it is noted and very useful going forward. =)



On Fri, Oct 4, 2013 at 10:32 PM, Ralf Gommers <ralf.gommers at gmail.com>wrote:

>
>
>
> On Fri, Oct 4, 2013 at 1:33 PM, Juan Nunez-Iglesias <jni.soma at gmail.com>wrote:
>
>> On Fri, Oct 4, 2013 at 8:59 PM, Johannes Sch?nberger <jsch at demuc.de>wrote:
>>
>>> Are you sure you have SWIG installed?
>>>
>>
>> I wasn't and I didn't. =)
>>
>> Bloody hell scipy takes a long time to build. =)
>>
>
> $ time python setup.py build_ext -i
> real    12m6.843s
> user    6m3.244s
> sys     0m13.124s
>
> $ time ../Bento/bentomaker build -i -j   # -j == parallel build (on 4
> cores here)
> real    1m46.466s
> user    2m54.628s
> sys     0m10.900s
>
> Blame distutils (and start using Bento) :)
>
> Ralf
>
>
>
>
>>  Juan.
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>
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From jni.soma at gmail.com  Fri Oct  4 09:07:39 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Fri, 4 Oct 2013 23:07:39 +1000
Subject: umfpack error
In-Reply-To: <CA+JHcKRQExrnGo+kg1qaQWhi0GR-+G9VfQ4qMMxbnDZHm8HCMA@mail.gmail.com>
References: <CA+JHcKSZZKrP5y_3R+CQh5UartSuJdJf_Z86u6e9V-P+0kRD9A@mail.gmail.com>
 <762baf0e-52c2-488b-ac8b-9e5e7caa4dc9@googlegroups.com> <CA+JHcKT88aF2yDOYO5=mkLd1CUzs01QOjhv3fS_wABv1CZ+SBQ@mail.gmail.com>
 <CA+JHcKTtp5ZOjZi6dbTsMJ4mTFbBkvMeyAS3qVF60aj8xz9fbg@mail.gmail.com>
 <1EDEEF3D-F300-4D8B-B463-65C69896B567@demuc.de> <CA+JHcKQ_GD-O2tzUWzUn6jAu2GxpNo4+5z_fHxO2r=e64-PZ1Q@mail.gmail.com>
 <CABL7CQiw04+TcHpMF5CWym54RaDkHwiv9PvfZozOPt=U-AqyQA@mail.gmail.com> <CA+JHcKRQExrnGo+kg1qaQWhi0GR-+G9VfQ4qMMxbnDZHm8HCMA@mail.gmail.com>
Message-ID: <CA+JHcKQYxwU0xcML+-DcaXJtq3Cbsy1ZVS_swXk18K2eyGwFxg@mail.gmail.com>

Ok so I'm having trouble actually suppressing this thing. The problem is
that to detect whether umfpack is present we try to build the
UmfpackContect() object:

try:
    from scipy.sparse.linalg.dsolve import umfpack
    UmfpackContext = umfpack.UmfpackContext()except:
    UmfpackContext = None


The constructor raises an ImportError, which we duly catch (although that
line should really specify the error type, but whatever). Unfortunately,
the UmfpackContext class has a destructor (__del__) which then tries to
delete some objects that were never created and raises an AttributeError ?
which, since we are already in a try: except: clause, gets ignored, hence
the message to stderr.

Basically this is a bug in scipy I think?

The standard approach is to temporarily redirect stderr to /dev/null, and
this works interactively:

In [1]: from scipy.sparse.linalg.dsolve import umfpack

In [2]: try:
    UC = umfpack.UmfpackContext()except ImportError:
    print 'hello'
   ...:
hello
Exception AttributeError: "'UmfpackContext' object has no attribute
'_symbolic'" in <bound method UmfpackContext.__del__ of
<scipy.sparse.linalg.dsolve.umfpack.umfpack.UmfpackContext object at
0x103938250>> ignored

In [3]: import sys, os

In [4]: null = open(os.devnull, 'w')

In [5]: null.write('hello!')

In [6]: sys.stdout.write('hello!')
hello!
In [7]: sys.stderr.write('hello')
hello
In [8]: sys.stderr = null

In [9]: sys.stderr.write('hello')

In [10]: try:
    UC = umfpack.UmfpackContext()except ImportError:
    print 'hello'
   ....:
hello

In [11]: sys.stderr = sys.__stderr__

In [12]: sys.stderr.write('hello')
hello


However, doing this in the code doesn't work, even when I try to flush the
redirected stderr! (I'm not even sure that makes sense!)

sys.stderr = open(os.devnull, 'w')try:
    from scipy.sparse.linalg.dsolve import umfpack
    UmfpackContext = umfpack.UmfpackContext()except:
    UmfpackContext = Nonefinally:
    sys.stderr.flush()
    sys.stderr = sys.__stderr__


Thoughts/ideas?



On Fri, Oct 4, 2013 at 10:54 PM, Juan Nunez-Iglesias <jni.soma at gmail.com>wrote:

> Thanks! Although in this case I was using pip install *and* it was on an
> EC2 micro instance so I only have 1 CPU. =)
>
> But it is noted and very useful going forward. =)
>
>
>
> On Fri, Oct 4, 2013 at 10:32 PM, Ralf Gommers <ralf.gommers at gmail.com>wrote:
>
>>
>>
>>
>> On Fri, Oct 4, 2013 at 1:33 PM, Juan Nunez-Iglesias <jni.soma at gmail.com>wrote:
>>
>>> On Fri, Oct 4, 2013 at 8:59 PM, Johannes Sch?nberger <jsch at demuc.de>wrote:
>>>
>>>> Are you sure you have SWIG installed?
>>>>
>>>
>>> I wasn't and I didn't. =)
>>>
>>> Bloody hell scipy takes a long time to build. =)
>>>
>>
>> $ time python setup.py build_ext -i
>> real    12m6.843s
>> user    6m3.244s
>> sys     0m13.124s
>>
>> $ time ../Bento/bentomaker build -i -j   # -j == parallel build (on 4
>> cores here)
>> real    1m46.466s
>> user    2m54.628s
>> sys     0m10.900s
>>
>> Blame distutils (and start using Bento) :)
>>
>> Ralf
>>
>>
>>
>>
>>>  Juan.
>>>
>>> --
>>> You received this message because you are subscribed to the Google
>>> Groups "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>> For more options, visit https://groups.google.com/groups/opt_out.
>>>
>>
>>  --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>
>
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From jni.soma at gmail.com  Sun Oct  6 03:18:04 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Sun, 6 Oct 2013 18:18:04 +1100
Subject: umfpack error
In-Reply-To: <ead13bc1-12c5-46d3-8ae0-49452a2e4a51@googlegroups.com>
References: <CA+JHcKSZZKrP5y_3R+CQh5UartSuJdJf_Z86u6e9V-P+0kRD9A@mail.gmail.com>
 <762baf0e-52c2-488b-ac8b-9e5e7caa4dc9@googlegroups.com> <CA+JHcKT88aF2yDOYO5=mkLd1CUzs01QOjhv3fS_wABv1CZ+SBQ@mail.gmail.com>
 <CA+JHcKTtp5ZOjZi6dbTsMJ4mTFbBkvMeyAS3qVF60aj8xz9fbg@mail.gmail.com>
 <1EDEEF3D-F300-4D8B-B463-65C69896B567@demuc.de> <CA+JHcKQ_GD-O2tzUWzUn6jAu2GxpNo4+5z_fHxO2r=e64-PZ1Q@mail.gmail.com>
 <CABL7CQiw04+TcHpMF5CWym54RaDkHwiv9PvfZozOPt=U-AqyQA@mail.gmail.com>
 <CA+JHcKRQExrnGo+kg1qaQWhi0GR-+G9VfQ4qMMxbnDZHm8HCMA@mail.gmail.com>
 <CA+JHcKQYxwU0xcML+-DcaXJtq3Cbsy1ZVS_swXk18K2eyGwFxg@mail.gmail.com> <ead13bc1-12c5-46d3-8ae0-49452a2e4a51@googlegroups.com>
Message-ID: <CA+JHcKT=Y7J3cD+6_aoXh3M_omWo-Hc-fzZ8CKnFGujfgBan1w@mail.gmail.com>

I'm in favor of the API change for 0.9, but otherwise we can always go the
deprecation route, and:
- not change the order
- add deprecation warning iff user calls random_walker without explicitly
specifying mode
- add the change in priority to the to-do list.

In the meantime, I did manage to suppress the error message that comes up
on import, at least.

https://github.com/scikit-image/scikit-image/pull/759


On Sat, Oct 5, 2013 at 9:41 AM, Josh Warner <silvertrumpet999 at gmail.com>wrote:

> This would probably involve an API change, but instead of importing
> umfpack *at all* we could try `import pyamg` first. If pyamg is
> available, we wouldn't even attempt to import umfpack, instead using
> `'cg_mg'` instead of `'cg'`. This sidesteps stderr issues.
>
> The approach only works because the results are equivalent, differing only
> in speed/memory. I don't know why we default to the worst brute force
> option, either. Seems like we could default to `None` and attempt a
> fallback scheme of pyamg -> umfpack -> brute force in order, with a
> different warning structure.
>
> On Friday, October 4, 2013 8:07:39 AM UTC-5, Juan Nunez-Iglesias wrote:
>
>> Ok so I'm having trouble actually suppressing this thing. The problem is
>> that to detect whether umfpack is present we try to build the
>> UmfpackContect() object:
>>
>> try:
>>     from scipy.sparse.linalg.dsolve import umfpack
>>     UmfpackContext = umfpack.UmfpackContext()except:
>>     UmfpackContext = None
>>
>>
>> The constructor raises an ImportError, which we duly catch (although that
>> line should really specify the error type, but whatever). Unfortunately,
>> the UmfpackContext class has a destructor (__del__) which then tries to
>> delete some objects that were never created and raises an AttributeError ?
>> which, since we are already in a try: except: clause, gets ignored, hence
>> the message to stderr.
>>
>> Basically this is a bug in scipy I think?
>>
>> The standard approach is to temporarily redirect stderr to /dev/null, and
>> this works interactively:
>>
>> In [1]: from scipy.sparse.linalg.dsolve import umfpack
>>
>> In [2]: try:
>>     UC = umfpack.UmfpackContext()except ImportError:
>>     print 'hello'
>>    ...:
>> hello
>> Exception AttributeError: "'UmfpackContext' object has no attribute '_symbolic'" in <bound method UmfpackContext.__del__ of <scipy.sparse.linalg.dsolve.**umfpack.umfpack.UmfpackContext object at 0x103938250>> ignored
>>
>> In [3]: import sys, os
>>
>> In [4]: null = open(os.devnull, 'w')
>>
>> In [5]: null.write('hello!')
>>
>> In [6]: sys.stdout.write('hello!')
>> hello!
>> In [7]: sys.stderr.write('hello')
>> hello
>> In [8]: sys.stderr = null
>>
>> In [9]: sys.stderr.write('hello')
>>
>> In [10]: try:
>>     UC = umfpack.UmfpackContext()except ImportError:
>>     print 'hello'
>>    ....:
>> hello
>>
>> In [11]: sys.stderr = sys.__stderr__
>>
>> In [12]: sys.stderr.write('hello')
>> hello
>>
>>
>> However, doing this in the code doesn't work, even when I try to flush
>> the redirected stderr! (I'm not even sure that makes sense!)
>>
>> sys.stderr = open(os.devnull, 'w')try:
>>     from scipy.sparse.linalg.dsolve import umfpack
>>     UmfpackContext = umfpack.UmfpackContext()except:
>>     UmfpackContext = Nonefinally:
>>     sys.stderr.flush()
>>     sys.stderr = sys.__stderr__
>>
>>
>> Thoughts/ideas?
>>
>>
>>
>> On Fri, Oct 4, 2013 at 10:54 PM, Juan Nunez-Iglesias <jni.... at gmail.com>wrote:
>>
>>> Thanks! Although in this case I was using pip install *and* it was on an
>>> EC2 micro instance so I only have 1 CPU. =)
>>>
>>> But it is noted and very useful going forward. =)
>>>
>>>
>>>
>>> On Fri, Oct 4, 2013 at 10:32 PM, Ralf Gommers <ralf.g... at gmail.com>wrote:
>>>
>>>>
>>>>
>>>>
>>>> On Fri, Oct 4, 2013 at 1:33 PM, Juan Nunez-Iglesias <jni.... at gmail.com>wrote:
>>>>
>>>> On Fri, Oct 4, 2013 at 8:59 PM, Johannes Sch?nberger <js... at demuc.de>wrote:
>>>>>
>>>>>> Are you sure you have SWIG installed?
>>>>>>
>>>>>
>>>>> I wasn't and I didn't. =)
>>>>>
>>>>> Bloody hell scipy takes a long time to build. =)
>>>>>
>>>>
>>>> $ time python setup.py build_ext -i
>>>> real    12m6.843s
>>>> user    6m3.244s
>>>> sys     0m13.124s
>>>>
>>>> $ time ../Bento/bentomaker build -i -j   # -j == parallel build (on 4
>>>> cores here)
>>>> real    1m46.466s
>>>> user    2m54.628s
>>>> sys     0m10.900s
>>>>
>>>> Blame distutils (and start using Bento) :)
>>>>
>>>> Ralf
>>>>
>>>>
>>>>
>>>>
>>>>>  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...@**googlegroups.com.
>>>>>
>>>>> For more options, visit https://groups.google.com/**groups/opt_out<https://groups.google.com/groups/opt_out>
>>>>> .
>>>>>
>>>>
>>>>  --
>>>> You received this message because you are subscribed to the Google
>>>> Groups "scikit-image" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>> an email to scikit-image...@**googlegroups.com.
>>>>
>>>> For more options, visit https://groups.google.com/**groups/opt_out<https://groups.google.com/groups/opt_out>
>>>> .
>>>>
>>>
>>>
>>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
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>
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From deil.christoph at googlemail.com  Tue Oct  8 10:43:47 2013
From: deil.christoph at googlemail.com (Christoph Deil)
Date: Tue, 8 Oct 2013 16:43:47 +0200
Subject: Richardson-Lucy deconvolution
Message-ID: <16AA6E8C-EDE8-42C7-B1D7-25AD4127DB67@gmail.com>

Hi,

I wanted to try out Richardson-Lucy deconvolution on some astronomy images.

Is this already available in some scientific Python package?

Would it be a welcome addition for scikit-image?
It seems very easy to implement looking at this description and I could give it a try.
http://en.wikipedia.org/wiki/Richardson?Lucy_deconvolution

Christoph


From cjgohlke at gmail.com  Tue Oct  8 22:55:28 2013
From: cjgohlke at gmail.com (Christoph Gohlke)
Date: Tue, 08 Oct 2013 19:55:28 -0700
Subject: Richardson-Lucy deconvolution
In-Reply-To: <16AA6E8C-EDE8-42C7-B1D7-25AD4127DB67@gmail.com>
References: <16AA6E8C-EDE8-42C7-B1D7-25AD4127DB67@gmail.com>
Message-ID: <5254C5A0.4060504@gmail.com>

On 10/8/2013 7:43 AM, Christoph Deil wrote:
> Hi,
>
> I wanted to try out Richardson-Lucy deconvolution on some astronomy images.
>
> Is this already available in some scientific Python package?
>
> Would it be a welcome addition for scikit-image?
> It seems very easy to implement looking at this description and I could give it a try.
> http://en.wikipedia.org/wiki/Richardson??????Lucy_deconvolution
>
> Christoph
>


There are implementations for microscopy images in the following Python 
packages:

IOCBio <http://code.google.com/p/iocbio/>
See also "Application of regularized Richardson??????Lucy algorithm for 
deconvolution of confocal microscopy images"
DOI: 10.1111/j.1365-2818.2011.03486.x

Python-microscopy <http://code.google.com/p/python-microscopy>

Christoph


From jni.soma at gmail.com  Tue Oct  8 22:41:22 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Wed, 9 Oct 2013 13:41:22 +1100
Subject: Richardson-Lucy deconvolution
In-Reply-To: <16AA6E8C-EDE8-42C7-B1D7-25AD4127DB67@gmail.com>
References: <16AA6E8C-EDE8-42C7-B1D7-25AD4127DB67@gmail.com>
Message-ID: <CA+JHcKQ8xm=DapPBgcpwybD-anoaLX8afocgHzGFxSuGxLD6+w@mail.gmail.com>

Hi Christoph,

I don't know of any Python implementations, and I agree with you that it
looks reasonable to implement well in the scipy stack. I'd vote in favor of
adding it to scikit-image (potentially in a new "deconvolution" module),
but we'll have to hear from the other devs before we make a decision.

Juan.



On Wed, Oct 9, 2013 at 1:43 AM, Christoph Deil <
deil.christoph at googlemail.com> wrote:

> Hi,
>
> I wanted to try out Richardson-Lucy deconvolution on some astronomy images.
>
> Is this already available in some scientific Python package?
>
> Would it be a welcome addition for scikit-image?
> It seems very easy to implement looking at this description and I could
> give it a try.
> http://en.wikipedia.org/wiki/Richardson?Lucy_deconvolution
>
> Christoph
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>
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From isaac.gerg at gergltd.com  Fri Oct 11 10:24:55 2013
From: isaac.gerg at gergltd.com (Isaac Gerg)
Date: Fri, 11 Oct 2013 07:24:55 -0700 (PDT)
Subject: CIELUV Transformations
Message-ID: <b20c6a2c-fe5f-43e5-b7ac-ebebde42724b@googlegroups.com>

Feature request here.

Could CIELUV transformation be added?  CIELAB was developed for reflective 
media while CIELUV is for light emitting sources like monitors.  Seems that 
CIELUV would be a more appropriate perceptually uniform colorspace to 
support.

Thanks in advance,
Isaac
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From isaac.gerg at gergltd.com  Fri Oct 11 11:38:25 2013
From: isaac.gerg at gergltd.com (Isaac Gerg)
Date: Fri, 11 Oct 2013 08:38:25 -0700 (PDT)
Subject: CIELUV Transformations
In-Reply-To: <CABDkGQmR6ZtVOdQZMKxgvSmYoeCbCp==KR+6w_+nGyLLN9jwwg@mail.gmail.com>
References: <b20c6a2c-fe5f-43e5-b7ac-ebebde42724b@googlegroups.com>
 <CABDkGQmR6ZtVOdQZMKxgvSmYoeCbCp==KR+6w_+nGyLLN9jwwg@mail.gmail.com>
Message-ID: <fc4457ee-8489-4cbb-8e85-fcce63e78678@googlegroups.com>

I am limited on time but am happy to provide code if someone can put it 
into github for me.

On Friday, October 11, 2013 11:08:50 AM UTC-4, Stefan van der Walt wrote:
>
> Hi Isaac 
>
> On Fri, Oct 11, 2013 at 4:24 PM, Isaac Gerg <isaac... at gergltd.com<javascript:>> 
> wrote: 
> > Could CIELUV transformation be added?  CIELAB was developed for 
> reflective 
> > media while CIELUV is for light emitting sources like monitors.  Seems 
> that 
> > CIELUV would be a more appropriate perceptually uniform colorspace to 
> > support. 
>
> Would you like to have a go at adding it?  It can probably done by 
> simply adding the weights--we have all the tools in place already. 
> We'll also help with the pull request, as necessary. 
>
> Regards 
> St?fan 
>
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From stefan at sun.ac.za  Fri Oct 11 11:08:50 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Fri, 11 Oct 2013 17:08:50 +0200
Subject: CIELUV Transformations
In-Reply-To: <b20c6a2c-fe5f-43e5-b7ac-ebebde42724b@googlegroups.com>
References: <b20c6a2c-fe5f-43e5-b7ac-ebebde42724b@googlegroups.com>
Message-ID: <CABDkGQmR6ZtVOdQZMKxgvSmYoeCbCp==KR+6w_+nGyLLN9jwwg@mail.gmail.com>

Hi Isaac

On Fri, Oct 11, 2013 at 4:24 PM, Isaac Gerg <isaac.gerg at gergltd.com> wrote:
> Could CIELUV transformation be added?  CIELAB was developed for reflective
> media while CIELUV is for light emitting sources like monitors.  Seems that
> CIELUV would be a more appropriate perceptually uniform colorspace to
> support.

Would you like to have a go at adding it?  It can probably done by
simply adding the weights--we have all the tools in place already.
We'll also help with the pull request, as necessary.

Regards
St?fan


From jsch at demuc.de  Fri Oct 11 11:13:12 2013
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Fri, 11 Oct 2013 17:13:12 +0200
Subject: Release time
In-Reply-To: <524C4E05.4030408@sciunto.org>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com> <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com> <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de> <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com> <583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de> <CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com> <9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de> <3370D65E-B530-4B57-B71D-AC8549A7791B@demuc.de> <CAF+hgui_p38G0duCHNCez85xa0ThkP9modmnESqEerxfyhy88A@mail.gmail.com> <CABDkGQkQNHUB=UVZzMsssanpqDqmMURNbSZ-iaW8vFKboQK_oA@mail.gmail.com> <524C4E05.4030408@sciunto.org>
Message-ID: <6B47F231-F251-469D-9EC7-2BB1D9317992@demuc.de>

Do we plan to push 0.9 to the public this weekend?

There are only a few minor outstanding issues: https://github.com/scikit-image/scikit-image/issues?milestone=2&state=open


From fboulogne at sciunto.org  Fri Oct 11 11:24:52 2013
From: fboulogne at sciunto.org (=?ISO-8859-1?Q?Fran=E7ois_Boulogne?=)
Date: Fri, 11 Oct 2013 17:24:52 +0200
Subject: Release time
In-Reply-To: <6B47F231-F251-469D-9EC7-2BB1D9317992@demuc.de>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com> <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com> <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de> <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com> <583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de> <CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com> <9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de> <3370D65E-B530-4B57-B71D-AC8549A7791B@demuc.de> <CAF+hgui_p38G0duCHNCez85xa0ThkP9modmnESqEerxfyhy88A@mail.gmail.com> <CABDkGQkQNHUB=UVZzMsssanpqDqmMURNbSZ-iaW8vFKboQK_oA@mail.gmail.com> <524C4E05.4030408@sciunto.org> <6B47F231-F251-469D-9EC7-2BB1D9317992@demuc.de>
Message-ID: <52581844.7050303@sciunto.org>

Le 11/10/2013 17:13, Johannes Sch?nberger a ?crit :
> Do we plan to push 0.9 to the public this weekend?
>
> There are only a few minor outstanding issues: https://github.com/scikit-image/scikit-image/issues?milestone=2&state=open
>
I think this one must be in 0.9, it's a bugfix.
https://github.com/scikit-image/scikit-image/pull/675

But, I'm not sure I'll have enough time before the release to look at
your last comment.

Cheers,

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



From jsch at demuc.de  Fri Oct 11 11:36:17 2013
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Fri, 11 Oct 2013 17:36:17 +0200
Subject: Release time
In-Reply-To: <52581844.7050303@sciunto.org>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com> <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com> <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de> <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com> <583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de> <CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com> <9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de> <3370D65E-B530-4B57-B71D-AC8549A7791B@demuc.de> <CAF+hgui_p38G0duCHNCez85xa0ThkP9modmnESqEerxfyhy88A@mail.gmail.com> <CABDkGQkQNHUB=UVZzMsssanpqDqmMURNbSZ-iaW8vFKboQK_oA@mail.gmail.com> <524C4E05.4030408@sciunto.org> <6B47F231-F251-469D-9EC7-2BB1D9317992@demuc.de> <52581844.7050303@sciunto.org>
Message-ID: <4AF09CB6-2652-4777-99CC-0CB21D0A1ADE@demuc.de>

Do you want me to send a PR against your branch?

Am 11.10.2013 um 17:24 schrieb Fran?ois Boulogne <fboulogne at sciunto.org>:

> Le 11/10/2013 17:13, Johannes Sch?nberger a ?crit :
>> Do we plan to push 0.9 to the public this weekend?
>> 
>> There are only a few minor outstanding issues: https://github.com/scikit-image/scikit-image/issues?milestone=2&state=open
>> 
> I think this one must be in 0.9, it's a bugfix.
> https://github.com/scikit-image/scikit-image/pull/675
> 
> But, I'm not sure I'll have enough time before the release to look at
> your last comment.
> 
> Cheers,
> 
> -- 
> Fran?ois Boulogne.
> http://www.sciunto.org
> GPG fingerprint: 25F6 C971 4875 A6C1 EDD1  75C8 1AA7 216E 32D5 F22F
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
> 



From fboulogne at sciunto.org  Fri Oct 11 11:55:48 2013
From: fboulogne at sciunto.org (=?ISO-8859-1?Q?Fran=E7ois_Boulogne?=)
Date: Fri, 11 Oct 2013 17:55:48 +0200
Subject: Release time
In-Reply-To: <4AF09CB6-2652-4777-99CC-0CB21D0A1ADE@demuc.de>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com> <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com> <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de> <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com> <583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de> <CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com> <9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de> <3370D65E-B530-4B57-B71D-AC8549A7791B@demuc.de> <CAF+hgui_p38G0duCHNCez85xa0ThkP9modmnESqEerxfyhy88A@mail.gmail.com> <CABDkGQkQNHUB=UVZzMsssanpqDqmMURNbSZ-iaW8vFKboQK_oA@mail.gmail.com> <524C4E05.4030408@sciunto.org> <6B47F231-F251-469D-9EC7-2BB1D9317992@demuc.de> <52581844.7050303@sciunto.org> <4AF09CB6-2652-4777-99CC-0CB21D0A1ADE@demuc.de>
Message-ID: <52581F84.5000006@sciunto.org>

Le 11/10/2013 17:36, Johannes Sch?nberger a ?crit :
> Do you want me to send a PR against your branch?
>

You can if you rather prefer. Thanks.

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



From stefan at sun.ac.za  Fri Oct 11 12:39:17 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Fri, 11 Oct 2013 18:39:17 +0200
Subject: Release time
In-Reply-To: <CAKAks=H_WcBG5vqWL0rZEEHa5=wEKiJ0OJViWF+eU5okconSEg@mail.gmail.com>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com>
 <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com>
 <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de> <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com>
 <583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de> <CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com>
 <9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de> <3370D65E-B530-4B57-B71D-AC8549A7791B@demuc.de>
 <CAF+hgui_p38G0duCHNCez85xa0ThkP9modmnESqEerxfyhy88A@mail.gmail.com>
 <CABDkGQkQNHUB=UVZzMsssanpqDqmMURNbSZ-iaW8vFKboQK_oA@mail.gmail.com>
 <524C4E05.4030408@sciunto.org> <6B47F231-F251-469D-9EC7-2BB1D9317992@demuc.de>
 <CAKAks=H_WcBG5vqWL0rZEEHa5=wEKiJ0OJViWF+eU5okconSEg@mail.gmail.com>
Message-ID: <CABDkGQmgKA-PuiVMdtrzESZj4C9bifoCjKx+p6HoQg37W5Kn9A@mail.gmail.com>

On Fri, Oct 11, 2013 at 5:15 PM, Chintak Sheth <chintaksheth at gmail.com> wrote:
> Can we include exemplar based inpainting?
> https://github.com/scikit-image/scikit-image/pull/706

We need more eyes on this--I am not sure whether this is optimized in
the right places.  Anyone willing to review Chintak's PR?

St?fan


From stefan at sun.ac.za  Fri Oct 11 12:40:14 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Fri, 11 Oct 2013 18:40:14 +0200
Subject: Release time
In-Reply-To: <6B47F231-F251-469D-9EC7-2BB1D9317992@demuc.de>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com>
 <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com>
 <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de> <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com>
 <583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de> <CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com>
 <9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de> <3370D65E-B530-4B57-B71D-AC8549A7791B@demuc.de>
 <CAF+hgui_p38G0duCHNCez85xa0ThkP9modmnESqEerxfyhy88A@mail.gmail.com>
 <CABDkGQkQNHUB=UVZzMsssanpqDqmMURNbSZ-iaW8vFKboQK_oA@mail.gmail.com>
 <524C4E05.4030408@sciunto.org> <6B47F231-F251-469D-9EC7-2BB1D9317992@demuc.de>
Message-ID: <CABDkGQ=3ZSGxqqEfuvfGDwezmK9x-bfM0zy3AUOQRnCDaydpcg@mail.gmail.com>

On Fri, Oct 11, 2013 at 5:13 PM, Johannes Sch?nberger <jsch at demuc.de> wrote:
> Do we plan to push 0.9 to the public this weekend?

I finished the Debian packaging last weekend, so there's nothing
stopping us from a distribution point of view.

> There are only a few minor outstanding issues: https://github.com/scikit-image/scikit-image/issues?milestone=2&state=open

I'll work through these... everyone who has got some spare cycles,
please glance at it!

Thanks
St?fan


From jsch at demuc.de  Fri Oct 11 12:55:17 2013
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Fri, 11 Oct 2013 18:55:17 +0200
Subject: Release time
In-Reply-To: <52581F84.5000006@sciunto.org>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com> <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com> <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de> <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com> <583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de> <CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com> <9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de> <3370D65E-B530-4B57-B71D-AC8549A7791B@demuc.de> <CAF+hgui_p38G0duCHNCez85xa0ThkP9modmnESqEerxfyhy88A@mail.gmail.com> <CABDkGQkQNHUB=UVZzMsssanpqDqmMURNbSZ-iaW8vFKboQK_oA@mail.gmail.com> <524C4E05.4030408@sciunto.org> <6B47F231-F251-469D-9EC7-2BB1D9317992@demuc.de> <52581844.7050303@sciunto.org> <4AF09CB6-2652-4777-99CC-0CB21D0A1ADE@demuc.de> <52581F84.5000006@sciunto.org>
Message-ID: <CC3C9750-7F98-4029-8F8F-1E4C5A377FDD@demuc.de>

>> 
>> Do you want me to send a PR against your branch?
>> 
> 
> You can if you rather prefer. Thanks.

See https://github.com/sciunto/scikit-image/pull/2.


From stefan at sun.ac.za  Fri Oct 11 13:22:57 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Fri, 11 Oct 2013 19:22:57 +0200
Subject: CIELUV Transformations
In-Reply-To: <fc4457ee-8489-4cbb-8e85-fcce63e78678@googlegroups.com>
References: <b20c6a2c-fe5f-43e5-b7ac-ebebde42724b@googlegroups.com>
 <CABDkGQmR6ZtVOdQZMKxgvSmYoeCbCp==KR+6w_+nGyLLN9jwwg@mail.gmail.com> <fc4457ee-8489-4cbb-8e85-fcce63e78678@googlegroups.com>
Message-ID: <CABDkGQkttiCurekV9a=Xi70G4WQt_Dn3AAm_OOxo2LmwGVePCQ@mail.gmail.com>

On Fri, Oct 11, 2013 at 5:38 PM, Isaac Gerg <isaac.gerg at gergltd.com> wrote:
> I am limited on time but am happy to provide code if someone can put it into
> github for me.

Sure, a patch is just fine.

Thanks!
St?fan


From chintaksheth at gmail.com  Fri Oct 11 11:15:18 2013
From: chintaksheth at gmail.com (Chintak Sheth)
Date: Fri, 11 Oct 2013 20:45:18 +0530
Subject: Release time
In-Reply-To: <6B47F231-F251-469D-9EC7-2BB1D9317992@demuc.de>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com>
	<178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de>
	<CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com>
	<C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de>
	<CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com>
	<583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de>
	<CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com>
	<9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de>
	<3370D65E-B530-4B57-B71D-AC8549A7791B@demuc.de>
	<CAF+hgui_p38G0duCHNCez85xa0ThkP9modmnESqEerxfyhy88A@mail.gmail.com>
	<CABDkGQkQNHUB=UVZzMsssanpqDqmMURNbSZ-iaW8vFKboQK_oA@mail.gmail.com>
	<524C4E05.4030408@sciunto.org>
	<6B47F231-F251-469D-9EC7-2BB1D9317992@demuc.de>
Message-ID: <CAKAks=H_WcBG5vqWL0rZEEHa5=wEKiJ0OJViWF+eU5okconSEg@mail.gmail.com>

Can we include exemplar based inpainting?
https://github.com/scikit-image/scikit-image/pull/706

Thanks
Chintak


On Fri, Oct 11, 2013 at 8:43 PM, Johannes Sch?nberger <jsch at demuc.de> wrote:

> Do we plan to push 0.9 to the public this weekend?
>
> There are only a few minor outstanding issues:
> https://github.com/scikit-image/scikit-image/issues?milestone=2&state=open
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>



-- 
Chintak
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From marianne.corvellec at ens-lyon.org  Sat Oct 12 20:57:33 2013
From: marianne.corvellec at ens-lyon.org (Marianne Corvellec)
Date: Sat, 12 Oct 2013 17:57:33 -0700 (PDT)
Subject: Release time
In-Reply-To: <CABDkGQ=3ZSGxqqEfuvfGDwezmK9x-bfM0zy3AUOQRnCDaydpcg@mail.gmail.com>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com>
 <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com>
 <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de> <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com>
 <583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de> <CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com>
 <9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de> <3370D65E-B530-4B57-B71D-AC8549A7791B@demuc.de>
 <CAF+hgui_p38G0duCHNCez85xa0ThkP9modmnESqEerxfyhy88A@mail.gmail.com>
 <CABDkGQkQNHUB=UVZzMsssanpqDqmMURNbSZ-iaW8vFKboQK_oA@mail.gmail.com>
 <524C4E05.4030408@sciunto.org> <6B47F231-F251-469D-9EC7-2BB1D9317992@demuc.de>
 <CABDkGQ=3ZSGxqqEfuvfGDwezmK9x-bfM0zy3AUOQRnCDaydpcg@mail.gmail.com>
Message-ID: <65c13bd3-b5a7-4606-b67b-83d862082125@googlegroups.com>

Hi anyone-with-time-this-weekend,

Please let me know whether my last commit wraps it up for that still open 
issue:
https://github.com/scikit-image/scikit-image/pull/624

Somehow I don't get the expected warnings when calling deprecated 
functions... x-( 

Happy Canadian Thanksgiving!

Marianne

On Friday, October 11, 2013 12:40:14 PM UTC-4, Stefan van der Walt wrote:
>
> On Fri, Oct 11, 2013 at 5:13 PM, Johannes Sch?nberger <js... at demuc.de<javascript:>> 
> wrote: 
> > Do we plan to push 0.9 to the public this weekend? 
>
> I finished the Debian packaging last weekend, so there's nothing 
> stopping us from a distribution point of view. 
>
> > There are only a few minor outstanding issues: 
> https://github.com/scikit-image/scikit-image/issues?milestone=2&state=open 
>
> I'll work through these... everyone who has got some spare cycles, 
> please glance at it! 
>
> Thanks 
> St?fan 
>
-------------- next part --------------
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From jsch at demuc.de  Sun Oct 13 02:22:41 2013
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Sun, 13 Oct 2013 08:22:41 +0200
Subject: Release time
In-Reply-To: <65c13bd3-b5a7-4606-b67b-83d862082125@googlegroups.com>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com> <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com> <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de> <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com> <583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de> <CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com> <9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de> <3370D65E-B530-4B57-B71D-AC8549A7791B@demuc.de> <CAF+hgui_p38G0duCHNCez85xa0ThkP9modmnESqEerxfyhy88A@mail.gmail.com> <CABDkGQkQNHUB=UVZzMsssanpqDqmMURNbSZ-iaW8vFKboQK_oA@mail.gmail.com> <524C4E05.4030408@sciunto.org> <6B47F231-F251-469D-9EC7-2BB1D9317992@demuc.de> <CABDkGQ=3ZSGxqqEfuvfGDwezmK9x-bfM0zy3AUOQRnCDaydpcg@mail.gmail.com> <65c13bd3-b5a7-4606-b67b-83d862082125@googlegroups.com>
Message-ID: <D778DFBE-8C62-466A-B92F-005BD03C28A9@demuc.de>

Marianne

Thanks that's perfect. We need to also add that deprecation to `TODO.txt`.

Thanks and happy Thanksgiving from Germany :-)
Johannes

Am 13.10.2013 um 02:57 schrieb Marianne Corvellec <marianne.corvellec at ens-lyon.org>:

> Hi anyone-with-time-this-weekend,
> 
> Please let me know whether my last commit wraps it up for that still open issue:
> https://github.com/scikit-image/scikit-image/pull/624
> 
> Somehow I don't get the expected warnings when calling deprecated functions... x-( 
> 
> Happy Canadian Thanksgiving!
> 
> Marianne
> 
> On Friday, October 11, 2013 12:40:14 PM UTC-4, Stefan van der Walt wrote:
> On Fri, Oct 11, 2013 at 5:13 PM, Johannes Sch?nberger <js... at demuc.de> wrote: 
> > Do we plan to push 0.9 to the public this weekend? 
> 
> I finished the Debian packaging last weekend, so there's nothing 
> stopping us from a distribution point of view. 
> 
> > There are only a few minor outstanding issues: https://github.com/scikit-image/scikit-image/issues?milestone=2&state=open 
> 
> I'll work through these... everyone who has got some spare cycles, 
> please glance at it! 
> 
> Thanks 
> St?fan 
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.



From jsch at demuc.de  Sun Oct 13 14:04:43 2013
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Sun, 13 Oct 2013 20:04:43 +0200
Subject: Release time
In-Reply-To: <D778DFBE-8C62-466A-B92F-005BD03C28A9@demuc.de>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com> <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com> <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de> <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com> <583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de> <CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com> <9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de> <3370D65E-B530-4B57-B71D-AC8549A7791B@demuc.de> <CAF+hgui_p38G0duCHNCez85xa0ThkP9modmnESqEerxfyhy88A@mail.gmail.com> <CABDkGQkQNHUB=UVZzMsssanpqDqmMURNbSZ-iaW8vFKboQK_oA@mail.gmail.com> <524C4E05.4030408@sciunto.org> <6B47F231-F251-469D-9EC7-2BB1D9317992@demuc.de> <CABDkGQ=3ZSGxqqEfuvfGDwezmK9x-bfM0zy3AUOQRnCDaydpcg@mail.gmail.com> <65c13bd3-b5a7-4606-b67b-83d862082125@googlegroups.com> <D778DFBE-8C62-466A-B92F-005BD03C28A9@demuc.de>
Message-ID: <F1D6BCC0-F232-4FF3-BF24-3A15581D38F9@demuc.de>

We are getting close. Only 2 minor issues left!

Am 13.10.2013 um 08:22 schrieb Johannes Sch?nberger <jsch at demuc.de>:

> Marianne
> 
> Thanks that's perfect. We need to also add that deprecation to `TODO.txt`.
> 
> Thanks and happy Thanksgiving from Germany :-)
> Johannes
> 
> Am 13.10.2013 um 02:57 schrieb Marianne Corvellec <marianne.corvellec at ens-lyon.org>:
> 
>> Hi anyone-with-time-this-weekend,
>> 
>> Please let me know whether my last commit wraps it up for that still open issue:
>> https://github.com/scikit-image/scikit-image/pull/624
>> 
>> Somehow I don't get the expected warnings when calling deprecated functions... x-( 
>> 
>> Happy Canadian Thanksgiving!
>> 
>> Marianne
>> 
>> On Friday, October 11, 2013 12:40:14 PM UTC-4, Stefan van der Walt wrote:
>> On Fri, Oct 11, 2013 at 5:13 PM, Johannes Sch?nberger <js... at demuc.de> wrote: 
>>> Do we plan to push 0.9 to the public this weekend? 
>> 
>> I finished the Debian packaging last weekend, so there's nothing 
>> stopping us from a distribution point of view. 
>> 
>>> There are only a few minor outstanding issues: https://github.com/scikit-image/scikit-image/issues?milestone=2&state=open 
>> 
>> I'll work through these... everyone who has got some spare cycles, 
>> please glance at it! 
>> 
>> Thanks 
>> St?fan 
>> 
>> -- 
>> You received this message because you are subscribed to the Google Groups "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/groups/opt_out.
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
> 



From jean.kossaifi at gmail.com  Mon Oct 14 09:38:35 2013
From: jean.kossaifi at gmail.com (Jean K)
Date: Mon, 14 Oct 2013 06:38:35 -0700 (PDT)
Subject: Build error
Message-ID: <bf919e01-769b-44fd-9451-42371ad439a3@googlegroups.com>

Hi all,

I'm trying to build scikit-image locally, in my git folder, and to just add 
it to my PYTHONPATH.
I checked that all the requirements were met (confirmed by pip install -r 
requirements.txt).
However, when I do 

> python setup.py build_ext -i 

I get an error.
I must be missing something but can't really figure out what...
 
This is the output I get:

> non-existing path in 'skimage/_shared': 'tests'
> non-existing path in 'skimage/_shared': 'geometry.c'
> non-existing path in 'skimage/_shared': 'interpolation.c'
> non-existing path in 'skimage/_shared': 'transform.c'
> non-existing path in 'skimage/draw': '_draw.c'
> non-existing path in 'skimage/feature': 'corner_cy.c'
> non-existing path in 'skimage/feature': 'censure_cy.c'
> non-existing path in 'skimage/feature': '_brief_cy.c'
> non-existing path in 'skimage/feature': '_texture.c'
> non-existing path in 'skimage/feature': '_template.c'
> cython -o /homes/jk712/scikit-image/skimage/filter/_ctmf.c 
> /homes/jk712/scikit-image/skimage/filter/_ctmf.pyx
> Traceback (most recent call last):
>   File "setup.py", line 146, in <module>
>     cmdclass={'build_py': build_py},
>   File "/usr/lib/python2.7/dist-packages/numpy/distutils/core.py", line 
> 152, in setup
>     config = configuration()
>   File "setup.py", line 48, in configuration
>     config.add_subpackage('skimage')
>   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", 
> line 1003, in add_subpackage
>     caller_level = 2)
>   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", 
> line 972, in get_subpackage
>     caller_level = caller_level + 1)
>   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", 
> line 909, in _get_configuration_from_setup_py
>     config = setup_module.configuration(*args)
>   File "skimage/setup.py", line 14, in configuration
>     config.add_subpackage('filter')
>   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", 
> line 1003, in add_subpackage
>     caller_level = 2)
>   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", 
> line 972, in get_subpackage
>     caller_level = caller_level + 1)
>   File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", 
> line 909, in _get_configuration_from_setup_py
>     config = setup_module.configuration(*args)
>   File "skimage/filter/setup.py", line 15, in configuration
>     cython(['_ctmf.pyx'], working_path=base_path)
>   File "/homes/jk712/scikit-image/skimage/_build.py", line 49, in cython
>     subprocess.call(['cython', '-o', c_file, pyxfile])
>   File "/usr/lib/python2.7/subprocess.py", line 524, in call
>     return Popen(*popenargs, **kwargs).wait()
>   File "/usr/lib/python2.7/subprocess.py", line 711, in __init__
>     errread, errwrite)
>   File "/usr/lib/python2.7/subprocess.py", line 1308, in _execute_child
>     raise child_exception
> OSError: [Errno 2] No such file or directory



Apparently the problem would be coming from a missing file _template.c

>  > /usr/lib/python2.7/subprocess.py(524)call()
>     523     """
> --> 524     return Popen(*popenargs, **kwargs).wait()
>     525 
>
 

> ipdb> print popenargs
> (['cython', '-o', '/homes/jk712/scikit-image/skimage/feature/_template.c', 
> '/homes/jk712/scikit-image/skimage/feature/_template.pyx'],)
>
 

> ipdb> print kwargs
> {}


On the other hand, 

> easy_install --prefix ~/usr scikit-image 

works. 

Any idea of what is going on?

Thanks,

Jean 

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From jean.kossaifi at gmail.com  Mon Oct 14 11:21:50 2013
From: jean.kossaifi at gmail.com (Jean K)
Date: Mon, 14 Oct 2013 16:21:50 +0100
Subject: Build error
In-Reply-To: <CABDkGQ=godpjAM5-W1reuYj=LpHOovfZkoWg4n7xiX7Ho8CWKw@mail.gmail.com>
References: <bf919e01-769b-44fd-9451-42371ad439a3@googlegroups.com>
	<CABDkGQ=godpjAM5-W1reuYj=LpHOovfZkoWg4n7xiX7Ho8CWKw@mail.gmail.com>
Message-ID: <CA+gx=EdE4Pp9h+QErvtvtXR7VpWth70+jxe_fn4zZJw_A2yMxg@mail.gmail.com>

You are absolutely right, thanks!
I had already installed Cython locally but didn't add it properly to the
PATH.

However after I fixed it I got another error:

>  [...]

building extension "skimage.segmentation._felzenszwalb_cy" sources
> building extension "skimage.segmentation._quickshift" sources
> building extension "skimage.segmentation._slic" sources
> building data_files sources
> build_src: building npy-pkg config files
> customize UnixCCompiler
> customize UnixCCompiler using build_ext
> building 'skimage._shared.geometry' extension
> compiling C sources
> C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g
> -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC
> creating build
> creating build/temp.linux-x86_64-2.7
> compile options: '-I/usr/lib/python2.7/dist-packages/numpy/core/include
> -I/usr/include/python2.7 -c'
> x86_64-linux-gnu-gcc: geometry.c
> x86_64-linux-gnu-gcc: error: geometry.c: No such file or directory
> x86_64-linux-gnu-gcc: fatal error: no input files
> compilation terminated.
> x86_64-linux-gnu-gcc: error: geometry.c: No such file or directory
> x86_64-linux-gnu-gcc: fatal error: no input files
> compilation terminated.
> error: Command "x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing
> -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC
> -I/usr/lib/python2.7/dist-packages/numpy/core/include
> -I/usr/include/python2.7 -c geometry.c -o
> build/temp.linux-x86_64-2.7/geometry.o" failed with exit status 4


Any idea?

Thanks,

Jean


2013/10/14 St?fan van der Walt <stefan at sun.ac.za>

> On Mon, Oct 14, 2013 at 3:38 PM, Jean K <jean.kossaifi at gmail.com> wrote:
> >> ipdb> print popenargs
> >> (['cython', '-o',
> '/homes/jk712/scikit-image/skimage/feature/_template.c',
> >> '/homes/jk712/scikit-image/skimage/feature/_template.pyx'],)
>
> It looks like cython wasn't installed correctly.  Could you try the
> "cython" command from the terminal?
>
> St?fan
>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "scikit-image" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/scikit-image/zV05Huop18c/unsubscribe.
> To unsubscribe from this group and all of its topics, send an email to
> scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>
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From stefan at sun.ac.za  Mon Oct 14 10:39:12 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 14 Oct 2013 16:39:12 +0200
Subject: Build error
In-Reply-To: <bf919e01-769b-44fd-9451-42371ad439a3@googlegroups.com>
References: <bf919e01-769b-44fd-9451-42371ad439a3@googlegroups.com>
Message-ID: <CABDkGQ=godpjAM5-W1reuYj=LpHOovfZkoWg4n7xiX7Ho8CWKw@mail.gmail.com>

On Mon, Oct 14, 2013 at 3:38 PM, Jean K <jean.kossaifi at gmail.com> wrote:
>> ipdb> print popenargs
>> (['cython', '-o', '/homes/jk712/scikit-image/skimage/feature/_template.c',
>> '/homes/jk712/scikit-image/skimage/feature/_template.pyx'],)

It looks like cython wasn't installed correctly.  Could you try the
"cython" command from the terminal?

St?fan


From jean.kossaifi at gmail.com  Mon Oct 14 12:06:03 2013
From: jean.kossaifi at gmail.com (Jean K)
Date: Mon, 14 Oct 2013 17:06:03 +0100
Subject: Build error
In-Reply-To: <CABDkGQm4fN2zJUqMSWLxnF7eRChvgGPYEUC8rMz1LR9CPnBOeQ@mail.gmail.com>
References: <bf919e01-769b-44fd-9451-42371ad439a3@googlegroups.com>
	<CABDkGQ=godpjAM5-W1reuYj=LpHOovfZkoWg4n7xiX7Ho8CWKw@mail.gmail.com>
	<CA+gx=EdE4Pp9h+QErvtvtXR7VpWth70+jxe_fn4zZJw_A2yMxg@mail.gmail.com>
	<CABDkGQm4fN2zJUqMSWLxnF7eRChvgGPYEUC8rMz1LR9CPnBOeQ@mail.gmail.com>
Message-ID: <CA+gx=EfHaymj4_7jfCGNWJBcNwSHBcATsu8f0_8jdLwj=TMoQQ@mail.gmail.com>

Yes

> % cython -V
> Cython version 0.19.2


I did python setup.py clean before installing but still get the same
error...


2013/10/14 St?fan van der Walt <stefan at sun.ac.za>

> On Mon, Oct 14, 2013 at 5:21 PM, Jean K <jean.kossaifi at gmail.com> wrote:
> > You are absolutely right, thanks!
> > I had already installed Cython locally but didn't add it properly to the
> > PATH.
> >
> > However after I fixed it I got another error:
>
> Do you have Cython v0.19 installed?  If so, then perhaps try a clean build.
>
> St?fan
>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "scikit-image" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/scikit-image/zV05Huop18c/unsubscribe.
> To unsubscribe from this group and all of its topics, send an email to
> scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>
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From stefan at sun.ac.za  Mon Oct 14 11:24:29 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 14 Oct 2013 17:24:29 +0200
Subject: Build error
In-Reply-To: <CA+gx=EdE4Pp9h+QErvtvtXR7VpWth70+jxe_fn4zZJw_A2yMxg@mail.gmail.com>
References: <bf919e01-769b-44fd-9451-42371ad439a3@googlegroups.com>
 <CABDkGQ=godpjAM5-W1reuYj=LpHOovfZkoWg4n7xiX7Ho8CWKw@mail.gmail.com> <CA+gx=EdE4Pp9h+QErvtvtXR7VpWth70+jxe_fn4zZJw_A2yMxg@mail.gmail.com>
Message-ID: <CABDkGQm4fN2zJUqMSWLxnF7eRChvgGPYEUC8rMz1LR9CPnBOeQ@mail.gmail.com>

On Mon, Oct 14, 2013 at 5:21 PM, Jean K <jean.kossaifi at gmail.com> wrote:
> You are absolutely right, thanks!
> I had already installed Cython locally but didn't add it properly to the
> PATH.
>
> However after I fixed it I got another error:

Do you have Cython v0.19 installed?  If so, then perhaps try a clean build.

St?fan


From stefan at sun.ac.za  Mon Oct 14 11:28:22 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 14 Oct 2013 17:28:22 +0200
Subject: Richardson-Lucy deconvolution
In-Reply-To: <16AA6E8C-EDE8-42C7-B1D7-25AD4127DB67@gmail.com>
References: <16AA6E8C-EDE8-42C7-B1D7-25AD4127DB67@gmail.com>
Message-ID: <CABDkGQ=HYX_ZXYpxMqBcG3LyZfXkfkXVFVfjXCPgdJBG+EU8Yw@mail.gmail.com>

Hi Christoph

On Tue, Oct 8, 2013 at 4:43 PM, Christoph Deil
<deil.christoph at googlemail.com> wrote:
> I wanted to try out Richardson-Lucy deconvolution on some astronomy images.

This would make for a nice addition to the existing inverse filtering
options (which are, frankly, pretty badly implemented).  Those were
some of the first pieces of code written, and could do with some love.

St?fan


From jsch at demuc.de  Mon Oct 14 11:40:14 2013
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Mon, 14 Oct 2013 17:40:14 +0200
Subject: Release time
In-Reply-To: <F1D6BCC0-F232-4FF3-BF24-3A15581D38F9@demuc.de>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com> <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com> <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de> <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com> <583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de> <CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com> <9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de> <3370D65E-B530-4B57-B71D-AC8549A7791B@demuc.de> <CAF+hgui_p38G0duCHNCez85xa0ThkP9modmnESqEerxfyhy88A@mail.gmail.com> <CABDkGQkQNHUB=UVZzMsssanpqDqmMURNbSZ-iaW8vFKboQK_oA@mail.gmail.com> <524C4E05.4030408@sciunto.org> <6B47F231-F251-469D-9EC7-2BB1D9317992@demuc.de> <CABDkGQ=3ZSGxqqEfuvfGDwezmK9x-bfM0zy3AUOQRnCDaydpcg@mail.gmail.com> <65c13bd3-b5a7-4606-b67b-83d862082125@googlegroups.com> <D778DFBE-8C62-466A-B92F-005BD03C28A9@demuc.de> <F1D6BCC0-F232-4FF3-BF24-3A15581D38F9@demuc.de>
Message-ID: <4AD1AFF6-40E7-470D-AEE1-918E1FECEC02@demuc.de>

It seems we closed all remaining issues.

Is there anything else that is stopping us from releasing 0.9?

Should we put a hold on merging new features apart from bug fixes for a window of maybe 10 days for a 0.9.1 release?

Am 13.10.2013 um 20:04 schrieb Johannes Sch?nberger <jsch at demuc.de>:

> We are getting close. Only 2 minor issues left!
> 
> Am 13.10.2013 um 08:22 schrieb Johannes Sch?nberger <jsch at demuc.de>:
> 
>> Marianne
>> 
>> Thanks that's perfect. We need to also add that deprecation to `TODO.txt`.
>> 
>> Thanks and happy Thanksgiving from Germany :-)
>> Johannes
>> 
>> Am 13.10.2013 um 02:57 schrieb Marianne Corvellec <marianne.corvellec at ens-lyon.org>:
>> 
>>> Hi anyone-with-time-this-weekend,
>>> 
>>> Please let me know whether my last commit wraps it up for that still open issue:
>>> https://github.com/scikit-image/scikit-image/pull/624
>>> 
>>> Somehow I don't get the expected warnings when calling deprecated functions... x-( 
>>> 
>>> Happy Canadian Thanksgiving!
>>> 
>>> Marianne
>>> 
>>> On Friday, October 11, 2013 12:40:14 PM UTC-4, Stefan van der Walt wrote:
>>> On Fri, Oct 11, 2013 at 5:13 PM, Johannes Sch?nberger <js... at demuc.de> wrote: 
>>>> Do we plan to push 0.9 to the public this weekend? 
>>> 
>>> I finished the Debian packaging last weekend, so there's nothing 
>>> stopping us from a distribution point of view. 
>>> 
>>>> There are only a few minor outstanding issues: https://github.com/scikit-image/scikit-image/issues?milestone=2&state=open 
>>> 
>>> I'll work through these... everyone who has got some spare cycles, 
>>> please glance at it! 
>>> 
>>> Thanks 
>>> St?fan 
>>> 
>>> -- 
>>> You received this message because you are subscribed to the Google Groups "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
>>> For more options, visit https://groups.google.com/groups/opt_out.
>> 
>> -- 
>> You received this message because you are subscribed to the Google Groups "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/groups/opt_out.
>> 
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
> 



From silvertrumpet999 at gmail.com  Mon Oct 14 20:48:06 2013
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Mon, 14 Oct 2013 17:48:06 -0700 (PDT)
Subject: Release time
In-Reply-To: <525C12DD.3070608@sciunto.org>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com> <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de> <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com> <583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de> <CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com> <9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de> <3370D65E-B530-4B57-B71D-AC8549A7791B@demuc.de> <CAF+hgui_p38G0duCHNCez85xa0ThkP9modmnESqEerxfyhy88A@mail.gmail.com> <CABDkGQkQNHUB=UVZzMsssanpqDqmMURNbSZ-iaW8vFKboQK_oA@mail.gmail.com> <524C4E05.4030408@sciunto.org> <6B47F231-F251-469D-9EC7-2BB1D9317992@demuc.de> <CABDkGQ=3ZSGxqqEfuvfGDwezmK9x-bfM0zy3AUOQRnCDaydpcg@mail.gmail.com> <65c13bd3-b5a7-4606-b67b-83d862082125@googlegroups.com> <D778DFBE-8C62-466A-B92F-005BD03C28A9@demuc.de> <F1D6BCC0-F232-4FF3-BF24-3A15581D38F9@demuc.de> <4AD1AFF6-40E7-470D-AEE1-918E1FECEC02@demuc.de>
 <525C12DD.3070608@sciunto.org>
Message-ID: <24323453-b6b5-4f45-929b-882743fee33c@googlegroups.com>

Yes, even deprecated functions need to be tested until they are removed. 
We've added a few new deprecations recently, and those will happily warn 
users until 0.10 is released.

On Monday, October 14, 2013 10:50:53 AM UTC-5, Fran?ois Boulogne wrote:
>
> Le 14/10/2013 17:40, Johannes Sch?nberger a ?crit : 
> > It seems we closed all remaining issues. 
> > 
> > Is there anything else that is stopping us from releasing 0.9? 
>
> Reading travis logs, it seems we are using deprecated functions in 
> tests. I think it's related to recent deprecations but I didn't looked 
> in details yet. Are you aware of that, and do you plan to fix this for 
> the next release? 
>
>
>
> -- 
> Fran?ois Boulogne. 
> http://www.sciunto.org 
> GPG fingerprint: 25F6 C971 4875 A6C1 EDD1  75C8 1AA7 216E 32D5 F22F 
>
>
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From jean.kossaifi at gmail.com  Mon Oct 14 12:49:40 2013
From: jean.kossaifi at gmail.com (Jean K)
Date: Mon, 14 Oct 2013 17:49:40 +0100
Subject: Build error
In-Reply-To: <52CDDFB3-F060-4392-B604-EB40C5908622@demuc.de>
References: <bf919e01-769b-44fd-9451-42371ad439a3@googlegroups.com>
	<CABDkGQ=godpjAM5-W1reuYj=LpHOovfZkoWg4n7xiX7Ho8CWKw@mail.gmail.com>
	<CA+gx=EdE4Pp9h+QErvtvtXR7VpWth70+jxe_fn4zZJw_A2yMxg@mail.gmail.com>
	<CABDkGQm4fN2zJUqMSWLxnF7eRChvgGPYEUC8rMz1LR9CPnBOeQ@mail.gmail.com>
	<CA+gx=EfHaymj4_7jfCGNWJBcNwSHBcATsu8f0_8jdLwj=TMoQQ@mail.gmail.com>
	<52CDDFB3-F060-4392-B604-EB40C5908622@demuc.de>
Message-ID: <CA+gx=EdbrggWTGuDdDJfkCpeh0tya+9vD5bY1j8L6ong-EGU3Q@mail.gmail.com>

Great, it works now!

Thanks a lot,

Sorry for the spam.

Cheers,

Jean


2013/10/14 Johannes Sch?nberger <jsch at demuc.de>

> Try ``make clean``.
>
> Am 14.10.2013 um 18:06 schrieb Jean K <jean.kossaifi at gmail.com>:
>
> > Yes
> > % cython -V
> > Cython version 0.19.2
> >
> > I did python setup.py clean before installing but still get the same
> error...
> >
> >
> > 2013/10/14 St?fan van der Walt <stefan at sun.ac.za>
> > On Mon, Oct 14, 2013 at 5:21 PM, Jean K <jean.kossaifi at gmail.com> wrote:
> > > You are absolutely right, thanks!
> > > I had already installed Cython locally but didn't add it properly to
> the
> > > PATH.
> > >
> > > However after I fixed it I got another error:
> >
> > Do you have Cython v0.19 installed?  If so, then perhaps try a clean
> build.
> >
> > St?fan
> >
> > --
> > You received this message because you are subscribed to a topic in the
> Google Groups "scikit-image" group.
> > To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/scikit-image/zV05Huop18c/unsubscribe.
> > To unsubscribe from this group and all of its topics, send an email to
> scikit-image+unsubscribe at googlegroups.com.
> > For more options, visit https://groups.google.com/groups/opt_out.
> >
> >
> > --
> > You received this message because you are subscribed to the Google
> Groups "scikit-image" group.
> > To unsubscribe from this group and stop receiving emails from it, send
> an email to scikit-image+unsubscribe at googlegroups.com.
> > For more options, visit https://groups.google.com/groups/opt_out.
>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "scikit-image" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/scikit-image/zV05Huop18c/unsubscribe.
> To unsubscribe from this group and all of its topics, send an email to
> scikit-image+unsubscribe at googlegroups.com.
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>
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From fboulogne at sciunto.org  Mon Oct 14 11:50:53 2013
From: fboulogne at sciunto.org (=?ISO-8859-1?Q?Fran=E7ois_Boulogne?=)
Date: Mon, 14 Oct 2013 17:50:53 +0200
Subject: Release time
In-Reply-To: <4AD1AFF6-40E7-470D-AEE1-918E1FECEC02@demuc.de>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com> <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de> <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com> <583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de> <CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com> <9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de> <3370D65E-B530-4B57-B71D-AC8549A7791B@demuc.de> <CAF+hgui_p38G0duCHNCez85xa0ThkP9modmnESqEerxfyhy88A@mail.gmail.com> <CABDkGQkQNHUB=UVZzMsssanpqDqmMURNbSZ-iaW8vFKboQK_oA@mail.gmail.com> <524C4E05.4030408@sciunto.org> <6B47F231-F251-469D-9EC7-2BB1D9317992@demuc.de> <CABDkGQ=3ZSGxqqEfuvfGDwezmK9x-bfM0zy3AUOQRnCDaydpcg@mail.gmail.com> <65c13bd3-b5a7-4606-b67b-83d862082125@googlegroups.com> <D778DFBE-8C62-466A-B92F-005BD03C28A9@demuc.de> <F1D6BCC0-F232-4FF3-BF24-3A15581D38F9@demuc.de> <4AD1AFF6-40E7-470D-AEE1-918E1FECEC02@demuc.de>
Message-ID: <525C12DD.3070608@sciunto.org>

Le 14/10/2013 17:40, Johannes Sch?nberger a ?crit :
> It seems we closed all remaining issues.
>
> Is there anything else that is stopping us from releasing 0.9?

Reading travis logs, it seems we are using deprecated functions in
tests. I think it's related to recent deprecations but I didn't looked
in details yet. Are you aware of that, and do you plan to fix this for
the next release?



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



From jsch at demuc.de  Mon Oct 14 12:11:32 2013
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Mon, 14 Oct 2013 18:11:32 +0200
Subject: Build error
In-Reply-To: <CA+gx=EfHaymj4_7jfCGNWJBcNwSHBcATsu8f0_8jdLwj=TMoQQ@mail.gmail.com>
References: <bf919e01-769b-44fd-9451-42371ad439a3@googlegroups.com> <CABDkGQ=godpjAM5-W1reuYj=LpHOovfZkoWg4n7xiX7Ho8CWKw@mail.gmail.com> <CA+gx=EdE4Pp9h+QErvtvtXR7VpWth70+jxe_fn4zZJw_A2yMxg@mail.gmail.com> <CABDkGQm4fN2zJUqMSWLxnF7eRChvgGPYEUC8rMz1LR9CPnBOeQ@mail.gmail.com> <CA+gx=EfHaymj4_7jfCGNWJBcNwSHBcATsu8f0_8jdLwj=TMoQQ@mail.gmail.com>
Message-ID: <52CDDFB3-F060-4392-B604-EB40C5908622@demuc.de>

Try ``make clean``.

Am 14.10.2013 um 18:06 schrieb Jean K <jean.kossaifi at gmail.com>:

> Yes
> % cython -V
> Cython version 0.19.2
> 
> I did python setup.py clean before installing but still get the same error... 
> 
> 
> 2013/10/14 St?fan van der Walt <stefan at sun.ac.za>
> On Mon, Oct 14, 2013 at 5:21 PM, Jean K <jean.kossaifi at gmail.com> wrote:
> > You are absolutely right, thanks!
> > I had already installed Cython locally but didn't add it properly to the
> > PATH.
> >
> > However after I fixed it I got another error:
> 
> Do you have Cython v0.19 installed?  If so, then perhaps try a clean build.
> 
> St?fan
> 
> --
> You received this message because you are subscribed to a topic in the Google Groups "scikit-image" group.
> To unsubscribe from this topic, visit https://groups.google.com/d/topic/scikit-image/zV05Huop18c/unsubscribe.
> To unsubscribe from this group and all of its topics, send an email to scikit-image+unsubscribe at googlegroups.com.
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> 
> 
> -- 
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From jsch at demuc.de  Mon Oct 14 12:27:14 2013
From: jsch at demuc.de (=?windows-1252?Q?Johannes_Sch=F6nberger?=)
Date: Mon, 14 Oct 2013 18:27:14 +0200
Subject: Release time
In-Reply-To: <525C12DD.3070608@sciunto.org>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com> <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de> <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com> <583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de> <CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com> <9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de> <3370D65E-B530-4B57-B71D-AC8549A7791B@demuc.de> <CAF+hgui_p38G0duCHNCez85xa0ThkP9modmnESqEerxfyhy88A@mail.gmail.com> <CABDkGQkQNHUB=UVZzMsssanpqDqmMURNbSZ-iaW8vFKboQK_oA@mail.gmail.com> <524C4E05.4030408@sciunto.org> <6B47F231-F251-469D-9EC7-2BB1D9317992@demuc.de> <CABDkGQ=3ZSGxqqEfuvfGDwezmK9x-bfM0zy3AUOQRnCDaydpcg@mail.gmail.com> <65c13bd3-b5a7-4606-b67b-83d862082125@googlegroups.com> <D778DFBE-8C62-466A-B92F-005BD03C28A9@demuc.de> <F1D6BCC0-F232-4FF3-BF24-3A15581D38F9@demuc.de> <4AD1AFF6-40E7-470D-AEE1-918E1FECEC02@demuc.de> <525C12DD.3070608@sciunto.org>
Message-ID: <8B535563-06DF-43D5-909A-0ED8DFC703BC@demuc.de>

> Reading travis logs, it seems we are using deprecated functions in
> tests. I think it's related to recent deprecations but I didn't looked
> in details yet. Are you aware of that, and do you plan to fix this for
> the next release?

I filed another issue which removes all deprecated functions that are due for 0.9. The rest of the deprecated function calls used in tests should be removed when their corresponding functions are removed in the 0.10 cycle imo?


From stefan at sun.ac.za  Mon Oct 14 13:50:35 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 14 Oct 2013 19:50:35 +0200
Subject: Release time
In-Reply-To: <4AD1AFF6-40E7-470D-AEE1-918E1FECEC02@demuc.de>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com>
 <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com>
 <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de> <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com>
 <583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de> <CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com>
 <9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de> <3370D65E-B530-4B57-B71D-AC8549A7791B@demuc.de>
 <CAF+hgui_p38G0duCHNCez85xa0ThkP9modmnESqEerxfyhy88A@mail.gmail.com>
 <CABDkGQkQNHUB=UVZzMsssanpqDqmMURNbSZ-iaW8vFKboQK_oA@mail.gmail.com>
 <524C4E05.4030408@sciunto.org> <6B47F231-F251-469D-9EC7-2BB1D9317992@demuc.de>
 <CABDkGQ=3ZSGxqqEfuvfGDwezmK9x-bfM0zy3AUOQRnCDaydpcg@mail.gmail.com>
 <65c13bd3-b5a7-4606-b67b-83d862082125@googlegroups.com> <D778DFBE-8C62-466A-B92F-005BD03C28A9@demuc.de>
 <F1D6BCC0-F232-4FF3-BF24-3A15581D38F9@demuc.de> <4AD1AFF6-40E7-470D-AEE1-918E1FECEC02@demuc.de>
Message-ID: <CABDkGQm1qxrGHGb1=1DH1Br33HmpeKFp7O-VEWJ=g1PLOBt8Kw@mail.gmail.com>

On Mon, Oct 14, 2013 at 5:40 PM, Johannes Sch?nberger <jsch at demuc.de> wrote:
> It seems we closed all remaining issues.

Thank you everyone, especially Johannes for being so active in driving
this release.

> Is there anything else that is stopping us from releasing 0.9?

I think we're ready!  Unless there's anything else, I can tag the
release later tonight.

> Should we put a hold on merging new features apart from bug fixes for a window of maybe 10 days for a 0.9.1 release?

How about we make a 0.9.x branch where we cherry-pick any serious bugs
affecting 0.9.0?

St?fan


From jsch at demuc.de  Tue Oct 15 09:25:38 2013
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Tue, 15 Oct 2013 15:25:38 +0200
Subject: Release time
In-Reply-To: <CABDkGQm1qxrGHGb1=1DH1Br33HmpeKFp7O-VEWJ=g1PLOBt8Kw@mail.gmail.com>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com> <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com> <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de> <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com> <583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de> <CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com> <9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de> <3370D65E-B530-4B57-B71D-AC8549A7791B@demuc.de> <CAF+hgui_p38G0duCHNCez85xa0ThkP9modmnESqEerxfyhy88A@mail.gmail.com> <CABDkGQkQNHUB=UVZzMsssanpqDqmMURNbSZ-iaW8vFKboQK_oA@mail.gmail.com> <524C4E05.4030408@sciunto.org> <6B47F231-F251-469D-9EC7-2BB1D9317992@demuc.de> <CABDkGQ=3ZSGxqqEfuvfGDwezmK9x-bfM0zy3AUOQRnCDaydpcg@mail.gmail.com> <65c13bd3-b5a7-4606-b67b-83d862082125@googlegroups.com> <D778DFBE-8C62-466A-B92F-005BD03C28A9@demuc.de> <F1D6BCC0-F232-4FF3-BF24-3A15581D38F9@demuc.de> <4AD1AFF6-40E7-470D-AEE1-918E1FECEC02@demuc.de> <CABDkGQm1qxrGHGb1=1DH1Br33HmpeKFp7O-VEWJ=g1PLOBt8Kw@mail.gmail.com>
Message-ID: <29349511-94C6-49DD-8BE1-2790ACF6C253@demuc.de>

I think I fixed the two remaining issues reported by Christoph, thanks for reporting them!

> How about we make a 0.9.x branch where we cherry-pick any serious bugs
> affecting 0.9.0?

Good idea.


From francesc at continuum.io  Tue Oct 15 10:59:55 2013
From: francesc at continuum.io (Francesc Alted)
Date: Tue, 15 Oct 2013 16:59:55 +0200
Subject: Operations on disk-based images
Message-ID: <CANF6gwog1+FdEReU=3Yn9EAoT2q1X7AD3AcocZ0ska0coWdSCA@mail.gmail.com>

Hi,

We are trying to deal with very large images (they typically do not fit
in-memory), and for visualizing purposes, I am trying to use some
downsampling before sending the bits to the graphics render.

Our files are typically in HDF5 (or NetCDF4) format, so the data on-disk is
accessible randomly (i.e. they support indexes a la NumPy), and I noticed
that the recently added `skimage.transform.downscale_local_mean()` function
(which is just perfect for our purposes) also works with these on-disk
arrays.  The problem is that the function takes *ages* to finish.  My guess
is that this is mainly a consequence of the fact that accessing data
on-disk without too much care about data locality, is much more expensive
than doing the same in-memory.

I suppose the only solution is to rewrite the algorithms we are interested
in so that leveraging spatial locality would be critical, but I wanted to
report that here just in case someone has some insight on what to do in
this case.

Thanks,

-- 
Francesc Alted
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From isaac.gerg at gergltd.com  Wed Oct 16 15:52:26 2013
From: isaac.gerg at gergltd.com (Isaac Gerg)
Date: Wed, 16 Oct 2013 12:52:26 -0700 (PDT)
Subject: CIELUV Transformations
In-Reply-To: <CABDkGQkttiCurekV9a=Xi70G4WQt_Dn3AAm_OOxo2LmwGVePCQ@mail.gmail.com>
References: <b20c6a2c-fe5f-43e5-b7ac-ebebde42724b@googlegroups.com>
 <CABDkGQmR6ZtVOdQZMKxgvSmYoeCbCp==KR+6w_+nGyLLN9jwwg@mail.gmail.com> <fc4457ee-8489-4cbb-8e85-fcce63e78678@googlegroups.com>
 <CABDkGQkttiCurekV9a=Xi70G4WQt_Dn3AAm_OOxo2LmwGVePCQ@mail.gmail.com>
Message-ID: <9450c9e5-5951-421b-92fe-c159ccbdbef1@googlegroups.com>

I have completed the changes to colorconv.py so that luv is now supported. 
 Whom do I email the file to so that it can be included in the repo?

Isaac

On Friday, October 11, 2013 1:22:57 PM UTC-4, Stefan van der Walt wrote:
>
> On Fri, Oct 11, 2013 at 5:38 PM, Isaac Gerg <isaac... at gergltd.com<javascript:>> 
> wrote: 
> > I am limited on time but am happy to provide code if someone can put it 
> into 
> > github for me. 
>
> Sure, a patch is just fine. 
>
> Thanks! 
> St?fan 
>
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From isaac.gerg at gergltd.com  Wed Oct 16 17:29:40 2013
From: isaac.gerg at gergltd.com (Isaac Gerg)
Date: Wed, 16 Oct 2013 14:29:40 -0700 (PDT)
Subject: CIELUV Transformations
In-Reply-To: <9450c9e5-5951-421b-92fe-c159ccbdbef1@googlegroups.com>
References: <b20c6a2c-fe5f-43e5-b7ac-ebebde42724b@googlegroups.com>
 <CABDkGQmR6ZtVOdQZMKxgvSmYoeCbCp==KR+6w_+nGyLLN9jwwg@mail.gmail.com> <fc4457ee-8489-4cbb-8e85-fcce63e78678@googlegroups.com>
 <CABDkGQkttiCurekV9a=Xi70G4WQt_Dn3AAm_OOxo2LmwGVePCQ@mail.gmail.com>
 <9450c9e5-5951-421b-92fe-c159ccbdbef1@googlegroups.com>
Message-ID: <0e4613db-ea50-4342-962c-20d1a8e8dd90@googlegroups.com>

I don't want to propagate false information and must correct myself from my 
initial post on this thread.

According to "Principles of Color Technology" by Roy S. Berns, it is a myth 
that" CIELAB was recommended for large color differences and tha tCIELUV 
was recommended for small color differences."  It is also a myth that 
"CIELAB is recommended for reflecting samples while CIELUV is recommended 
for sources and displays."  The second myth is what I originally stated as 
fact but is incorrect. 

In my literature review, several sources state these two myths are truths 
but provide no citations

Isaac

On Wednesday, October 16, 2013 3:52:26 PM UTC-4, Isaac Gerg wrote:
>
> I have completed the changes to colorconv.py so that luv is now supported. 
>  Whom do I email the file to so that it can be included in the repo?
>
> Isaac
>
> On Friday, October 11, 2013 1:22:57 PM UTC-4, Stefan van der Walt wrote:
>>
>> On Fri, Oct 11, 2013 at 5:38 PM, Isaac Gerg <isaac... at gergltd.com> 
>> wrote: 
>> > I am limited on time but am happy to provide code if someone can put it 
>> into 
>> > github for me. 
>>
>> Sure, a patch is just fine. 
>>
>> Thanks! 
>> St?fan 
>>
>
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From stefan at sun.ac.za  Wed Oct 16 09:11:29 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 16 Oct 2013 15:11:29 +0200
Subject: Release time
In-Reply-To: <29349511-94C6-49DD-8BE1-2790ACF6C253@demuc.de>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com>
 <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com>
 <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de> <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com>
 <583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de> <CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com>
 <9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de> <3370D65E-B530-4B57-B71D-AC8549A7791B@demuc.de>
 <CAF+hgui_p38G0duCHNCez85xa0ThkP9modmnESqEerxfyhy88A@mail.gmail.com>
 <CABDkGQkQNHUB=UVZzMsssanpqDqmMURNbSZ-iaW8vFKboQK_oA@mail.gmail.com>
 <524C4E05.4030408@sciunto.org> <6B47F231-F251-469D-9EC7-2BB1D9317992@demuc.de>
 <CABDkGQ=3ZSGxqqEfuvfGDwezmK9x-bfM0zy3AUOQRnCDaydpcg@mail.gmail.com>
 <65c13bd3-b5a7-4606-b67b-83d862082125@googlegroups.com> <D778DFBE-8C62-466A-B92F-005BD03C28A9@demuc.de>
 <F1D6BCC0-F232-4FF3-BF24-3A15581D38F9@demuc.de> <4AD1AFF6-40E7-470D-AEE1-918E1FECEC02@demuc.de>
 <CABDkGQm1qxrGHGb1=1DH1Br33HmpeKFp7O-VEWJ=g1PLOBt8Kw@mail.gmail.com> <29349511-94C6-49DD-8BE1-2790ACF6C253@demuc.de>
Message-ID: <CABDkGQmwLH6ZQaD0AF=5-DJGEB0Q-ybtpkE6pwwE2P4Ma-_6AQ@mail.gmail.com>

On Tue, Oct 15, 2013 at 3:25 PM, Johannes Sch?nberger <jsch at demuc.de> wrote:
> I think I fixed the two remaining issues reported by Christoph, thanks for reporting them!

Alright!  Everything's gone quiet... so I'm starting the countdown to
the release.  Speak now or hold your deprecations until 0.10!

St?fan


From mtrent at gmail.com  Thu Oct 17 14:40:14 2013
From: mtrent at gmail.com (Matthew Trentacoste)
Date: Thu, 17 Oct 2013 11:40:14 -0700 (PDT)
Subject: CIELUV Transformations
In-Reply-To: <9450c9e5-5951-421b-92fe-c159ccbdbef1@googlegroups.com>
References: <b20c6a2c-fe5f-43e5-b7ac-ebebde42724b@googlegroups.com>
 <CABDkGQmR6ZtVOdQZMKxgvSmYoeCbCp==KR+6w_+nGyLLN9jwwg@mail.gmail.com> <fc4457ee-8489-4cbb-8e85-fcce63e78678@googlegroups.com>
 <CABDkGQkttiCurekV9a=Xi70G4WQt_Dn3AAm_OOxo2LmwGVePCQ@mail.gmail.com>
 <9450c9e5-5951-421b-92fe-c159ccbdbef1@googlegroups.com>
Message-ID: <8467a84d-0e4f-4b3f-b10c-6a8220a1e588@googlegroups.com>

I saw the initial email and was working on an implementation myself, and 
wrote all the test cases.  If you want to send it to me, I can integrate it 
with mine and make sure it passes all the tests.

On Wednesday, October 16, 2013 12:52:26 PM UTC-7, Isaac Gerg wrote:
>
> I have completed the changes to colorconv.py so that luv is now supported. 
>  Whom do I email the file to so that it can be included in the repo?
>
> Isaac
>
> On Friday, October 11, 2013 1:22:57 PM UTC-4, Stefan van der Walt wrote:
>>
>> On Fri, Oct 11, 2013 at 5:38 PM, Isaac Gerg <isaac... at gergltd.com> 
>> wrote: 
>> > I am limited on time but am happy to provide code if someone can put it 
>> into 
>> > github for me. 
>>
>> Sure, a patch is just fine. 
>>
>> Thanks! 
>> St?fan 
>>
>
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From guillaume at mitotic-machine.org  Thu Oct 17 08:25:57 2013
From: guillaume at mitotic-machine.org (Guillaume Gay)
Date: Thu, 17 Oct 2013 14:25:57 +0200
Subject: `min_size` argument in Feltzenswalb segmentation has no effect
Message-ID: <525FD755.4010805@mitotic-machine.org>

Hi all,

The title says it, with a recent 0.9dev version of skimage, I can't see 
an effect of the `min_size` argument in Felzenszwalb segmentation. BTW 
the meaning of this argument is not very clear in the doc.  It's the 
first time I use this function, so I don't know wether this is a 
regression or not.

Reading the code, I fail to understand how this all works....

Here is a notebook showing the (lack of) effect of min_size:

http://nbviewer.ipython.org/7023716


Cheers, good luck with the realease


Guillaume



From jni.soma at gmail.com  Thu Oct 17 00:57:04 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Thu, 17 Oct 2013 15:57:04 +1100
Subject: Release time
In-Reply-To: <CABDkGQmwLH6ZQaD0AF=5-DJGEB0Q-ybtpkE6pwwE2P4Ma-_6AQ@mail.gmail.com>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com>
 <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com>
 <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de> <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com>
 <583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de> <CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com>
 <9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de> <3370D65E-B530-4B57-B71D-AC8549A7791B@demuc.de>
 <CAF+hgui_p38G0duCHNCez85xa0ThkP9modmnESqEerxfyhy88A@mail.gmail.com>
 <CABDkGQkQNHUB=UVZzMsssanpqDqmMURNbSZ-iaW8vFKboQK_oA@mail.gmail.com>
 <524C4E05.4030408@sciunto.org> <6B47F231-F251-469D-9EC7-2BB1D9317992@demuc.de>
 <CABDkGQ=3ZSGxqqEfuvfGDwezmK9x-bfM0zy3AUOQRnCDaydpcg@mail.gmail.com>
 <65c13bd3-b5a7-4606-b67b-83d862082125@googlegroups.com> <D778DFBE-8C62-466A-B92F-005BD03C28A9@demuc.de>
 <F1D6BCC0-F232-4FF3-BF24-3A15581D38F9@demuc.de> <4AD1AFF6-40E7-470D-AEE1-918E1FECEC02@demuc.de>
 <CABDkGQm1qxrGHGb1=1DH1Br33HmpeKFp7O-VEWJ=g1PLOBt8Kw@mail.gmail.com>
 <29349511-94C6-49DD-8BE1-2790ACF6C253@demuc.de> <CABDkGQmwLH6ZQaD0AF=5-DJGEB0Q-ybtpkE6pwwE2P4Ma-_6AQ@mail.gmail.com>
Message-ID: <CA+JHcKS2drzT7xUaReZH=kw_8Ku-BMPkYFT6RCcFM_qywRLADw@mail.gmail.com>

Hi Stefan,

It just occurred to me that this comment of mine:
https://github.com/scikit-image/scikit-image/pull/674#issuecomment-22308750

was ignored. As I mention in the comment, the refactoring of regionprops
actually resulted in an API change. Seems fixable... Do you want me to
tackle it? Here's the error it gives:

/Users/nuneziglesiasj/venv/husc/lib/python2.7/site-packages/husc/features.py
in object_features(bin_im, im, erode)
    141                                  'MaxIntensity', 'Solidity'],
    142                                 intensity_image=im)
--> 143     feats = np.array([props.values() for props in feats], np.float)
    144     feature_quantiles = mquantiles(feats, [0.05, 0.25, 0.5,
0.75, 0.95],
    145                                    axis=0)

AttributeError: '_RegionProperties' object has no attribute 'values'


I think it would be fixable by adding a .values() function (which would be
deprecated from the beginning) that returns whatever regionprops were
originally requested.

@ahojnnes might have something to add...

Juan.



On Thu, Oct 17, 2013 at 12:11 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> On Tue, Oct 15, 2013 at 3:25 PM, Johannes Sch?nberger <jsch at demuc.de>
> wrote:
> > I think I fixed the two remaining issues reported by Christoph, thanks
> for reporting them!
>
> Alright!  Everything's gone quiet... so I'm starting the countdown to
> the release.  Speak now or hold your deprecations until 0.10!
>
> St?fan
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>
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From stefan at sun.ac.za  Thu Oct 17 10:06:20 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 17 Oct 2013 16:06:20 +0200
Subject: `min_size` argument in Feltzenswalb segmentation has no effect
In-Reply-To: <525FD755.4010805@mitotic-machine.org>
References: <525FD755.4010805@mitotic-machine.org>
Message-ID: <CABDkGQkt3L-Zm_hBJ=8JqiE-AtB5s2m2svUQCPMiLANUU+LBWA@mail.gmail.com>

Hi Guillaume

On Thu, Oct 17, 2013 at 2:25 PM, Guillaume Gay
<guillaume at mitotic-machine.org> wrote:
> The title says it, with a recent 0.9dev version of skimage, I can't see an
> effect of the `min_size` argument in Felzenszwalb segmentation. BTW the
> meaning of this argument is not very clear in the doc.  It's the first time
> I use this function, so I don't know wether this is a regression or not.
>
> Reading the code, I fail to understand how this all works....

I can verify the bug, but the code looks okay, so it's something a bit
more subtle.  I'll have a look at this again later.  We may have to
include this as a 0.9.1 bugfix.

https://github.com/scikit-image/scikit-image/issues/793

St?fan


From cjgohlke at gmail.com  Sat Oct 19 12:40:06 2013
From: cjgohlke at gmail.com (Christoph Gohlke)
Date: Sat, 19 Oct 2013 09:40:06 -0700
Subject: ANN: scikit-image 0.9.0
In-Reply-To: <CABDkGQmBjBMzqe2XyF8C5cM-V_fUqAS=2pwiY9=MFVs3Er3Wtw@mail.gmail.com>
References: <CABDkGQmBjBMzqe2XyF8C5cM-V_fUqAS=2pwiY9=MFVs3Er3Wtw@mail.gmail.com>
Message-ID: <5262B5E6.8080704@gmail.com>

Hello,

scikit-image-0.9.0.tar.gz is missing the file 
skimage\color\tests\ciede2000_test_data.txt causing test errors.

Christoph


On 10/19/2013 7:28 AM, St??????fan van der Walt wrote:
> Announcement: scikits-image 0.9.0
> =================================
>
> We're happy to announce the release of scikit-image v0.9.0!
>
> 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
> ------------
>
> `scikit-image` now runs without translation under both Python 2 and 3.
>
> In addition to several bug fixes, speed improvements and examples, the 204 pull
> requests merged for this release include the following new features (PR number
> in brackets):
>
> Segmentation:
>
> - 3D support in SLIC segmentation (#546)
> - SLIC voxel spacing (#719)
> - Generalized anisotropic spacing support for random_walker (#775)
> - Yen threshold method (#686)
>
> Transforms and filters:
>
> - SART algorithm for tomography reconstruction (#584)
> - Gabor filters (#371)
> - Hough transform for ellipses (#597)
> - Fast resampling of nD arrays (#511)
> - Rotation axis center for Radon transforms with inverses. (#654)
> - Reconstruction circle in inverse Radon transform (#567)
> - Pixelwise image adjustment curves and methods (#505)
>
> Feature detection:
>
> - [experimental API] BRIEF feature descriptor (#591)
> - [experimental API] Censure (STAR) Feature Detector (#668)
> - Octagon structural element (#669)
> - Add non rotation invariant uniform LBPs (#704)
>
> Color and noise:
>
> - Add deltaE color comparison and lab2lch conversion (#665)
> - Isotropic denoising (#653)
> - Generator to add various types of random noise to images (#625)
> - Color deconvolution for immunohistochemical images (#441)
> - Color label visualization (#485)
>
> Drawing and visualization:
>
> - Wu's anti-aliased circle, line, bezier curve (#709)
> - Linked image viewers and docked plugins (#575)
> - Rotated ellipse + bezier curve drawing (#510)
> - PySide & PyQt4 compatibility in skimage-viewer (#551)
>
> Other:
>
> - Python 3 support without 2to3. (#620)
> - 3D Marching Cubes (#469)
> - Line, Circle, Ellipse total least squares fitting and RANSAC algorithm (#440)
> - N-dimensional array padding (#577)
> - Add a wrapper around `scipy.ndimage.gaussian_filter` with useful
> default behaviors. (#712)
> - Predefined structuring elements for 3D morphology (#484)
>
>
> API changes
> -----------
>
> The following backward-incompatible API changes were made between 0.8 and 0.9:
>
> - No longer wrap ``imread`` output in an ``Image`` class
> - Change default value of `sigma` parameter in ``skimage.segmentation.slic``
>    to 0
> - ``hough_circle`` now returns a stack of arrays that are the same size as the
>    input image. Set the ``full_output`` flag to True for the old behavior.
> - The following functions were deprecated over two releases:
>    `skimage.filter.denoise_tv_chambolle`,
>    `skimage.morphology.is_local_maximum`, `skimage.transform.hough`,
>    `skimage.transform.probabilistic_hough`,`skimage.transform.hough_peaks`.
>    Their functionality still exists, but under different names.
>
>
> 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:
>
> - Ankit Agrawal
> - K.-Michael Aye
> - Chris Beaumont
> - Fran??????ois Boulogne
> - Luis Pedro Coelho
> - Marianne Corvellec
> - Olivier Debeir
> - Ferdinand Deger
> - Kemal Eren
> - Jostein B?????? Fl??????ystad
> - Christoph Gohlke
> - Emmanuelle Gouillart
> - Christian Horea
> - Thouis (Ray) Jones
> - Almar Klein
> - Xavier Moles Lopez
> - Alexis Mignon
> - Juan Nunez-Iglesias
> - Zachary Pincus
> - Nicolas Pinto
> - Davin Potts
> - Malcolm Reynolds
> - Umesh Sharma
> - Johannes Sch??????nberger
> - Chintak Sheth
> - Kirill Shklovsky
> - Steven Silvester
> - Matt Terry
> - Riaan van den Dool
> - St??????fan van der Walt
> - Josh Warner
> - Adam Wisniewski
> - Yang Zetian
> - Tony S Yu
>


From stefan at sun.ac.za  Sat Oct 19 08:34:29 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sat, 19 Oct 2013 14:34:29 +0200
Subject: Release time
In-Reply-To: <CAON2ciJAtVYffHaHeqyhEZATBFU3LwOiVQ8dcHEgP5Zf_qhdCw@mail.gmail.com>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com>
 <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com>
 <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de> <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com>
 <583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de> <CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com>
 <9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de> <3370D65E-B530-4B57-B71D-AC8549A7791B@demuc.de>
 <CAF+hgui_p38G0duCHNCez85xa0ThkP9modmnESqEerxfyhy88A@mail.gmail.com>
 <CABDkGQkQNHUB=UVZzMsssanpqDqmMURNbSZ-iaW8vFKboQK_oA@mail.gmail.com>
 <524C4E05.4030408@sciunto.org> <6B47F231-F251-469D-9EC7-2BB1D9317992@demuc.de>
 <CABDkGQ=3ZSGxqqEfuvfGDwezmK9x-bfM0zy3AUOQRnCDaydpcg@mail.gmail.com>
 <65c13bd3-b5a7-4606-b67b-83d862082125@googlegroups.com> <D778DFBE-8C62-466A-B92F-005BD03C28A9@demuc.de>
 <F1D6BCC0-F232-4FF3-BF24-3A15581D38F9@demuc.de> <4AD1AFF6-40E7-470D-AEE1-918E1FECEC02@demuc.de>
 <CABDkGQm1qxrGHGb1=1DH1Br33HmpeKFp7O-VEWJ=g1PLOBt8Kw@mail.gmail.com>
 <29349511-94C6-49DD-8BE1-2790ACF6C253@demuc.de> <CABDkGQmwLH6ZQaD0AF=5-DJGEB0Q-ybtpkE6pwwE2P4Ma-_6AQ@mail.gmail.com>
 <CA+JHcKS2drzT7xUaReZH=kw_8Ku-BMPkYFT6RCcFM_qywRLADw@mail.gmail.com> <CAON2ciJAtVYffHaHeqyhEZATBFU3LwOiVQ8dcHEgP5Zf_qhdCw@mail.gmail.com>
Message-ID: <CABDkGQ=9Zx=xT5nuy7bQ4ocJE40eoDsjYt1-ObgF7pBhF7Ohgw@mail.gmail.com>

On Sat, Oct 19, 2013 at 12:37 PM, Ankit Agrawal <aaaagrawal at gmail.com> wrote:
> Any updates about the 0.9 release?

Just waiting for GitHub to come back online to push the tags.

St?fan


From aaaagrawal at gmail.com  Sat Oct 19 06:37:34 2013
From: aaaagrawal at gmail.com (Ankit Agrawal)
Date: Sat, 19 Oct 2013 16:07:34 +0530
Subject: Release time
In-Reply-To: <CA+JHcKS2drzT7xUaReZH=kw_8Ku-BMPkYFT6RCcFM_qywRLADw@mail.gmail.com>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com>
	<178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de>
	<CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com>
	<C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de>
	<CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com>
	<583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de>
	<CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com>
	<9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de>
	<3370D65E-B530-4B57-B71D-AC8549A7791B@demuc.de>
	<CAF+hgui_p38G0duCHNCez85xa0ThkP9modmnESqEerxfyhy88A@mail.gmail.com>
	<CABDkGQkQNHUB=UVZzMsssanpqDqmMURNbSZ-iaW8vFKboQK_oA@mail.gmail.com>
	<524C4E05.4030408@sciunto.org>
	<6B47F231-F251-469D-9EC7-2BB1D9317992@demuc.de>
	<CABDkGQ=3ZSGxqqEfuvfGDwezmK9x-bfM0zy3AUOQRnCDaydpcg@mail.gmail.com>
	<65c13bd3-b5a7-4606-b67b-83d862082125@googlegroups.com>
	<D778DFBE-8C62-466A-B92F-005BD03C28A9@demuc.de>
	<F1D6BCC0-F232-4FF3-BF24-3A15581D38F9@demuc.de>
	<4AD1AFF6-40E7-470D-AEE1-918E1FECEC02@demuc.de>
	<CABDkGQm1qxrGHGb1=1DH1Br33HmpeKFp7O-VEWJ=g1PLOBt8Kw@mail.gmail.com>
	<29349511-94C6-49DD-8BE1-2790ACF6C253@demuc.de>
	<CABDkGQmwLH6ZQaD0AF=5-DJGEB0Q-ybtpkE6pwwE2P4Ma-_6AQ@mail.gmail.com>
	<CA+JHcKS2drzT7xUaReZH=kw_8Ku-BMPkYFT6RCcFM_qywRLADw@mail.gmail.com>
Message-ID: <CAON2ciJAtVYffHaHeqyhEZATBFU3LwOiVQ8dcHEgP5Zf_qhdCw@mail.gmail.com>

Any updates about the 0.9 release?

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


On Thu, Oct 17, 2013 at 10:27 AM, Juan Nunez-Iglesias <jni.soma at gmail.com>wrote:

> Hi Stefan,
>
> It just occurred to me that this comment of mine:
> https://github.com/scikit-image/scikit-image/pull/674#issuecomment-22308750
>
> was ignored. As I mention in the comment, the refactoring of regionprops
> actually resulted in an API change. Seems fixable... Do you want me to
> tackle it? Here's the error it gives:
>
> /Users/nuneziglesiasj/venv/husc/lib/python2.7/site-packages/husc/features.py in object_features(bin_im, im, erode)
>     141                                  'MaxIntensity', 'Solidity'],
>     142                                 intensity_image=im)
> --> 143     feats = np.array([props.values() for props in feats], np.float)
>     144     feature_quantiles = mquantiles(feats, [0.05, 0.25, 0.5, 0.75, 0.95],
>     145                                    axis=0)
>
> AttributeError: '_RegionProperties' object has no attribute 'values'
>
>
> I think it would be fixable by adding a .values() function (which would be
> deprecated from the beginning) that returns whatever regionprops were
> originally requested.
>
> @ahojnnes might have something to add...
>
> Juan.
>
>
>
> On Thu, Oct 17, 2013 at 12:11 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:
>
>> On Tue, Oct 15, 2013 at 3:25 PM, Johannes Sch?nberger <jsch at demuc.de>
>> wrote:
>> > I think I fixed the two remaining issues reported by Christoph, thanks
>> for reporting them!
>>
>> Alright!  Everything's gone quiet... so I'm starting the countdown to
>> the release.  Speak now or hold your deprecations until 0.10!
>>
>> St?fan
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
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From stefan at sun.ac.za  Sat Oct 19 10:28:26 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sat, 19 Oct 2013 16:28:26 +0200
Subject: ANN: scikit-image 0.9.0
Message-ID: <CABDkGQmBjBMzqe2XyF8C5cM-V_fUqAS=2pwiY9=MFVs3Er3Wtw@mail.gmail.com>

Announcement: scikits-image 0.9.0
=================================

We're happy to announce the release of scikit-image v0.9.0!

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
------------

`scikit-image` now runs without translation under both Python 2 and 3.

In addition to several bug fixes, speed improvements and examples, the 204 pull
requests merged for this release include the following new features (PR number
in brackets):

Segmentation:

- 3D support in SLIC segmentation (#546)
- SLIC voxel spacing (#719)
- Generalized anisotropic spacing support for random_walker (#775)
- Yen threshold method (#686)

Transforms and filters:

- SART algorithm for tomography reconstruction (#584)
- Gabor filters (#371)
- Hough transform for ellipses (#597)
- Fast resampling of nD arrays (#511)
- Rotation axis center for Radon transforms with inverses. (#654)
- Reconstruction circle in inverse Radon transform (#567)
- Pixelwise image adjustment curves and methods (#505)

Feature detection:

- [experimental API] BRIEF feature descriptor (#591)
- [experimental API] Censure (STAR) Feature Detector (#668)
- Octagon structural element (#669)
- Add non rotation invariant uniform LBPs (#704)

Color and noise:

- Add deltaE color comparison and lab2lch conversion (#665)
- Isotropic denoising (#653)
- Generator to add various types of random noise to images (#625)
- Color deconvolution for immunohistochemical images (#441)
- Color label visualization (#485)

Drawing and visualization:

- Wu's anti-aliased circle, line, bezier curve (#709)
- Linked image viewers and docked plugins (#575)
- Rotated ellipse + bezier curve drawing (#510)
- PySide & PyQt4 compatibility in skimage-viewer (#551)

Other:

- Python 3 support without 2to3. (#620)
- 3D Marching Cubes (#469)
- Line, Circle, Ellipse total least squares fitting and RANSAC algorithm (#440)
- N-dimensional array padding (#577)
- Add a wrapper around `scipy.ndimage.gaussian_filter` with useful
default behaviors. (#712)
- Predefined structuring elements for 3D morphology (#484)


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

The following backward-incompatible API changes were made between 0.8 and 0.9:

- No longer wrap ``imread`` output in an ``Image`` class
- Change default value of `sigma` parameter in ``skimage.segmentation.slic``
  to 0
- ``hough_circle`` now returns a stack of arrays that are the same size as the
  input image. Set the ``full_output`` flag to True for the old behavior.
- The following functions were deprecated over two releases:
  `skimage.filter.denoise_tv_chambolle`,
  `skimage.morphology.is_local_maximum`, `skimage.transform.hough`,
  `skimage.transform.probabilistic_hough`,`skimage.transform.hough_peaks`.
  Their functionality still exists, but under different names.


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:

- Ankit Agrawal
- K.-Michael Aye
- Chris Beaumont
- Fran?ois Boulogne
- Luis Pedro Coelho
- Marianne Corvellec
- Olivier Debeir
- Ferdinand Deger
- Kemal Eren
- Jostein B? Fl?ystad
- Christoph Gohlke
- Emmanuelle Gouillart
- Christian Horea
- Thouis (Ray) Jones
- Almar Klein
- Xavier Moles Lopez
- Alexis Mignon
- Juan Nunez-Iglesias
- Zachary Pincus
- Nicolas Pinto
- Davin Potts
- Malcolm Reynolds
- Umesh Sharma
- Johannes Sch?nberger
- Chintak Sheth
- Kirill Shklovsky
- Steven Silvester
- Matt Terry
- Riaan van den Dool
- St?fan van der Walt
- Josh Warner
- Adam Wisniewski
- Yang Zetian
- Tony S Yu


From jsch at demuc.de  Sat Oct 19 11:50:20 2013
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Sat, 19 Oct 2013 17:50:20 +0200
Subject: ANN: scikit-image 0.9.0
In-Reply-To: <CABDkGQmBjBMzqe2XyF8C5cM-V_fUqAS=2pwiY9=MFVs3Er3Wtw@mail.gmail.com>
References: <CABDkGQmBjBMzqe2XyF8C5cM-V_fUqAS=2pwiY9=MFVs3Er3Wtw@mail.gmail.com>
Message-ID: <EA295BD9-465E-4CAA-A358-B3A73FBEC0D5@demuc.de>

Kudos to everyone involved in this release! Thanks Stefan for making this nice feature list.

Am 19.10.2013 um 16:28 schrieb St?fan van der Walt <stefan at sun.ac.za>:

> Announcement: scikits-image 0.9.0
> =================================
> 
> We're happy to announce the release of scikit-image v0.9.0!
> 
> 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
> ------------
> 
> `scikit-image` now runs without translation under both Python 2 and 3.
> 
> In addition to several bug fixes, speed improvements and examples, the 204 pull
> requests merged for this release include the following new features (PR number
> in brackets):
> 
> Segmentation:
> 
> - 3D support in SLIC segmentation (#546)
> - SLIC voxel spacing (#719)
> - Generalized anisotropic spacing support for random_walker (#775)
> - Yen threshold method (#686)
> 
> Transforms and filters:
> 
> - SART algorithm for tomography reconstruction (#584)
> - Gabor filters (#371)
> - Hough transform for ellipses (#597)
> - Fast resampling of nD arrays (#511)
> - Rotation axis center for Radon transforms with inverses. (#654)
> - Reconstruction circle in inverse Radon transform (#567)
> - Pixelwise image adjustment curves and methods (#505)
> 
> Feature detection:
> 
> - [experimental API] BRIEF feature descriptor (#591)
> - [experimental API] Censure (STAR) Feature Detector (#668)
> - Octagon structural element (#669)
> - Add non rotation invariant uniform LBPs (#704)
> 
> Color and noise:
> 
> - Add deltaE color comparison and lab2lch conversion (#665)
> - Isotropic denoising (#653)
> - Generator to add various types of random noise to images (#625)
> - Color deconvolution for immunohistochemical images (#441)
> - Color label visualization (#485)
> 
> Drawing and visualization:
> 
> - Wu's anti-aliased circle, line, bezier curve (#709)
> - Linked image viewers and docked plugins (#575)
> - Rotated ellipse + bezier curve drawing (#510)
> - PySide & PyQt4 compatibility in skimage-viewer (#551)
> 
> Other:
> 
> - Python 3 support without 2to3. (#620)
> - 3D Marching Cubes (#469)
> - Line, Circle, Ellipse total least squares fitting and RANSAC algorithm (#440)
> - N-dimensional array padding (#577)
> - Add a wrapper around `scipy.ndimage.gaussian_filter` with useful
> default behaviors. (#712)
> - Predefined structuring elements for 3D morphology (#484)
> 
> 
> API changes
> -----------
> 
> The following backward-incompatible API changes were made between 0.8 and 0.9:
> 
> - No longer wrap ``imread`` output in an ``Image`` class
> - Change default value of `sigma` parameter in ``skimage.segmentation.slic``
>  to 0
> - ``hough_circle`` now returns a stack of arrays that are the same size as the
>  input image. Set the ``full_output`` flag to True for the old behavior.
> - The following functions were deprecated over two releases:
>  `skimage.filter.denoise_tv_chambolle`,
>  `skimage.morphology.is_local_maximum`, `skimage.transform.hough`,
>  `skimage.transform.probabilistic_hough`,`skimage.transform.hough_peaks`.
>  Their functionality still exists, but under different names.
> 
> 
> 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:
> 
> - Ankit Agrawal
> - K.-Michael Aye
> - Chris Beaumont
> - Fran?ois Boulogne
> - Luis Pedro Coelho
> - Marianne Corvellec
> - Olivier Debeir
> - Ferdinand Deger
> - Kemal Eren
> - Jostein B? Fl?ystad
> - Christoph Gohlke
> - Emmanuelle Gouillart
> - Christian Horea
> - Thouis (Ray) Jones
> - Almar Klein
> - Xavier Moles Lopez
> - Alexis Mignon
> - Juan Nunez-Iglesias
> - Zachary Pincus
> - Nicolas Pinto
> - Davin Potts
> - Malcolm Reynolds
> - Umesh Sharma
> - Johannes Sch?nberger
> - Chintak Sheth
> - Kirill Shklovsky
> - Steven Silvester
> - Matt Terry
> - Riaan van den Dool
> - St?fan van der Walt
> - Josh Warner
> - Adam Wisniewski
> - Yang Zetian
> - Tony S Yu
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
> 



From jsch at demuc.de  Sat Oct 19 12:01:15 2013
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Sat, 19 Oct 2013 18:01:15 +0200
Subject: ANN: scikit-image 0.9.0
In-Reply-To: <EA295BD9-465E-4CAA-A358-B3A73FBEC0D5@demuc.de>
References: <CABDkGQmBjBMzqe2XyF8C5cM-V_fUqAS=2pwiY9=MFVs3Er3Wtw@mail.gmail.com> <EA295BD9-465E-4CAA-A358-B3A73FBEC0D5@demuc.de>
Message-ID: <8BD8C00B-1B90-4C4E-A354-DBBC74216AF5@demuc.de>

Did you also announce the release on other relevant mailing lists?

Am 19.10.2013 um 17:50 schrieb Johannes Sch?nberger <jsch at demuc.de>:

> Kudos to everyone involved in this release! Thanks Stefan for making this nice feature list.
> 
> Am 19.10.2013 um 16:28 schrieb St?fan van der Walt <stefan at sun.ac.za>:
> 
>> Announcement: scikits-image 0.9.0
>> =================================
>> 
>> We're happy to announce the release of scikit-image v0.9.0!
>> 
>> 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
>> ------------
>> 
>> `scikit-image` now runs without translation under both Python 2 and 3.
>> 
>> In addition to several bug fixes, speed improvements and examples, the 204 pull
>> requests merged for this release include the following new features (PR number
>> in brackets):
>> 
>> Segmentation:
>> 
>> - 3D support in SLIC segmentation (#546)
>> - SLIC voxel spacing (#719)
>> - Generalized anisotropic spacing support for random_walker (#775)
>> - Yen threshold method (#686)
>> 
>> Transforms and filters:
>> 
>> - SART algorithm for tomography reconstruction (#584)
>> - Gabor filters (#371)
>> - Hough transform for ellipses (#597)
>> - Fast resampling of nD arrays (#511)
>> - Rotation axis center for Radon transforms with inverses. (#654)
>> - Reconstruction circle in inverse Radon transform (#567)
>> - Pixelwise image adjustment curves and methods (#505)
>> 
>> Feature detection:
>> 
>> - [experimental API] BRIEF feature descriptor (#591)
>> - [experimental API] Censure (STAR) Feature Detector (#668)
>> - Octagon structural element (#669)
>> - Add non rotation invariant uniform LBPs (#704)
>> 
>> Color and noise:
>> 
>> - Add deltaE color comparison and lab2lch conversion (#665)
>> - Isotropic denoising (#653)
>> - Generator to add various types of random noise to images (#625)
>> - Color deconvolution for immunohistochemical images (#441)
>> - Color label visualization (#485)
>> 
>> Drawing and visualization:
>> 
>> - Wu's anti-aliased circle, line, bezier curve (#709)
>> - Linked image viewers and docked plugins (#575)
>> - Rotated ellipse + bezier curve drawing (#510)
>> - PySide & PyQt4 compatibility in skimage-viewer (#551)
>> 
>> Other:
>> 
>> - Python 3 support without 2to3. (#620)
>> - 3D Marching Cubes (#469)
>> - Line, Circle, Ellipse total least squares fitting and RANSAC algorithm (#440)
>> - N-dimensional array padding (#577)
>> - Add a wrapper around `scipy.ndimage.gaussian_filter` with useful
>> default behaviors. (#712)
>> - Predefined structuring elements for 3D morphology (#484)
>> 
>> 
>> API changes
>> -----------
>> 
>> The following backward-incompatible API changes were made between 0.8 and 0.9:
>> 
>> - No longer wrap ``imread`` output in an ``Image`` class
>> - Change default value of `sigma` parameter in ``skimage.segmentation.slic``
>> to 0
>> - ``hough_circle`` now returns a stack of arrays that are the same size as the
>> input image. Set the ``full_output`` flag to True for the old behavior.
>> - The following functions were deprecated over two releases:
>> `skimage.filter.denoise_tv_chambolle`,
>> `skimage.morphology.is_local_maximum`, `skimage.transform.hough`,
>> `skimage.transform.probabilistic_hough`,`skimage.transform.hough_peaks`.
>> Their functionality still exists, but under different names.
>> 
>> 
>> 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:
>> 
>> - Ankit Agrawal
>> - K.-Michael Aye
>> - Chris Beaumont
>> - Fran?ois Boulogne
>> - Luis Pedro Coelho
>> - Marianne Corvellec
>> - Olivier Debeir
>> - Ferdinand Deger
>> - Kemal Eren
>> - Jostein B? Fl?ystad
>> - Christoph Gohlke
>> - Emmanuelle Gouillart
>> - Christian Horea
>> - Thouis (Ray) Jones
>> - Almar Klein
>> - Xavier Moles Lopez
>> - Alexis Mignon
>> - Juan Nunez-Iglesias
>> - Zachary Pincus
>> - Nicolas Pinto
>> - Davin Potts
>> - Malcolm Reynolds
>> - Umesh Sharma
>> - Johannes Sch?nberger
>> - Chintak Sheth
>> - Kirill Shklovsky
>> - Steven Silvester
>> - Matt Terry
>> - Riaan van den Dool
>> - St?fan van der Walt
>> - Josh Warner
>> - Adam Wisniewski
>> - Yang Zetian
>> - Tony S Yu
>> 
>> -- 
>> You received this message because you are subscribed to the Google Groups "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/groups/opt_out.
>> 
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
> 



From jsch at demuc.de  Sat Oct 19 12:04:31 2013
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Sat, 19 Oct 2013 18:04:31 +0200
Subject: ANN: scikit-image 0.9.0
In-Reply-To: <8BD8C00B-1B90-4C4E-A354-DBBC74216AF5@demuc.de>
References: <CABDkGQmBjBMzqe2XyF8C5cM-V_fUqAS=2pwiY9=MFVs3Er3Wtw@mail.gmail.com> <EA295BD9-465E-4CAA-A358-B3A73FBEC0D5@demuc.de> <8BD8C00B-1B90-4C4E-A354-DBBC74216AF5@demuc.de>
Message-ID: <F89F7488-5A1E-43E3-8B51-12109CB6482F@demuc.de>

I just noticed you included the compiled Cython files in the archive. Is this intended?

Am 19.10.2013 um 18:01 schrieb Johannes Sch?nberger <jsch at demuc.de>:

> Did you also announce the release on other relevant mailing lists?
> 
> Am 19.10.2013 um 17:50 schrieb Johannes Sch?nberger <jsch at demuc.de>:
> 
>> Kudos to everyone involved in this release! Thanks Stefan for making this nice feature list.
>> 
>> Am 19.10.2013 um 16:28 schrieb St?fan van der Walt <stefan at sun.ac.za>:
>> 
>>> Announcement: scikits-image 0.9.0
>>> =================================
>>> 
>>> We're happy to announce the release of scikit-image v0.9.0!
>>> 
>>> 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
>>> ------------
>>> 
>>> `scikit-image` now runs without translation under both Python 2 and 3.
>>> 
>>> In addition to several bug fixes, speed improvements and examples, the 204 pull
>>> requests merged for this release include the following new features (PR number
>>> in brackets):
>>> 
>>> Segmentation:
>>> 
>>> - 3D support in SLIC segmentation (#546)
>>> - SLIC voxel spacing (#719)
>>> - Generalized anisotropic spacing support for random_walker (#775)
>>> - Yen threshold method (#686)
>>> 
>>> Transforms and filters:
>>> 
>>> - SART algorithm for tomography reconstruction (#584)
>>> - Gabor filters (#371)
>>> - Hough transform for ellipses (#597)
>>> - Fast resampling of nD arrays (#511)
>>> - Rotation axis center for Radon transforms with inverses. (#654)
>>> - Reconstruction circle in inverse Radon transform (#567)
>>> - Pixelwise image adjustment curves and methods (#505)
>>> 
>>> Feature detection:
>>> 
>>> - [experimental API] BRIEF feature descriptor (#591)
>>> - [experimental API] Censure (STAR) Feature Detector (#668)
>>> - Octagon structural element (#669)
>>> - Add non rotation invariant uniform LBPs (#704)
>>> 
>>> Color and noise:
>>> 
>>> - Add deltaE color comparison and lab2lch conversion (#665)
>>> - Isotropic denoising (#653)
>>> - Generator to add various types of random noise to images (#625)
>>> - Color deconvolution for immunohistochemical images (#441)
>>> - Color label visualization (#485)
>>> 
>>> Drawing and visualization:
>>> 
>>> - Wu's anti-aliased circle, line, bezier curve (#709)
>>> - Linked image viewers and docked plugins (#575)
>>> - Rotated ellipse + bezier curve drawing (#510)
>>> - PySide & PyQt4 compatibility in skimage-viewer (#551)
>>> 
>>> Other:
>>> 
>>> - Python 3 support without 2to3. (#620)
>>> - 3D Marching Cubes (#469)
>>> - Line, Circle, Ellipse total least squares fitting and RANSAC algorithm (#440)
>>> - N-dimensional array padding (#577)
>>> - Add a wrapper around `scipy.ndimage.gaussian_filter` with useful
>>> default behaviors. (#712)
>>> - Predefined structuring elements for 3D morphology (#484)
>>> 
>>> 
>>> API changes
>>> -----------
>>> 
>>> The following backward-incompatible API changes were made between 0.8 and 0.9:
>>> 
>>> - No longer wrap ``imread`` output in an ``Image`` class
>>> - Change default value of `sigma` parameter in ``skimage.segmentation.slic``
>>> to 0
>>> - ``hough_circle`` now returns a stack of arrays that are the same size as the
>>> input image. Set the ``full_output`` flag to True for the old behavior.
>>> - The following functions were deprecated over two releases:
>>> `skimage.filter.denoise_tv_chambolle`,
>>> `skimage.morphology.is_local_maximum`, `skimage.transform.hough`,
>>> `skimage.transform.probabilistic_hough`,`skimage.transform.hough_peaks`.
>>> Their functionality still exists, but under different names.
>>> 
>>> 
>>> 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:
>>> 
>>> - Ankit Agrawal
>>> - K.-Michael Aye
>>> - Chris Beaumont
>>> - Fran?ois Boulogne
>>> - Luis Pedro Coelho
>>> - Marianne Corvellec
>>> - Olivier Debeir
>>> - Ferdinand Deger
>>> - Kemal Eren
>>> - Jostein B? Fl?ystad
>>> - Christoph Gohlke
>>> - Emmanuelle Gouillart
>>> - Christian Horea
>>> - Thouis (Ray) Jones
>>> - Almar Klein
>>> - Xavier Moles Lopez
>>> - Alexis Mignon
>>> - Juan Nunez-Iglesias
>>> - Zachary Pincus
>>> - Nicolas Pinto
>>> - Davin Potts
>>> - Malcolm Reynolds
>>> - Umesh Sharma
>>> - Johannes Sch?nberger
>>> - Chintak Sheth
>>> - Kirill Shklovsky
>>> - Steven Silvester
>>> - Matt Terry
>>> - Riaan van den Dool
>>> - St?fan van der Walt
>>> - Josh Warner
>>> - Adam Wisniewski
>>> - Yang Zetian
>>> - Tony S Yu
>>> 
>>> -- 
>>> You received this message because you are subscribed to the Google Groups "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
>>> For more options, visit https://groups.google.com/groups/opt_out.
>>> 
>> 
>> -- 
>> You received this message because you are subscribed to the Google Groups "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/groups/opt_out.
>> 
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
> 



From stefan at sun.ac.za  Sat Oct 19 13:36:10 2013
From: stefan at sun.ac.za (=?iso-8859-1?Q?St=E9fan?= van der Walt)
Date: Sat, 19 Oct 2013 19:36:10 +0200
Subject: ANN: scikit-image 0.9.0
In-Reply-To: <F89F7488-5A1E-43E3-8B51-12109CB6482F@demuc.de>
References: <CABDkGQmBjBMzqe2XyF8C5cM-V_fUqAS=2pwiY9=MFVs3Er3Wtw@mail.gmail.com>
 <EA295BD9-465E-4CAA-A358-B3A73FBEC0D5@demuc.de>
 <8BD8C00B-1B90-4C4E-A354-DBBC74216AF5@demuc.de>
 <F89F7488-5A1E-43E3-8B51-12109CB6482F@demuc.de>
Message-ID: <20131019173610.GA16971@shinobi>

On Sat, 19 Oct 2013 18:04:31 +0200, Johannes Sch??????nberger wrote:
> I just noticed you included the compiled Cython files in the archive. Is this intended?

Yes, this is the way we've done it in the past.  We can consider leaving it
out in the future, then the user just needs to have Cython installed (it
is listed as a build dependency anyway).

However, I did not mean to leave out the file mentioned by Christoph.  I tried
to upload a fixed v0.9.1 and then v0.9.2 now, but PyPi keeps giving me an MD5
error.  Johannes, could you try from your end?

I've placed all the changes in the v0.9.x branch of scikit-image/scikit-image
and also pushed the tags.

Unfortunately, I may not have much internet connectivity for the next 24 hrs.

Cheers
St??????fan



From jsch at demuc.de  Sat Oct 19 14:40:16 2013
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Sat, 19 Oct 2013 20:40:16 +0200
Subject: ANN: scikit-image 0.9.0
In-Reply-To: <20131019173610.GA16971@shinobi>
References: <CABDkGQmBjBMzqe2XyF8C5cM-V_fUqAS=2pwiY9=MFVs3Er3Wtw@mail.gmail.com> <EA295BD9-465E-4CAA-A358-B3A73FBEC0D5@demuc.de> <8BD8C00B-1B90-4C4E-A354-DBBC74216AF5@demuc.de> <F89F7488-5A1E-43E3-8B51-12109CB6482F@demuc.de> <20131019173610.GA16971@shinobi>
Message-ID: <B9619353-D2C1-4A4C-826E-4FE87603D864@demuc.de>

> Yes, this is the way we've done it in the past.  We can consider leaving it
> out in the future, then the user just needs to have Cython installed (it
> is listed as a build dependency anyway).
> 
> However, I did not mean to leave out the file mentioned by Christoph.  I tried
> to upload a fixed v0.9.1 and then v0.9.2 now, but PyPi keeps giving me an MD5
> error.  Johannes, could you try from your end?
> 
> I've placed all the changes in the v0.9.x branch of scikit-image/scikit-image
> and also pushed the tags.

I pushed the v0.9.1 version. You may remove the v0.9.2 version.

I hope everything works now?


From stefan at sun.ac.za  Sat Oct 19 15:43:57 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sat, 19 Oct 2013 21:43:57 +0200
Subject: ANN: scikit-image 0.9.0
In-Reply-To: <B9619353-D2C1-4A4C-826E-4FE87603D864@demuc.de>
References: <CABDkGQmBjBMzqe2XyF8C5cM-V_fUqAS=2pwiY9=MFVs3Er3Wtw@mail.gmail.com>
	<EA295BD9-465E-4CAA-A358-B3A73FBEC0D5@demuc.de>
	<8BD8C00B-1B90-4C4E-A354-DBBC74216AF5@demuc.de>
	<F89F7488-5A1E-43E3-8B51-12109CB6482F@demuc.de>
	<20131019173610.GA16971@shinobi>
	<B9619353-D2C1-4A4C-826E-4FE87603D864@demuc.de>
Message-ID: <CABDkGQks3h3SBT4PE57iCqP-MY2+UpJn5wcveShrSe7xMgiKAw@mail.gmail.com>

On 19 Oct 2013 20:40, "Johannes Sch?nberger" <jsch at demuc.de> wrote:
>
> > Yes, this is the way we've done it in the past.  We can consider
leaving it
> > out in the future, then the user just needs to have Cython installed (it
> > is listed as a build dependency anyway).
> >
> > However, I did not mean to leave out the file mentioned by Christoph.
 I tried
> > to upload a fixed v0.9.1 and then v0.9.2 now, but PyPi keeps giving me
an MD5
> > error.  Johannes, could you try from your end?
> >
> > I've placed all the changes in the v0.9.x branch of
scikit-image/scikit-image
> > and also pushed the tags.
>
> I pushed the v0.9.1 version. You may remove the v0.9.2 version.

Thanks, you rock. I've removed 0.9.2.

Cheers
St?fan
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From jsch at demuc.de  Sun Oct 20 10:15:07 2013
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Sun, 20 Oct 2013 16:15:07 +0200
Subject: ANN: scikit-image 0.9.0
In-Reply-To: <CABDkGQks3h3SBT4PE57iCqP-MY2+UpJn5wcveShrSe7xMgiKAw@mail.gmail.com>
References: <CABDkGQmBjBMzqe2XyF8C5cM-V_fUqAS=2pwiY9=MFVs3Er3Wtw@mail.gmail.com> <EA295BD9-465E-4CAA-A358-B3A73FBEC0D5@demuc.de> <8BD8C00B-1B90-4C4E-A354-DBBC74216AF5@demuc.de> <F89F7488-5A1E-43E3-8B51-12109CB6482F@demuc.de> <20131019173610.GA16971@shinobi> <B9619353-D2C1-4A4C-826E-4FE87603D864@demuc.de> <CABDkGQks3h3SBT4PE57iCqP-MY2+UpJn5wcveShrSe7xMgiKAw@mail.gmail.com>
Message-ID: <CEF885E3-F7EC-4B6F-8C7A-F5707CFA71A9@demuc.de>

> Thanks, you rock. I've removed 0.9.2.

I guess, you forgot to push the updated tags.

Did you have time to send ANN to other mailing lists or do you want me to do it?

Johannes


From stefan at sun.ac.za  Sun Oct 20 13:44:38 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 20 Oct 2013 19:44:38 +0200
Subject: ANN: scikit-image 0.9.0
In-Reply-To: <CEF885E3-F7EC-4B6F-8C7A-F5707CFA71A9@demuc.de>
References: <CABDkGQmBjBMzqe2XyF8C5cM-V_fUqAS=2pwiY9=MFVs3Er3Wtw@mail.gmail.com>
	<EA295BD9-465E-4CAA-A358-B3A73FBEC0D5@demuc.de>
	<8BD8C00B-1B90-4C4E-A354-DBBC74216AF5@demuc.de>
	<F89F7488-5A1E-43E3-8B51-12109CB6482F@demuc.de>
	<20131019173610.GA16971@shinobi>
	<B9619353-D2C1-4A4C-826E-4FE87603D864@demuc.de>
	<CABDkGQks3h3SBT4PE57iCqP-MY2+UpJn5wcveShrSe7xMgiKAw@mail.gmail.com>
	<CEF885E3-F7EC-4B6F-8C7A-F5707CFA71A9@demuc.de>
Message-ID: <CABDkGQmTEsk65dw_fCgzOeTA04F=zomXhKuSasQe8SoPNSUm9A@mail.gmail.com>

On 20 Oct 2013 16:15, "Johannes Sch?nberger" <jsch at demuc.de> wrote:
>
> > Thanks, you rock. I've removed 0.9.2.
>
> I guess, you forgot to push the updated tags.

I can't untag from a public repository, so any further release will have to
be 0.9.3.

> Did you have time to send ANN to other mailing lists or do you want me to
do it?

I sent one to scipy-user, but please go ahead and post anywhere else you
see fit. Just use the latest version of the release notes (s removed from
name).

Thanks
St?fan
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From jsch at demuc.de  Sun Oct 20 13:51:49 2013
From: jsch at demuc.de (=?windows-1252?Q?Johannes_Sch=F6nberger?=)
Date: Sun, 20 Oct 2013 19:51:49 +0200
Subject: ANN: scikit-image 0.9.0
In-Reply-To: <CABDkGQmTEsk65dw_fCgzOeTA04F=zomXhKuSasQe8SoPNSUm9A@mail.gmail.com>
References: <CABDkGQmBjBMzqe2XyF8C5cM-V_fUqAS=2pwiY9=MFVs3Er3Wtw@mail.gmail.com> <EA295BD9-465E-4CAA-A358-B3A73FBEC0D5@demuc.de> <8BD8C00B-1B90-4C4E-A354-DBBC74216AF5@demuc.de> <F89F7488-5A1E-43E3-8B51-12109CB6482F@demuc.de> <20131019173610.GA16971@shinobi> <B9619353-D2C1-4A4C-826E-4FE87603D864@demuc.de> <CABDkGQks3h3SBT4PE57iCqP-MY2+UpJn5wcveShrSe7xMgiKAw@mail.gmail.com> <CEF885E3-F7EC-4B6F-8C7A-F5707CFA71A9@demuc.de> <CABDkGQmTEsk65dw_fCgzOeTA04F=zomXhKuSasQe8SoPNSUm9A@mail.gmail.com>
Message-ID: <0453EBC2-1AEC-4DFD-A4E3-EBD7BCB96AB3@demuc.de>

> I sent one to scipy-user, but please go ahead and post anywhere else you see fit. Just use the latest version of the release notes (s removed from name).

Strange? I did not receive it and cannot see it in the archives either.


From stefan at sun.ac.za  Mon Oct 21 02:46:35 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 21 Oct 2013 08:46:35 +0200
Subject: ANN: scikit-image 0.9.0
In-Reply-To: <0453EBC2-1AEC-4DFD-A4E3-EBD7BCB96AB3@demuc.de>
References: <CABDkGQmBjBMzqe2XyF8C5cM-V_fUqAS=2pwiY9=MFVs3Er3Wtw@mail.gmail.com>
 <EA295BD9-465E-4CAA-A358-B3A73FBEC0D5@demuc.de> <8BD8C00B-1B90-4C4E-A354-DBBC74216AF5@demuc.de>
 <F89F7488-5A1E-43E3-8B51-12109CB6482F@demuc.de> <20131019173610.GA16971@shinobi>
 <B9619353-D2C1-4A4C-826E-4FE87603D864@demuc.de> <CABDkGQks3h3SBT4PE57iCqP-MY2+UpJn5wcveShrSe7xMgiKAw@mail.gmail.com>
 <CEF885E3-F7EC-4B6F-8C7A-F5707CFA71A9@demuc.de> <CABDkGQmTEsk65dw_fCgzOeTA04F=zomXhKuSasQe8SoPNSUm9A@mail.gmail.com>
 <0453EBC2-1AEC-4DFD-A4E3-EBD7BCB96AB3@demuc.de>
Message-ID: <CABDkGQ=2tSpBgBv-4TPsYjNhaMdKZQ+=5wY-Q5kq9LAZf6RY1g@mail.gmail.com>

On 20 Oct 2013 19:51, "Johannes Sch?nberger" <jsch at demuc.de> wrote:
>
> > I sent one to scipy-user, but please go ahead and post anywhere else you see fit. Just use the latest version of the release notes (s removed from name).
>
> Strange? I did not receive it and cannot see it in the archives either.

Weird--it was sent from my system, but clearly did not get posted to
the list.  Let me try again.

St?fan


From stefan at sun.ac.za  Mon Oct 21 03:19:33 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 21 Oct 2013 09:19:33 +0200
Subject: CIELUV Transformations
In-Reply-To: <0e4613db-ea50-4342-962c-20d1a8e8dd90@googlegroups.com>
References: <b20c6a2c-fe5f-43e5-b7ac-ebebde42724b@googlegroups.com>
 <CABDkGQmR6ZtVOdQZMKxgvSmYoeCbCp==KR+6w_+nGyLLN9jwwg@mail.gmail.com>
 <fc4457ee-8489-4cbb-8e85-fcce63e78678@googlegroups.com> <CABDkGQkttiCurekV9a=Xi70G4WQt_Dn3AAm_OOxo2LmwGVePCQ@mail.gmail.com>
 <9450c9e5-5951-421b-92fe-c159ccbdbef1@googlegroups.com> <0e4613db-ea50-4342-962c-20d1a8e8dd90@googlegroups.com>
Message-ID: <CABDkGQk8HqwCsWoo-tBGrWeySKEXq9D0Wnogb=g_wQqKE7Mnww@mail.gmail.com>

On Wed, Oct 16, 2013 at 11:29 PM, Isaac Gerg <isaac.gerg at gergltd.com> wrote:
> According to "Principles of Color Technology" by Roy S. Berns, it is a myth
> that" CIELAB was recommended for large color differences and tha tCIELUV was
> recommended for small color differences."  It is also a myth that "CIELAB is
> recommended for reflecting samples while CIELUV is recommended for sources
> and displays."  The second myth is what I originally stated as fact but is
> incorrect.

This makes for good docstrings!

St?fan


From stefan at sun.ac.za  Mon Oct 21 03:25:55 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 21 Oct 2013 09:25:55 +0200
Subject: ANN: scikit-image 0.9.0
In-Reply-To: <CABDkGQ=2tSpBgBv-4TPsYjNhaMdKZQ+=5wY-Q5kq9LAZf6RY1g@mail.gmail.com>
References: <CABDkGQmBjBMzqe2XyF8C5cM-V_fUqAS=2pwiY9=MFVs3Er3Wtw@mail.gmail.com>
 <EA295BD9-465E-4CAA-A358-B3A73FBEC0D5@demuc.de> <8BD8C00B-1B90-4C4E-A354-DBBC74216AF5@demuc.de>
 <F89F7488-5A1E-43E3-8B51-12109CB6482F@demuc.de> <20131019173610.GA16971@shinobi>
 <B9619353-D2C1-4A4C-826E-4FE87603D864@demuc.de> <CABDkGQks3h3SBT4PE57iCqP-MY2+UpJn5wcveShrSe7xMgiKAw@mail.gmail.com>
 <CEF885E3-F7EC-4B6F-8C7A-F5707CFA71A9@demuc.de> <CABDkGQmTEsk65dw_fCgzOeTA04F=zomXhKuSasQe8SoPNSUm9A@mail.gmail.com>
 <0453EBC2-1AEC-4DFD-A4E3-EBD7BCB96AB3@demuc.de> <CABDkGQ=2tSpBgBv-4TPsYjNhaMdKZQ+=5wY-Q5kq9LAZf6RY1g@mail.gmail.com>
Message-ID: <CABDkGQmKnZ2_Uh+0oYayfQSf-KK9JVjSSULM8A_WL1+ooqCLKw@mail.gmail.com>

On Mon, Oct 21, 2013 at 8:46 AM, St?fan van der Walt <stefan at sun.ac.za> wrote:
> Weird--it was sent from my system, but clearly did not get posted to
> the list.  Let me try again.

I posted again--still doesn't look like it went through, but no
response from the list server either.  The numpy-discussion post went
through (I can see it in the archive).  If you are subscribed to
scipy-user, perhaps try to post there?

Thanks
St?fan


From jsch at demuc.de  Mon Oct 21 03:32:44 2013
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Mon, 21 Oct 2013 09:32:44 +0200
Subject: ANN: scikit-image 0.9.0
In-Reply-To: <CABDkGQmKnZ2_Uh+0oYayfQSf-KK9JVjSSULM8A_WL1+ooqCLKw@mail.gmail.com>
References: <CABDkGQmBjBMzqe2XyF8C5cM-V_fUqAS=2pwiY9=MFVs3Er3Wtw@mail.gmail.com> <EA295BD9-465E-4CAA-A358-B3A73FBEC0D5@demuc.de> <8BD8C00B-1B90-4C4E-A354-DBBC74216AF5@demuc.de> <F89F7488-5A1E-43E3-8B51-12109CB6482F@demuc.de> <20131019173610.GA16971@shinobi> <B9619353-D2C1-4A4C-826E-4FE87603D864@demuc.de> <CABDkGQks3h3SBT4PE57iCqP-MY2+UpJn5wcveShrSe7xMgiKAw@mail.gmail.com> <CEF885E3-F7EC-4B6F-8C7A-F5707CFA71A9@demuc.de> <CABDkGQmTEsk65dw_fCgzOeTA04F=zomXhKuSasQe8SoPNSUm9A@mail.gmail.com> <0453EBC2-1AEC-4DFD-A4E3-EBD7BCB96AB3@demuc.de> <CABDkGQ=2tSpBgBv-4TPsYjNhaMdKZQ+=5wY-Q5kq9LAZf6RY1g@mail.gmail.com> <CABDkGQmKnZ2_Uh+0oYayfQSf-KK9JVjSSULM8A_WL1+ooqCLKw@mail.gmail.com>
Message-ID: <93EFCAEA-317B-40FB-A24F-960E469F2493@demuc.de>

http://mail.scipy.org/pipermail/scipy-user/2013-October/035095.html

Am 21.10.2013 um 09:25 schrieb St?fan van der Walt <stefan at sun.ac.za>:

> On Mon, Oct 21, 2013 at 8:46 AM, St?fan van der Walt <stefan at sun.ac.za> wrote:
>> Weird--it was sent from my system, but clearly did not get posted to
>> the list.  Let me try again.
> 
> I posted again--still doesn't look like it went through, but no
> response from the list server either.  The numpy-discussion post went
> through (I can see it in the archive).  If you are subscribed to
> scipy-user, perhaps try to post there?
> 
> Thanks
> St?fan
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
> 



From isaac.gerg at gergltd.com  Wed Oct 23 08:14:20 2013
From: isaac.gerg at gergltd.com (Isaac Gerg)
Date: Wed, 23 Oct 2013 05:14:20 -0700 (PDT)
Subject: CIELUV Transformations
In-Reply-To: <CABDkGQk8HqwCsWoo-tBGrWeySKEXq9D0Wnogb=g_wQqKE7Mnww@mail.gmail.com>
References: <b20c6a2c-fe5f-43e5-b7ac-ebebde42724b@googlegroups.com>
 <CABDkGQmR6ZtVOdQZMKxgvSmYoeCbCp==KR+6w_+nGyLLN9jwwg@mail.gmail.com>
 <fc4457ee-8489-4cbb-8e85-fcce63e78678@googlegroups.com> <CABDkGQkttiCurekV9a=Xi70G4WQt_Dn3AAm_OOxo2LmwGVePCQ@mail.gmail.com>
 <9450c9e5-5951-421b-92fe-c159ccbdbef1@googlegroups.com> <0e4613db-ea50-4342-962c-20d1a8e8dd90@googlegroups.com>
 <CABDkGQk8HqwCsWoo-tBGrWeySKEXq9D0Wnogb=g_wQqKE7Mnww@mail.gmail.com>
Message-ID: <0bd73a5f-871e-451d-896d-264d4da462e3@googlegroups.com>

I am seeing some chatter on github about the differences between CIELUV and 
CIELAB.  My understanding is that the committee could not agree on a single 
standard and didnt feel they could approve CIELAB alone.

Isaac

On Monday, October 21, 2013 3:19:33 AM UTC-4, Stefan van der Walt wrote:
>
> On Wed, Oct 16, 2013 at 11:29 PM, Isaac Gerg <isaac... at gergltd.com<javascript:>> 
> wrote: 
> > According to "Principles of Color Technology" by Roy S. Berns, it is a 
> myth 
> > that" CIELAB was recommended for large color differences and tha tCIELUV 
> was 
> > recommended for small color differences."  It is also a myth that 
> "CIELAB is 
> > recommended for reflecting samples while CIELUV is recommended for 
> sources 
> > and displays."  The second myth is what I originally stated as fact but 
> is 
> > incorrect. 
>
> This makes for good docstrings! 
>
> St?fan 
>
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From jaime.frio at gmail.com  Wed Oct 23 11:56:25 2013
From: jaime.frio at gmail.com (=?ISO-8859-1?Q?Jaime_Fern=E1ndez_del_R=EDo?=)
Date: Wed, 23 Oct 2013 08:56:25 -0700
Subject: CIELUV Transformations
In-Reply-To: <CADnN3yVMo6WepifMSEusE_cJZo25jgMzHX1eTH512H2NOk6q6A@mail.gmail.com>
References: <b20c6a2c-fe5f-43e5-b7ac-ebebde42724b@googlegroups.com>
	<CABDkGQmR6ZtVOdQZMKxgvSmYoeCbCp==KR+6w_+nGyLLN9jwwg@mail.gmail.com>
	<fc4457ee-8489-4cbb-8e85-fcce63e78678@googlegroups.com>
	<CABDkGQkttiCurekV9a=Xi70G4WQt_Dn3AAm_OOxo2LmwGVePCQ@mail.gmail.com>
	<9450c9e5-5951-421b-92fe-c159ccbdbef1@googlegroups.com>
	<0e4613db-ea50-4342-962c-20d1a8e8dd90@googlegroups.com>
	<CABDkGQk8HqwCsWoo-tBGrWeySKEXq9D0Wnogb=g_wQqKE7Mnww@mail.gmail.com>
	<0bd73a5f-871e-451d-896d-264d4da462e3@googlegroups.com>
	<CABDkGQku-gvNYbOPwrC7mcd=0na9ZdZgo2EZV1aKzy1SwZaM3w@mail.gmail.com>
	<CADnN3yWWNLo1Yn=cF=t7mSq4aXgVdtO2udSuHpQxF8gpywFS8g@mail.gmail.com>
	<CABDkGQ=vkZjj-Mwr5rwFsbSMwJDkx3UX064-4TtSL-dr8AA=XA@mail.gmail.com>
	<CADnN3yVMo6WepifMSEusE_cJZo25jgMzHX1eTH512H2NOk6q6A@mail.gmail.com>
Message-ID: <CAPOWHWkC5uVLgsph2EW2ccV=eSa2Qv4oLhbYBB26oQpae3CSbw@mail.gmail.com>

I have a coworker that is a member of one of CIE's divisions, so I asked
him the LAB vs LUV question, and here's his reply:

"Yes, there is a simple historical explanation - LUV was championed by the
display industry while LAB was the favorite of "surface" industries (print,
materials manufacturing, ...). LUV has the beneficial property of having a
saturation predictor and of being related to the luminance-linear u'v'
chromaticity space. Let me know if you'd like more detail.

Today, I am not aware of LUV being used anywhere - LAB has won the battle
between the two and is used even for displays. Either that, or, where
higher performance is needed in terms of perceptual prediction accuracy,
CIECAM02 (a color appearance model) is used. It is significantly more
complex, but predicts more visual phenomena and allows for taking viewing
conditions better into account.

So, I'd say use LAB if what it does is good enough and CIECAM02 if it fails
(e.g., for gamut mapping LAB has serious hue non-uniformity)."

So, who's up for coding CIECAM02 color transformations, whatever that may
be? ;-)

Jaime

-- 
(\__/)
( O.o)
( > <) Este es Conejo. Copia a Conejo en tu firma y ay?dale en sus planes
de dominaci?n mundial.
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From isaac.gerg at gergltd.com  Wed Oct 23 09:25:54 2013
From: isaac.gerg at gergltd.com (Isaac Gerg)
Date: Wed, 23 Oct 2013 09:25:54 -0400
Subject: CIELUV Transformations
In-Reply-To: <CABDkGQku-gvNYbOPwrC7mcd=0na9ZdZgo2EZV1aKzy1SwZaM3w@mail.gmail.com>
References: <b20c6a2c-fe5f-43e5-b7ac-ebebde42724b@googlegroups.com>
 <CABDkGQmR6ZtVOdQZMKxgvSmYoeCbCp==KR+6w_+nGyLLN9jwwg@mail.gmail.com>
 <fc4457ee-8489-4cbb-8e85-fcce63e78678@googlegroups.com> <CABDkGQkttiCurekV9a=Xi70G4WQt_Dn3AAm_OOxo2LmwGVePCQ@mail.gmail.com>
 <9450c9e5-5951-421b-92fe-c159ccbdbef1@googlegroups.com> <0e4613db-ea50-4342-962c-20d1a8e8dd90@googlegroups.com>
 <CABDkGQk8HqwCsWoo-tBGrWeySKEXq9D0Wnogb=g_wQqKE7Mnww@mail.gmail.com>
 <0bd73a5f-871e-451d-896d-264d4da462e3@googlegroups.com> <CABDkGQku-gvNYbOPwrC7mcd=0na9ZdZgo2EZV1aKzy1SwZaM3w@mail.gmail.com>
Message-ID: <CADnN3yWWNLo1Yn=cF=t7mSq4aXgVdtO2udSuHpQxF8gpywFS8g@mail.gmail.com>

As I understand it, they simply could not agree on a single standard and
felt both must be approved.  That is as much as i can get out of the
literature.


On Wed, Oct 23, 2013 at 9:17 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> On Wed, Oct 23, 2013 at 2:14 PM, Isaac Gerg <isaac.gerg at gergltd.com>
> wrote:
> > I am seeing some chatter on github about the differences between CIELUV
> and
> > CIELAB.  My understanding is that the committee could not agree on a
> single
> > standard and didnt feel they could approve CIELAB alone.
>
> Did they provide some motivation as to why not, or why both standards
> are needed?
>
> St?fan
>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "scikit-image" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/scikit-image/DIRaSXJoEes/unsubscribe.
> To unsubscribe from this group and all of its topics, send an email to
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>
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From isaac.gerg at gergltd.com  Wed Oct 23 09:30:24 2013
From: isaac.gerg at gergltd.com (Isaac Gerg)
Date: Wed, 23 Oct 2013 09:30:24 -0400
Subject: CIELUV Transformations
In-Reply-To: <CABDkGQ=vkZjj-Mwr5rwFsbSMwJDkx3UX064-4TtSL-dr8AA=XA@mail.gmail.com>
References: <b20c6a2c-fe5f-43e5-b7ac-ebebde42724b@googlegroups.com>
 <CABDkGQmR6ZtVOdQZMKxgvSmYoeCbCp==KR+6w_+nGyLLN9jwwg@mail.gmail.com>
 <fc4457ee-8489-4cbb-8e85-fcce63e78678@googlegroups.com> <CABDkGQkttiCurekV9a=Xi70G4WQt_Dn3AAm_OOxo2LmwGVePCQ@mail.gmail.com>
 <9450c9e5-5951-421b-92fe-c159ccbdbef1@googlegroups.com> <0e4613db-ea50-4342-962c-20d1a8e8dd90@googlegroups.com>
 <CABDkGQk8HqwCsWoo-tBGrWeySKEXq9D0Wnogb=g_wQqKE7Mnww@mail.gmail.com>
 <0bd73a5f-871e-451d-896d-264d4da462e3@googlegroups.com> <CABDkGQku-gvNYbOPwrC7mcd=0na9ZdZgo2EZV1aKzy1SwZaM3w@mail.gmail.com>
 <CADnN3yWWNLo1Yn=cF=t7mSq4aXgVdtO2udSuHpQxF8gpywFS8g@mail.gmail.com> <CABDkGQ=vkZjj-Mwr5rwFsbSMwJDkx3UX064-4TtSL-dr8AA=XA@mail.gmail.com>
Message-ID: <CADnN3yVMo6WepifMSEusE_cJZo25jgMzHX1eTH512H2NOk6q6A@mail.gmail.com>

Unfortunately, I do not know.  You could check out Principles of Color
Technology by Berns and see if he talks more about it in his book.
 Additionally, you could email burns and ask him.  I dont have the time at
the moment to track this down.

Isaac
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From isaac.gerg at gergltd.com  Wed Oct 23 13:30:41 2013
From: isaac.gerg at gergltd.com (Isaac Gerg)
Date: Wed, 23 Oct 2013 13:30:41 -0400
Subject: CIELUV Transformations
In-Reply-To: <CAPOWHWkC5uVLgsph2EW2ccV=eSa2Qv4oLhbYBB26oQpae3CSbw@mail.gmail.com>
References: <b20c6a2c-fe5f-43e5-b7ac-ebebde42724b@googlegroups.com>
 <CABDkGQmR6ZtVOdQZMKxgvSmYoeCbCp==KR+6w_+nGyLLN9jwwg@mail.gmail.com>
 <fc4457ee-8489-4cbb-8e85-fcce63e78678@googlegroups.com> <CABDkGQkttiCurekV9a=Xi70G4WQt_Dn3AAm_OOxo2LmwGVePCQ@mail.gmail.com>
 <9450c9e5-5951-421b-92fe-c159ccbdbef1@googlegroups.com> <0e4613db-ea50-4342-962c-20d1a8e8dd90@googlegroups.com>
 <CABDkGQk8HqwCsWoo-tBGrWeySKEXq9D0Wnogb=g_wQqKE7Mnww@mail.gmail.com>
 <0bd73a5f-871e-451d-896d-264d4da462e3@googlegroups.com> <CABDkGQku-gvNYbOPwrC7mcd=0na9ZdZgo2EZV1aKzy1SwZaM3w@mail.gmail.com>
 <CADnN3yWWNLo1Yn=cF=t7mSq4aXgVdtO2udSuHpQxF8gpywFS8g@mail.gmail.com>
 <CABDkGQ=vkZjj-Mwr5rwFsbSMwJDkx3UX064-4TtSL-dr8AA=XA@mail.gmail.com>
 <CADnN3yVMo6WepifMSEusE_cJZo25jgMzHX1eTH512H2NOk6q6A@mail.gmail.com> <CAPOWHWkC5uVLgsph2EW2ccV=eSa2Qv4oLhbYBB26oQpae3CSbw@mail.gmail.com>
Message-ID: <CADnN3yUKQz+=y4=2K2-MhHu_Jmks9QFnWYBuOdaojze+h47qew@mail.gmail.com>

Good stuff -- thank you for sharing.


On Wed, Oct 23, 2013 at 11:56 AM, Jaime Fern?ndez del R?o <
jaime.frio at gmail.com> wrote:

> I have a coworker that is a member of one of CIE's divisions, so I asked
> him the LAB vs LUV question, and here's his reply:
>
> "Yes, there is a simple historical explanation - LUV was championed by the
> display industry while LAB was the favorite of "surface" industries (print,
> materials manufacturing, ...). LUV has the beneficial property of having a
> saturation predictor and of being related to the luminance-linear u'v'
> chromaticity space. Let me know if you'd like more detail.
>
> Today, I am not aware of LUV being used anywhere - LAB has won the battle
> between the two and is used even for displays. Either that, or, where
> higher performance is needed in terms of perceptual prediction accuracy,
> CIECAM02 (a color appearance model) is used. It is significantly more
> complex, but predicts more visual phenomena and allows for taking viewing
> conditions better into account.
>
> So, I'd say use LAB if what it does is good enough and CIECAM02 if it
> fails (e.g., for gamut mapping LAB has serious hue non-uniformity)."
>
> So, who's up for coding CIECAM02 color transformations, whatever that may
> be? ;-)
>
> Jaime
>
> --
> (\__/)
> ( O.o)
> ( > <) Este es Conejo. Copia a Conejo en tu firma y ay?dale en sus planes
> de dominaci?n mundial.
>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "scikit-image" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/scikit-image/DIRaSXJoEes/unsubscribe.
> To unsubscribe from this group and all of its topics, send an email to
> scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>
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From stefan at sun.ac.za  Wed Oct 23 09:17:14 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 23 Oct 2013 15:17:14 +0200
Subject: CIELUV Transformations
In-Reply-To: <0bd73a5f-871e-451d-896d-264d4da462e3@googlegroups.com>
References: <b20c6a2c-fe5f-43e5-b7ac-ebebde42724b@googlegroups.com>
 <CABDkGQmR6ZtVOdQZMKxgvSmYoeCbCp==KR+6w_+nGyLLN9jwwg@mail.gmail.com>
 <fc4457ee-8489-4cbb-8e85-fcce63e78678@googlegroups.com> <CABDkGQkttiCurekV9a=Xi70G4WQt_Dn3AAm_OOxo2LmwGVePCQ@mail.gmail.com>
 <9450c9e5-5951-421b-92fe-c159ccbdbef1@googlegroups.com> <0e4613db-ea50-4342-962c-20d1a8e8dd90@googlegroups.com>
 <CABDkGQk8HqwCsWoo-tBGrWeySKEXq9D0Wnogb=g_wQqKE7Mnww@mail.gmail.com> <0bd73a5f-871e-451d-896d-264d4da462e3@googlegroups.com>
Message-ID: <CABDkGQku-gvNYbOPwrC7mcd=0na9ZdZgo2EZV1aKzy1SwZaM3w@mail.gmail.com>

On Wed, Oct 23, 2013 at 2:14 PM, Isaac Gerg <isaac.gerg at gergltd.com> wrote:
> I am seeing some chatter on github about the differences between CIELUV and
> CIELAB.  My understanding is that the committee could not agree on a single
> standard and didnt feel they could approve CIELAB alone.

Did they provide some motivation as to why not, or why both standards
are needed?

St?fan


From stefan at sun.ac.za  Wed Oct 23 09:28:10 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 23 Oct 2013 15:28:10 +0200
Subject: CIELUV Transformations
In-Reply-To: <CADnN3yWWNLo1Yn=cF=t7mSq4aXgVdtO2udSuHpQxF8gpywFS8g@mail.gmail.com>
References: <b20c6a2c-fe5f-43e5-b7ac-ebebde42724b@googlegroups.com>
 <CABDkGQmR6ZtVOdQZMKxgvSmYoeCbCp==KR+6w_+nGyLLN9jwwg@mail.gmail.com>
 <fc4457ee-8489-4cbb-8e85-fcce63e78678@googlegroups.com> <CABDkGQkttiCurekV9a=Xi70G4WQt_Dn3AAm_OOxo2LmwGVePCQ@mail.gmail.com>
 <9450c9e5-5951-421b-92fe-c159ccbdbef1@googlegroups.com> <0e4613db-ea50-4342-962c-20d1a8e8dd90@googlegroups.com>
 <CABDkGQk8HqwCsWoo-tBGrWeySKEXq9D0Wnogb=g_wQqKE7Mnww@mail.gmail.com>
 <0bd73a5f-871e-451d-896d-264d4da462e3@googlegroups.com> <CABDkGQku-gvNYbOPwrC7mcd=0na9ZdZgo2EZV1aKzy1SwZaM3w@mail.gmail.com>
 <CADnN3yWWNLo1Yn=cF=t7mSq4aXgVdtO2udSuHpQxF8gpywFS8g@mail.gmail.com>
Message-ID: <CABDkGQ=vkZjj-Mwr5rwFsbSMwJDkx3UX064-4TtSL-dr8AA=XA@mail.gmail.com>

On Wed, Oct 23, 2013 at 3:25 PM, Isaac Gerg <isaac.gerg at gergltd.com> wrote:
> As I understand it, they simply could not agree on a single standard and
> felt both must be approved.  That is as much as i can get out of the
> literature.

But were arguments made on both sides that were so compelling, or did
they have different trade-offs?  I'm just trying to get a grip on the
situation.

St?fan


From google at terre-adelie.org  Thu Oct 24 03:03:22 2013
From: google at terre-adelie.org (Jerome Kieffer)
Date: Thu, 24 Oct 2013 09:03:22 +0200
Subject: Clarity
In-Reply-To: <CA+JHcKSBruYkQq6or1-4iJ_65jLcy26JhWVMf549Bnm8gwsbAA@mail.gmail.com>
References: <CA+JHcKSBruYkQq6or1-4iJ_65jLcy26JhWVMf549Bnm8gwsbAA@mail.gmail.com>
Message-ID: <20131024090322.6a9fc3cf.google@terre-adelie.org>

On Thu, 24 Oct 2013 17:27:55 +1100
Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:

> Hi guys,
> 
> Does anyone here have any ideas about what the Camera+ Clarity filter is
> doing? Some examples of the filter
> here<https://secure.flickr.com/photos/pierrewikberg/6983939966/>and
> here <http://obamapacman.com/2011/03/enhance-iphone-camera-clarity-video/>.
> 
> Might be a nice addition to skimage.exposure... =)

Looks like a contrast mask:
http://www.gimp.org/tutorials/ContrastMask/

Here is an old implementation, starting from a JPEG:
    def contrastMask(self, outfile):
        """Ceci est un filtre de debouchage de photographies, aussi appel? masque de contraste, 
        il permet de rattrapper une photo trop contrast?, un contre jour, ...
        ?crit par J?r?me Kieffer, avec l'aide de la liste python at aful, 
        en particulier A. Fayolles et F. Mantegazza avril 2006
        necessite numpy et PIL.
        
        @param: the name of the output file (JPEG)
        @return: filtered Photo instance
        """

        try:
            import numpy
#            import scipy.signal as signal
        except:
            logger.error("This filter needs the numpy library available on https://sourceforge.net/projects/numpy/files/")
            return

        t0 = time.time()
        dimX, dimY = self.pil.size

        ImageFile.MAXBLOCK = dimX * dimY
        img_array = numpy.fromstring(self.pil.tostring(), dtype="UInt8").astype("float32")
        img_array.shape = (dimY, dimX, 3)
        red, green, blue = img_array[:, :, 0], img_array[:, :, 1], img_array[:, :, 2]
        #nota: this is faster than desat2=(ar.max(axis=2)+ar.min(axis=2))/2
        desat_array = (numpy.minimum(numpy.minimum(red, green), blue) + numpy.maximum(numpy.maximum(red, green), blue)) / 2.0
        inv_desat = 255. - desat_array
        blured_inv_desat = self._gaussian.blur(inv_desat, config.ContrastMaskGaussianSize)
        bisi = numpy.round(blured_inv_desat).astype("uint8")
        k = Image.fromarray(bisi, "L").convert("RGB")
        S = ImageChops.screen(self.pil, k)
        M = ImageChops.multiply(self.pil, k)
        F = ImageChops.add(ImageChops.multiply(self.pil, S), ImageChops.multiply(ImageChops.invert(self.pil), M))
        exitJpeg = op.join(config.DefaultRepository, outfile)
        F.save(exitJpeg, quality=80, progressive=True, Optimize=True)
        try:
            os.chmod(exitJpeg, config.DefaultFileMode)
        except IOError:
            logger.error("Unable to chmod %s" % outfile)
        exifJpeg = Exif(exitJpeg)
        exifJpeg.read()
        self.exif.copy(exifJpeg)
        exifJpeg.comment = self.exif.comment

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


From orieux at iap.fr  Thu Oct 24 05:45:12 2013
From: orieux at iap.fr (=?utf-8?Q?Fran=C3=A7ois?= Orieux)
Date: Thu, 24 Oct 2013 11:45:12 +0200
Subject: Image deconvolution submission
Message-ID: <8738nrngt3.fsf@gaia.iap.fr>

Hi,

I plan to submit image deconvolution algorithms to skimage. Before the
pull request and peer review of the code I contact the mailing for a
first reaction and comments.

Fran?ois Orieux

-- 
IAP, CNRS-UPMC - Paris, France
+33 1 73 77 55 11
http://research.orieux.fr


From deil.christoph at googlemail.com  Thu Oct 24 07:43:12 2013
From: deil.christoph at googlemail.com (Christoph Deil)
Date: Thu, 24 Oct 2013 13:43:12 +0200
Subject: Image deconvolution submission
In-Reply-To: <8738nrngt3.fsf@gaia.iap.fr>
References: <8738nrngt3.fsf@gaia.iap.fr>
Message-ID: <DDBBC907-EE47-4C4A-95B9-1B76AC6AD0F5@gmail.com>


On Oct 24, 2013, at 11:45 AM, Fran?ois Orieux <orieux at iap.fr> wrote:

> Hi,
> 
> I plan to submit image deconvolution algorithms to skimage. Before the
> pull request and peer review of the code I contact the mailing for a
> first reaction and comments.

My first reaction: Yippie!

In case you haven't seen it, see Stefan van der Walt's comment here:
https://groups.google.com/d/msg/scikit-image/UMSc2loL5C8/X4F_2YKKunEJ

When you make the pull request, please mention it here. I'm definitely interested to try it out.

> 
> Fran?ois Orieux
> 
> -- 
> IAP, CNRS-UPMC - Paris, France
> +33 1 73 77 55 11
> http://research.orieux.fr
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.



From silvertrumpet999 at gmail.com  Thu Oct 24 19:09:23 2013
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Thu, 24 Oct 2013 16:09:23 -0700 (PDT)
Subject: Image deconvolution submission
In-Reply-To: <DDBBC907-EE47-4C4A-95B9-1B76AC6AD0F5@gmail.com>
References: <8738nrngt3.fsf@gaia.iap.fr>
 <DDBBC907-EE47-4C4A-95B9-1B76AC6AD0F5@gmail.com>
Message-ID: <8f303045-736a-437c-9aef-88ab33c7ea77@googlegroups.com>

It's been on the package to-do list for some time. Particularly blind 
deconvolution, but you have to walk before you run. At least, that's what 
they keep telling me...

I have a number of very basic Fourier-domain deconvolution algorithms 
which, if they aren't included, I can pitch in to fill out the suite. Just 
never seem to find the time to submit them ;)


On Thursday, October 24, 2013 6:43:12 AM UTC-5, Christoph Deil wrote:
>
>
> On Oct 24, 2013, at 11:45 AM, Fran?ois Orieux <ori... at iap.fr <javascript:>> 
> wrote: 
>
> > Hi, 
> > 
> > I plan to submit image deconvolution algorithms to skimage. Before the 
> > pull request and peer review of the code I contact the mailing for a 
> > first reaction and comments. 
>
> My first reaction: Yippie! 
>
> In case you haven't seen it, see Stefan van der Walt's comment here: 
> https://groups.google.com/d/msg/scikit-image/UMSc2loL5C8/X4F_2YKKunEJ 
>
> When you make the pull request, please mention it here. I'm definitely 
> interested to try it out. 
>
> > 
> > Fran?ois Orieux 
> > 
> > -- 
> > IAP, CNRS-UPMC - Paris, France 
> > +33 1 73 77 55 11 
> > http://research.orieux.fr 
> > 
> > -- 
> > You received this message because you are subscribed to the Google 
> Groups "scikit-image" group. 
> > To unsubscribe from this group and stop receiving emails from it, send 
> an email to scikit-image... at googlegroups.com <javascript:>. 
> > For more options, visit https://groups.google.com/groups/opt_out. 
>
>
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From silvertrumpet999 at gmail.com  Thu Oct 24 19:13:02 2013
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Thu, 24 Oct 2013 16:13:02 -0700 (PDT)
Subject: Clarity
In-Reply-To: <20131024090322.6a9fc3cf.google@terre-adelie.org>
References: <CA+JHcKSBruYkQq6or1-4iJ_65jLcy26JhWVMf549Bnm8gwsbAA@mail.gmail.com>
 <20131024090322.6a9fc3cf.google@terre-adelie.org>
Message-ID: <6f4bd457-cdcf-4e8c-b4d1-f8a523db534f@googlegroups.com>

I think that's on the right track.

But a naive contrast mask affects only the luminance. In the first example 
the colors are also very punched up; just looking this seems like more than 
a simple global contrast mask.

My guess? They're applying the equivalent of a contrast mask, but to each 
RGB channel separately. This is "wrong" from an image processing 
perspective, but in the world of Instagram it seems people are more 
interested in filters than reality.

I wouldn't be against this for advertising purposes, though I'd never do it 
to my own images.

On Thursday, October 24, 2013 2:03:22 AM UTC-5, Jerome Kieffer wrote:
>
> On Thu, 24 Oct 2013 17:27:55 +1100 
> Juan Nunez-Iglesias <jni.... at gmail.com <javascript:>> wrote: 
>
> > Hi guys, 
> > 
> > Does anyone here have any ideas about what the Camera+ Clarity filter is 
> > doing? Some examples of the filter 
> > here<https://secure.flickr.com/photos/pierrewikberg/6983939966/>and 
> > here <
> http://obamapacman.com/2011/03/enhance-iphone-camera-clarity-video/>. 
> > 
> > Might be a nice addition to skimage.exposure... =) 
>
> Looks like a contrast mask: 
> http://www.gimp.org/tutorials/ContrastMask/ 
>
> Here is an old implementation, starting from a JPEG: 
>     def contrastMask(self, outfile): 
>         """Ceci est un filtre de debouchage de photographies, aussi appel? 
> masque de contraste, 
>         il permet de rattrapper une photo trop contrast?, un contre jour, 
> ... 
>         ?crit par J?r?me Kieffer, avec l'aide de la liste python at aful, 
>         en particulier A. Fayolles et F. Mantegazza avril 2006 
>         necessite numpy et PIL. 
>         
>         @param: the name of the output file (JPEG) 
>         @return: filtered Photo instance 
>         """ 
>
>         try: 
>             import numpy 
> #            import scipy.signal as signal 
>         except: 
>             logger.error("This filter needs the numpy library available on 
> https://sourceforge.net/projects/numpy/files/") 
>             return 
>
>         t0 = time.time() 
>         dimX, dimY = self.pil.size 
>
>         ImageFile.MAXBLOCK = dimX * dimY 
>         img_array = numpy.fromstring(self.pil.tostring(), 
> dtype="UInt8").astype("float32") 
>         img_array.shape = (dimY, dimX, 3) 
>         red, green, blue = img_array[:, :, 0], img_array[:, :, 1], 
> img_array[:, :, 2] 
>         #nota: this is faster than 
> desat2=(ar.max(axis=2)+ar.min(axis=2))/2 
>         desat_array = (numpy.minimum(numpy.minimum(red, green), blue) + 
> numpy.maximum(numpy.maximum(red, green), blue)) / 2.0 
>         inv_desat = 255. - desat_array 
>         blured_inv_desat = self._gaussian.blur(inv_desat, 
> config.ContrastMaskGaussianSize) 
>         bisi = numpy.round(blured_inv_desat).astype("uint8") 
>         k = Image.fromarray(bisi, "L").convert("RGB") 
>         S = ImageChops.screen(self.pil, k) 
>         M = ImageChops.multiply(self.pil, k) 
>         F = ImageChops.add(ImageChops.multiply(self.pil, S), 
> ImageChops.multiply(ImageChops.invert(self.pil), M)) 
>         exitJpeg = op.join(config.DefaultRepository, outfile) 
>         F.save(exitJpeg, quality=80, progressive=True, Optimize=True) 
>         try: 
>             os.chmod(exitJpeg, config.DefaultFileMode) 
>         except IOError: 
>             logger.error("Unable to chmod %s" % outfile) 
>         exifJpeg = Exif(exitJpeg) 
>         exifJpeg.read() 
>         self.exif.copy(exifJpeg) 
>         exifJpeg.comment = self.exif.comment 
>
> -- 
> Jerome Kieffer <goo... at terre-adelie.org <javascript:>> 
>
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From jni.soma at gmail.com  Thu Oct 24 02:27:55 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Thu, 24 Oct 2013 17:27:55 +1100
Subject: Clarity
Message-ID: <CA+JHcKSBruYkQq6or1-4iJ_65jLcy26JhWVMf549Bnm8gwsbAA@mail.gmail.com>

Hi guys,

Does anyone here have any ideas about what the Camera+ Clarity filter is
doing? Some examples of the filter
here<https://secure.flickr.com/photos/pierrewikberg/6983939966/>and
here <http://obamapacman.com/2011/03/enhance-iphone-camera-clarity-video/>.

Might be a nice addition to skimage.exposure... =)

Juan.
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From mt at matttrent.com  Thu Oct 24 22:35:59 2013
From: mt at matttrent.com (Matthew Trentacoste)
Date: Thu, 24 Oct 2013 19:35:59 -0700
Subject: Clarity
In-Reply-To: <CA+JHcKQALbh-RvguGWxhiLf6c2_2YdNk7hTUseG-6kNtRXRqQA@mail.gmail.com>
References: <CA+JHcKSBruYkQq6or1-4iJ_65jLcy26JhWVMf549Bnm8gwsbAA@mail.gmail.com>
 <20131024090322.6a9fc3cf.google@terre-adelie.org> <6f4bd457-cdcf-4e8c-b4d1-f8a523db534f@googlegroups.com>
 <CA+JHcKQALbh-RvguGWxhiLf6c2_2YdNk7hTUseG-6kNtRXRqQA@mail.gmail.com>
Message-ID: <CAJU8MvQC2-aDouYQkyRjOG5TyQweB2xx076DhHtufnp+XLNZcw@mail.gmail.com>

Doing the computation per RGB channel would introduce chromatic shifts.  My
guess is that chromatic scaling is probably uniform (either across channels
or  adjusting the saturation of the image in a non-spatially variant
manner).

Some of the best of breed work on this topic is by Sylvain Paris, a
researcher also at Adobe:
http://people.csail.mit.edu/sparis/publi/2011/siggraph/

You can use it to boost certain spatial scales to increase local contrast
and reconstruct an image without artifacts.


On Thu, Oct 24, 2013 at 6:45 PM, Juan Nunez-Iglesias <jni.soma at gmail.com>wrote:

> Thanks Josh, Jerome,
>
> Actually what I'm really after is a good, *local* foreground/background
> correction. The local bit is what attracted me to Clarity even though it's
> not really what I'm after.
>
> Particularly of interest is something that will be robust to artifacts in
> the images.
>
> Juan.
>
> On Fri, Oct 25, 2013 at 10:13 AM, Josh Warner <silvertrumpet999 at gmail.com>wrote:
>
>> I think that's on the right track.
>>
>> But a naive contrast mask affects only the luminance. In the first
>> example the colors are also very punched up; just looking this seems like
>> more than a simple global contrast mask.
>>
>> My guess? They're applying the equivalent of a contrast mask, but to each
>> RGB channel separately. This is "wrong" from an image processing
>> perspective, but in the world of Instagram it seems people are more
>> interested in filters than reality.
>>
>> I wouldn't be against this for advertising purposes, though I'd never do
>> it to my own images.
>>
>> On Thursday, October 24, 2013 2:03:22 AM UTC-5, Jerome Kieffer wrote:
>>
>>> On Thu, 24 Oct 2013 17:27:55 +1100
>>> Juan Nunez-Iglesias <jni.... at gmail.com> wrote:
>>>
>>> > Hi guys,
>>> >
>>> > Does anyone here have any ideas about what the Camera+ Clarity filter
>>> is
>>> > doing? Some examples of the filter
>>> > here<https://secure.flickr.**com/photos/pierrewikberg/**6983939966/<https://secure.flickr.com/photos/pierrewikberg/6983939966/>>and
>>>
>>> > here <http://obamapacman.com/2011/**03/enhance-iphone-camera-**
>>> clarity-video/<http://obamapacman.com/2011/03/enhance-iphone-camera-clarity-video/>>.
>>>
>>> >
>>> > Might be a nice addition to skimage.exposure... =)
>>>
>>> Looks like a contrast mask:
>>> http://www.gimp.org/tutorials/**ContrastMask/<http://www.gimp.org/tutorials/ContrastMask/>
>>>
>>> Here is an old implementation, starting from a JPEG:
>>>     def contrastMask(self, outfile):
>>>         """Ceci est un filtre de debouchage de photographies, aussi
>>> appel? masque de contraste,
>>>         il permet de rattrapper une photo trop contrast?, un contre
>>> jour, ...
>>>         ?crit par J?r?me Kieffer, avec l'aide de la liste python at aful,
>>>         en particulier A. Fayolles et F. Mantegazza avril 2006
>>>         necessite numpy et PIL.
>>>
>>>         @param: the name of the output file (JPEG)
>>>         @return: filtered Photo instance
>>>         """
>>>
>>>         try:
>>>             import numpy
>>> #            import scipy.signal as signal
>>>         except:
>>>             logger.error("This filter needs the numpy library available
>>> on https://sourceforge.net/**projects/numpy/files/<https://sourceforge.net/projects/numpy/files/>")
>>>
>>>             return
>>>
>>>         t0 = time.time()
>>>         dimX, dimY = self.pil.size
>>>
>>>         ImageFile.MAXBLOCK = dimX * dimY
>>>         img_array = numpy.fromstring(self.pil.**tostring(),
>>> dtype="UInt8").astype("**float32")
>>>         img_array.shape = (dimY, dimX, 3)
>>>         red, green, blue = img_array[:, :, 0], img_array[:, :, 1],
>>> img_array[:, :, 2]
>>>         #nota: this is faster than desat2=(ar.max(axis=2)+ar.min(**axis=2))/2
>>>
>>>         desat_array = (numpy.minimum(numpy.minimum(**red, green), blue)
>>> + numpy.maximum(numpy.maximum(**red, green), blue)) / 2.0
>>>         inv_desat = 255. - desat_array
>>>         blured_inv_desat = self._gaussian.blur(inv_desat, config.**ContrastMaskGaussianSize)
>>>
>>>         bisi = numpy.round(blured_inv_desat).**astype("uint8")
>>>         k = Image.fromarray(bisi, "L").convert("RGB")
>>>         S = ImageChops.screen(self.pil, k)
>>>         M = ImageChops.multiply(self.pil, k)
>>>         F = ImageChops.add(ImageChops.**multiply(self.pil, S),
>>> ImageChops.multiply(**ImageChops.invert(self.pil), M))
>>>         exitJpeg = op.join(config.**DefaultRepository, outfile)
>>>         F.save(exitJpeg, quality=80, progressive=True, Optimize=True)
>>>         try:
>>>             os.chmod(exitJpeg, config.DefaultFileMode)
>>>         except IOError:
>>>             logger.error("Unable to chmod %s" % outfile)
>>>         exifJpeg = Exif(exitJpeg)
>>>         exifJpeg.read()
>>>         self.exif.copy(exifJpeg)
>>>         exifJpeg.comment = self.exif.comment
>>>
>>> --
>>> Jerome Kieffer <goo... at terre-adelie.org>
>>>
>>  --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>



-- 

[  matthew m trentacoste                                     ]
[                                                            ]
[  mt at matttrent.com                                          ]
[  http://matttrent.com                                      ]
[  twitter: @matttrent                                       ]
[  +1.415.326.3226                                           ]
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From yager.neil at gmail.com  Fri Oct 25 09:37:20 2013
From: yager.neil at gmail.com (Neil)
Date: Fri, 25 Oct 2013 06:37:20 -0700 (PDT)
Subject: import error on linux
In-Reply-To: <df835b83-2438-4b71-8f07-86303885af16@googlegroups.com>
References: <CAE5Ny9t1UMbvDOO+zrTR0NMasvP41QsjoG2gnsat5KPTHuMi_A@mail.gmail.com>
 <df835b83-2438-4b71-8f07-86303885af16@googlegroups.com>
Message-ID: <bcffc388-b907-4008-afc2-cfee40b87048@googlegroups.com>

Hi everyone,

I'm a little late on this, but I've just used scikit-image with a Raspberry 
Pi project, and I can confirm that everything works fine. I included a 
little installation recipe on the project page:

http://www.aicbt.com/disguise-detection/#program

Neil

On Tuesday, 1 October 2013 07:42:05 UTC+1, Payal Gupta wrote:
>
>
> hello everyone...
>
> my problem solved... 
> thanks to all.... :) :)
>
>
> On Friday, September 27, 2013 12:52:35 PM UTC+5:30, Payal Gupta wrote:
>>
>> hello....
>>
>> i am using skimage library on raspberry pi which have  linux platform but 
>> i cant import skimage module on this.
>>  
>> what do i do?
>> anybody know this prob.
>> reply
>>
>
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From jni.soma at gmail.com  Thu Oct 24 21:45:39 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Fri, 25 Oct 2013 12:45:39 +1100
Subject: Clarity
In-Reply-To: <6f4bd457-cdcf-4e8c-b4d1-f8a523db534f@googlegroups.com>
References: <CA+JHcKSBruYkQq6or1-4iJ_65jLcy26JhWVMf549Bnm8gwsbAA@mail.gmail.com>
 <20131024090322.6a9fc3cf.google@terre-adelie.org> <6f4bd457-cdcf-4e8c-b4d1-f8a523db534f@googlegroups.com>
Message-ID: <CA+JHcKQALbh-RvguGWxhiLf6c2_2YdNk7hTUseG-6kNtRXRqQA@mail.gmail.com>

Thanks Josh, Jerome,

Actually what I'm really after is a good, *local* foreground/background
correction. The local bit is what attracted me to Clarity even though it's
not really what I'm after.

Particularly of interest is something that will be robust to artifacts in
the images.

Juan.

On Fri, Oct 25, 2013 at 10:13 AM, Josh Warner <silvertrumpet999 at gmail.com>wrote:

> I think that's on the right track.
>
> But a naive contrast mask affects only the luminance. In the first example
> the colors are also very punched up; just looking this seems like more than
> a simple global contrast mask.
>
> My guess? They're applying the equivalent of a contrast mask, but to each
> RGB channel separately. This is "wrong" from an image processing
> perspective, but in the world of Instagram it seems people are more
> interested in filters than reality.
>
> I wouldn't be against this for advertising purposes, though I'd never do
> it to my own images.
>
> On Thursday, October 24, 2013 2:03:22 AM UTC-5, Jerome Kieffer wrote:
>
>> On Thu, 24 Oct 2013 17:27:55 +1100
>> Juan Nunez-Iglesias <jni.... at gmail.com> wrote:
>>
>> > Hi guys,
>> >
>> > Does anyone here have any ideas about what the Camera+ Clarity filter
>> is
>> > doing? Some examples of the filter
>> > here<https://secure.flickr.**com/photos/pierrewikberg/**6983939966/<https://secure.flickr.com/photos/pierrewikberg/6983939966/>>and
>>
>> > here <http://obamapacman.com/2011/**03/enhance-iphone-camera-**
>> clarity-video/<http://obamapacman.com/2011/03/enhance-iphone-camera-clarity-video/>>.
>>
>> >
>> > Might be a nice addition to skimage.exposure... =)
>>
>> Looks like a contrast mask:
>> http://www.gimp.org/tutorials/**ContrastMask/<http://www.gimp.org/tutorials/ContrastMask/>
>>
>> Here is an old implementation, starting from a JPEG:
>>     def contrastMask(self, outfile):
>>         """Ceci est un filtre de debouchage de photographies, aussi
>> appel? masque de contraste,
>>         il permet de rattrapper une photo trop contrast?, un contre jour,
>> ...
>>         ?crit par J?r?me Kieffer, avec l'aide de la liste python at aful,
>>         en particulier A. Fayolles et F. Mantegazza avril 2006
>>         necessite numpy et PIL.
>>
>>         @param: the name of the output file (JPEG)
>>         @return: filtered Photo instance
>>         """
>>
>>         try:
>>             import numpy
>> #            import scipy.signal as signal
>>         except:
>>             logger.error("This filter needs the numpy library available
>> on https://sourceforge.net/**projects/numpy/files/<https://sourceforge.net/projects/numpy/files/>")
>>
>>             return
>>
>>         t0 = time.time()
>>         dimX, dimY = self.pil.size
>>
>>         ImageFile.MAXBLOCK = dimX * dimY
>>         img_array = numpy.fromstring(self.pil.**tostring(),
>> dtype="UInt8").astype("**float32")
>>         img_array.shape = (dimY, dimX, 3)
>>         red, green, blue = img_array[:, :, 0], img_array[:, :, 1],
>> img_array[:, :, 2]
>>         #nota: this is faster than desat2=(ar.max(axis=2)+ar.min(**axis=2))/2
>>
>>         desat_array = (numpy.minimum(numpy.minimum(**red, green), blue)
>> + numpy.maximum(numpy.maximum(**red, green), blue)) / 2.0
>>         inv_desat = 255. - desat_array
>>         blured_inv_desat = self._gaussian.blur(inv_desat, config.**ContrastMaskGaussianSize)
>>
>>         bisi = numpy.round(blured_inv_desat).**astype("uint8")
>>         k = Image.fromarray(bisi, "L").convert("RGB")
>>         S = ImageChops.screen(self.pil, k)
>>         M = ImageChops.multiply(self.pil, k)
>>         F = ImageChops.add(ImageChops.**multiply(self.pil, S),
>> ImageChops.multiply(**ImageChops.invert(self.pil), M))
>>         exitJpeg = op.join(config.**DefaultRepository, outfile)
>>         F.save(exitJpeg, quality=80, progressive=True, Optimize=True)
>>         try:
>>             os.chmod(exitJpeg, config.DefaultFileMode)
>>         except IOError:
>>             logger.error("Unable to chmod %s" % outfile)
>>         exifJpeg = Exif(exitJpeg)
>>         exifJpeg.read()
>>         self.exif.copy(exifJpeg)
>>         exifJpeg.comment = self.exif.comment
>>
>> --
>> Jerome Kieffer <goo... at terre-adelie.org>
>>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>
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From stefan at sun.ac.za  Fri Oct 25 12:35:10 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Fri, 25 Oct 2013 18:35:10 +0200
Subject: import error on linux
In-Reply-To: <bcffc388-b907-4008-afc2-cfee40b87048@googlegroups.com>
References: <CAE5Ny9t1UMbvDOO+zrTR0NMasvP41QsjoG2gnsat5KPTHuMi_A@mail.gmail.com>
 <df835b83-2438-4b71-8f07-86303885af16@googlegroups.com> <bcffc388-b907-4008-afc2-cfee40b87048@googlegroups.com>
Message-ID: <CABDkGQnsMoznFQpWzmS-0n1_rAZdXXz5kjFtS73MkynqQOWzmA@mail.gmail.com>

On Fri, Oct 25, 2013 at 3:37 PM, Neil <yager.neil at gmail.com> wrote:
> I'm a little late on this, but I've just used scikit-image with a Raspberry
> Pi project, and I can confirm that everything works fine. I included a
> little installation recipe on the project page:
>
> http://www.aicbt.com/disguise-detection/#program

What a fun project!  You could perhaps even use skimage.transform to
help with the calibration.

St?fan


From stefan at sun.ac.za  Fri Oct 25 13:05:02 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Fri, 25 Oct 2013 19:05:02 +0200
Subject: Clarity
In-Reply-To: <CAJU8MvQC2-aDouYQkyRjOG5TyQweB2xx076DhHtufnp+XLNZcw@mail.gmail.com>
References: <CA+JHcKSBruYkQq6or1-4iJ_65jLcy26JhWVMf549Bnm8gwsbAA@mail.gmail.com>
 <20131024090322.6a9fc3cf.google@terre-adelie.org> <6f4bd457-cdcf-4e8c-b4d1-f8a523db534f@googlegroups.com>
 <CA+JHcKQALbh-RvguGWxhiLf6c2_2YdNk7hTUseG-6kNtRXRqQA@mail.gmail.com> <CAJU8MvQC2-aDouYQkyRjOG5TyQweB2xx076DhHtufnp+XLNZcw@mail.gmail.com>
Message-ID: <CABDkGQ=v9HiJYM-NkBEvE_EAxucJJR9D1Vs9-EH=RfxygVpA0g@mail.gmail.com>

On Fri, Oct 25, 2013 at 4:35 AM, Matthew Trentacoste <mt at matttrent.com> wrote:
> Some of the best of breed work on this topic is by Sylvain Paris, a
> researcher also at Adobe:
> http://people.csail.mit.edu/sparis/publi/2011/siggraph/

That looks really neat!

A little bit tongue in cheek:

http://nbviewer.ipython.org/urls/gist.github.com/stefanv/7158075/raw/0418080161f044ce11ba229ed5f58a860afbd7fd/gistfile1.txt

St?fan


From orieux at iap.fr  Fri Oct 25 17:59:48 2013
From: orieux at iap.fr (=?utf-8?Q?Fran=C3=A7ois?= Orieux)
Date: Fri, 25 Oct 2013 23:59:48 +0200
Subject: Image deconvolution submission
In-Reply-To: <DDBBC907-EE47-4C4A-95B9-1B76AC6AD0F5@gmail.com>
References: <8738nrngt3.fsf@gaia.iap.fr> <DDBBC907-EE47-4C4A-95B9-1B76AC6AD0F5@gmail.com>
Message-ID: <87bo2d106j.fsf@gaia.iap.fr>

Christoph Deil <deil.christoph at googlemail.com> writes:
> On Oct 24, 2013, at 11:45 AM, Fran?ois Orieux <orieux at iap.fr> wrote:
>> I plan to submit image deconvolution algorithms to skimage. Before the
>> pull request and peer review of the code I contact the mailing for a
>> first reaction and comments.
>
> When you make the pull request, please mention it here. I'm definitely
> interested to try it out.

Done !

https://github.com/scikit-image/scikit-image/pull/800

I'm clearly open to any suggestion to results in inclusion.

Regards, Fran?ois

-- 
IAP, CNRS-UPMC - Paris, France
+33 1 73 77 55 11
http://research.orieux.fr


From yager.neil at gmail.com  Sat Oct 26 04:06:49 2013
From: yager.neil at gmail.com (Neil)
Date: Sat, 26 Oct 2013 01:06:49 -0700 (PDT)
Subject: import error on linux
In-Reply-To: <CABDkGQnsMoznFQpWzmS-0n1_rAZdXXz5kjFtS73MkynqQOWzmA@mail.gmail.com>
References: <CAE5Ny9t1UMbvDOO+zrTR0NMasvP41QsjoG2gnsat5KPTHuMi_A@mail.gmail.com>
 <df835b83-2438-4b71-8f07-86303885af16@googlegroups.com> <bcffc388-b907-4008-afc2-cfee40b87048@googlegroups.com>
 <CABDkGQnsMoznFQpWzmS-0n1_rAZdXXz5kjFtS73MkynqQOWzmA@mail.gmail.com>
Message-ID: <bb9b302b-3e80-41d2-956f-56c82cae37b3@googlegroups.com>

Good idea - using transform.AffineTransform is much nicer. Updated.

Thanks, yes, it was a really fun project. I've always been on the software 
side, but there's a huge maker/DIY movement going on in 
hardware/electronics at the moment. Lots of cool opportunities for embedded 
image processing & computer vision applications. 

On Friday, 25 October 2013 17:35:10 UTC+1, Stefan van der Walt wrote:
>
> On Fri, Oct 25, 2013 at 3:37 PM, Neil <yager... at gmail.com <javascript:>> 
> wrote: 
> > I'm a little late on this, but I've just used scikit-image with a 
> Raspberry 
> > Pi project, and I can confirm that everything works fine. I included a 
> > little installation recipe on the project page: 
> > 
> > http://www.aicbt.com/disguise-detection/#program 
>
> What a fun project!  You could perhaps even use skimage.transform to 
> help with the calibration. 
>
> St?fan 
>
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From nhv at cape.com  Sat Oct 26 11:00:55 2013
From: nhv at cape.com (Norman Vine)
Date: Sat, 26 Oct 2013 11:00:55 -0400
Subject: Clarity
In-Reply-To: <CA+JHcKSBruYkQq6or1-4iJ_65jLcy26JhWVMf549Bnm8gwsbAA@mail.gmail.com>
References: <CA+JHcKSBruYkQq6or1-4iJ_65jLcy26JhWVMf549Bnm8gwsbAA@mail.gmail.com>
Message-ID: <C55050B2-AED9-4138-B431-46D8B669C7B8@cape.com>


On Oct 24, 2013, at 2:27 AM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:

> Hi guys,
> 
> Does anyone here have any ideas about what the Camera+ Clarity filter is doing? Some examples of the filter here and here.
> 
> Might be a nice addition to skimage.exposure... =)
> 
> Juan.
> 

see
http://code.google.com/p/imagestack/wiki/locallaplacian
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From jsch at demuc.de  Sun Oct 27 03:34:43 2013
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Sun, 27 Oct 2013 08:34:43 +0100
Subject: Release time
In-Reply-To: <CABDkGQ=9Zx=xT5nuy7bQ4ocJE40eoDsjYt1-ObgF7pBhF7Ohgw@mail.gmail.com>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com> <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com> <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de> <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com> <583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de> <CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com> <9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de> <3370D65E-B530-4B57-B71D-AC8549A7791B@demuc.de> <CAF+hgui_p38G0duCHNCez85xa0ThkP9modmnESqEerxfyhy88A@mail.gmail.com> <CABDkGQkQNHUB=UVZzMsssanpqDqmMURNbSZ-iaW8vFKboQK_oA@mail.gmail.com> <524C4E05.4030408@sciunto.org> <6B47F231-F251-469D-9EC7-2BB1D9317992@demuc.de> <CABDkGQ=3ZSGxqqEfuvfGDwezmK9x-bfM0zy3AUOQRnCDaydpcg@mail.gmail.com> <65c13bd3-b5a7-4606-b67b-83d862082125@googlegroups.com> <D778DFBE-8C62-466A-B92F-005BD03C28A9@demuc.de> <F1D6BCC0-F232-4FF3-BF24-3A15581D38F9@demuc.de> <4AD1AFF6-40E7-470D-AEE1-918E1FECEC02@demuc.de> <CABDkGQm1qxrGHGb1=1DH1Br33HmpeKFp7O-VEWJ=g1PLOBt8Kw@mail.gmail.com> <29349511-94C6-49DD-8BE1-2790ACF6C253@demuc.de> <CABDkGQmwLH6ZQaD0AF=5-DJGEB0Q-ybtpkE6pwwE2P4Ma-_6AQ@mail.gmail.com> <CA+JHcKS2drzT7xUaReZH=kw_8Ku-BMPkYFT6RCcFM_qywRLADw@mail.gmail.com> <CAON2ciJAtVYffHaHeqyhEZATBFU3LwOiVQ8dcHEgP5Zf_qhdCw@mail.gmail.com> <CABDkGQ=9Zx=xT5nuy7bQ4ocJE40eoDsjYt1-ObgF7pBhF7Ohgw@mail.gmail.com>
Message-ID: <C6941654-982F-4F45-8E3F-41801E421170@demuc.de>

Updated to 0.9.3 with a small bugfix.

	https://pypi.python.org/pypi/scikit-image

Am 19.10.2013 um 14:34 schrieb St?fan van der Walt <stefan at sun.ac.za>:

> On Sat, Oct 19, 2013 at 12:37 PM, Ankit Agrawal <aaaagrawal at gmail.com> wrote:
>> Any updates about the 0.9 release?
> 
> Just waiting for GitHub to come back online to push the tags.
> 
> St?fan
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
> 



From stefan at sun.ac.za  Sun Oct 27 04:55:09 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 27 Oct 2013 10:55:09 +0200
Subject: Release time
In-Reply-To: <C6941654-982F-4F45-8E3F-41801E421170@demuc.de>
References: <CABDkGQ=QgL6+8xy2oVQ1pTrcQnoWN=vzU8590K+eNrpYgEOuvw@mail.gmail.com>
 <178F8EDE-A4CA-406F-A5E7-AA658AE9E5BB@demuc.de> <CABDkGQmOU9BMPQ3b3m2voD0eNc9yfzS+s-6a1WAf0oXDobUeDw@mail.gmail.com>
 <C6DC3903-6AFC-40FD-8B73-BED327691522@demuc.de> <CABDkGQ=cgMfLSDmw1Q+p9A3BfAOnEBb4DVTtu01nCpAHDCFQNA@mail.gmail.com>
 <583BBF3D-5699-4FC1-BE86-6E06C8640F76@demuc.de> <CABDkGQmYsBD86Lq8CLZTV_PZyCZ-ZAOmxPgVkU0tndosOW9bCg@mail.gmail.com>
 <9874287C-C7E6-4C97-8F8E-79D64A70CA58@demuc.de> <3370D65E-B530-4B57-B71D-AC8549A7791B@demuc.de>
 <CAF+hgui_p38G0duCHNCez85xa0ThkP9modmnESqEerxfyhy88A@mail.gmail.com>
 <CABDkGQkQNHUB=UVZzMsssanpqDqmMURNbSZ-iaW8vFKboQK_oA@mail.gmail.com>
 <524C4E05.4030408@sciunto.org> <6B47F231-F251-469D-9EC7-2BB1D9317992@demuc.de>
 <CABDkGQ=3ZSGxqqEfuvfGDwezmK9x-bfM0zy3AUOQRnCDaydpcg@mail.gmail.com>
 <65c13bd3-b5a7-4606-b67b-83d862082125@googlegroups.com> <D778DFBE-8C62-466A-B92F-005BD03C28A9@demuc.de>
 <F1D6BCC0-F232-4FF3-BF24-3A15581D38F9@demuc.de> <4AD1AFF6-40E7-470D-AEE1-918E1FECEC02@demuc.de>
 <CABDkGQm1qxrGHGb1=1DH1Br33HmpeKFp7O-VEWJ=g1PLOBt8Kw@mail.gmail.com>
 <29349511-94C6-49DD-8BE1-2790ACF6C253@demuc.de> <CABDkGQmwLH6ZQaD0AF=5-DJGEB0Q-ybtpkE6pwwE2P4Ma-_6AQ@mail.gmail.com>
 <CA+JHcKS2drzT7xUaReZH=kw_8Ku-BMPkYFT6RCcFM_qywRLADw@mail.gmail.com>
 <CAON2ciJAtVYffHaHeqyhEZATBFU3LwOiVQ8dcHEgP5Zf_qhdCw@mail.gmail.com>
 <CABDkGQ=9Zx=xT5nuy7bQ4ocJE40eoDsjYt1-ObgF7pBhF7Ohgw@mail.gmail.com> <C6941654-982F-4F45-8E3F-41801E421170@demuc.de>
Message-ID: <CABDkGQkmixWa1GKg+myH2hJ6DksV9Q9Jhh+gSudYdBAQz=o4JA@mail.gmail.com>

On Sun, Oct 27, 2013 at 9:34 AM, Johannes Sch?nberger <jsch at demuc.de> wrote:
> Updated to 0.9.3 with a small bugfix.
>
>         https://pypi.python.org/pypi/scikit-image

Thanks, Johannes.  I am working on finalizing the Debian packaging.

St?fan


From jni.soma at gmail.com  Sun Oct 27 05:19:06 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Sun, 27 Oct 2013 20:19:06 +1100
Subject: Clarity
In-Reply-To: <CABDkGQ=v9HiJYM-NkBEvE_EAxucJJR9D1Vs9-EH=RfxygVpA0g@mail.gmail.com>
References: <CA+JHcKSBruYkQq6or1-4iJ_65jLcy26JhWVMf549Bnm8gwsbAA@mail.gmail.com>
 <20131024090322.6a9fc3cf.google@terre-adelie.org> <6f4bd457-cdcf-4e8c-b4d1-f8a523db534f@googlegroups.com>
 <CA+JHcKQALbh-RvguGWxhiLf6c2_2YdNk7hTUseG-6kNtRXRqQA@mail.gmail.com>
 <CAJU8MvQC2-aDouYQkyRjOG5TyQweB2xx076DhHtufnp+XLNZcw@mail.gmail.com> <CABDkGQ=v9HiJYM-NkBEvE_EAxucJJR9D1Vs9-EH=RfxygVpA0g@mail.gmail.com>
Message-ID: <CA+JHcKRxmCZ+TJyFOL08_apepMmGQC8s3U_Nbm8=y3PEM8bHiA@mail.gmail.com>

On Sat, Oct 26, 2013 at 4:05 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> A little bit tongue in cheek:
>
>
> http://nbviewer.ipython.org/urls/gist.github.com/stefanv/7158075/raw/0418080161f044ce11ba229ed5f58a860afbd7fd/gistfile1.txt
>

Awesome! =)
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From stefan at sun.ac.za  Sun Oct 27 16:55:17 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 27 Oct 2013 22:55:17 +0200
Subject: CIELUV Transformations
In-Reply-To: <CAPOWHWkC5uVLgsph2EW2ccV=eSa2Qv4oLhbYBB26oQpae3CSbw@mail.gmail.com>
References: <b20c6a2c-fe5f-43e5-b7ac-ebebde42724b@googlegroups.com>
 <CABDkGQmR6ZtVOdQZMKxgvSmYoeCbCp==KR+6w_+nGyLLN9jwwg@mail.gmail.com>
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 <9450c9e5-5951-421b-92fe-c159ccbdbef1@googlegroups.com> <0e4613db-ea50-4342-962c-20d1a8e8dd90@googlegroups.com>
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 <CADnN3yWWNLo1Yn=cF=t7mSq4aXgVdtO2udSuHpQxF8gpywFS8g@mail.gmail.com>
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Message-ID: <CABDkGQnAM2y8ErbE6D2NNP=JgAVfNswfzwoemJ43-MiDpXCujg@mail.gmail.com>

On Wed, Oct 23, 2013 at 5:56 PM, Jaime Fern?ndez del R?o
<jaime.frio at gmail.com> wrote:
> So, who's up for coding CIECAM02 color transformations, whatever that may
> be? ;-)

Let's see.  We need someone who understands the intricacies of color
spaces.  Now who could that be?

Thank you in advance!

St?fan


From kmichael.aye at gmail.com  Mon Oct 28 18:59:07 2013
From: kmichael.aye at gmail.com (Michael Aye)
Date: Mon, 28 Oct 2013 15:59:07 -0700 (PDT)
Subject: Kakadu JP2000 reader
Message-ID: <b0ab6704-f2c2-48c9-9fde-d904f198c59c@googlegroups.com>

Hi!
I was wondering if it would be possible to implement the Kakadu JP2000 
reader into scikit-image? I believe but am not sure that the reader only 
could be used without licensing fees? At least it's worth investigating 
because that reader is really the most powerful JP2000 reader out there and 
the only one that can deal with the large HiRISE images of the MRO 
spacecraft.
Failing the above, a work-around could be to implement or encapsulate 
system calls to the freely downloadable kdu-expand utilities, converting it 
to something that is compatible with your current import routines?

Best regards,
Michael
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From silvertrumpet999 at gmail.com  Mon Oct 28 19:25:54 2013
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Mon, 28 Oct 2013 16:25:54 -0700 (PDT)
Subject: Returning an image from the viewer
In-Reply-To: <CA+JHcKTfpiC8ADpquU6TfH0vjX1YSaDQR69SO34HbZXHd41UCA@mail.gmail.com>
References: <CA+JHcKTfpiC8ADpquU6TfH0vjX1YSaDQR69SO34HbZXHd41UCA@mail.gmail.com>
Message-ID: <e825243b-5db6-405c-a4dd-409c54efe37f@googlegroups.com>

There was some discussion about the save functionality in the original PR. 
I admit, I advocated to change "File -> Save As" from saving the overlay to 
saving the actual image the user sees... so feel free to send some blame 
for the present behavior my way.

There should be an option to add a Save Overlay *button* which should allow 
you to grab the overlay specifically. As to your second question: I think 
you can send data either to a file, or to a buffer which can be read out 
using `skimage.io.pop`. I've used this before, but my memory is a bit fuzzy 
on it now. If this isn't currently available for scripting like your 
hoped-for functionality example, I'm sure it could be implemented.

Thanks for the PR fixing the save dialog if it's RGB!


On Monday, October 28, 2013 2:19:03 AM UTC-5, Juan Nunez-Iglesias wrote:
>
> Hi all, but especially @tonysyu:
>
> I'm using the viewer for the first time to add some interactivity to my 
> work. Please forgive the noobish-ness: I've only ever worked on 
> command-line stuff. (Thanks btw to @tonysyu for his awesome SciPy lightning 
> talk, which inspired me to even dip my toes in this!)
>
> I'm running an RGB image through a bunch of thresholding and morphological 
> operations, and I want to fiddle with the parameters before getting back 
> the filter output. I'm running into the following problems:
>
> 1) The file > save as dialog saves a composite image of the overlay and 
> underlying image, where I just want the overlay.
> 2) The file > save as dialog actually crashes when the underlying image is 
> RGB! (PR forthcoming)
> 3) But most of all, I don't actually want to save the overlay, I just want 
> to return it to the calling process. How would one go about this? Here's my 
> code now:
>
> v = viewer.ImageViewer(rgbs[0])
> v += CentroPlugin()
> v.show()
>
>
> which works as expected. I'd like something like:
>
> v = viewer.ImageViewer(rgbs[0])
> v += CentroPlugin()
> overlay = v.show()
>
> Is this possible?
>
> Thanks,
>
> Juan.
>
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From jni.soma at gmail.com  Mon Oct 28 03:19:03 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Mon, 28 Oct 2013 18:19:03 +1100
Subject: Returning an image from the viewer
Message-ID: <CA+JHcKTfpiC8ADpquU6TfH0vjX1YSaDQR69SO34HbZXHd41UCA@mail.gmail.com>

Hi all, but especially @tonysyu:

I'm using the viewer for the first time to add some interactivity to my
work. Please forgive the noobish-ness: I've only ever worked on
command-line stuff. (Thanks btw to @tonysyu for his awesome SciPy lightning
talk, which inspired me to even dip my toes in this!)

I'm running an RGB image through a bunch of thresholding and morphological
operations, and I want to fiddle with the parameters before getting back
the filter output. I'm running into the following problems:

1) The file > save as dialog saves a composite image of the overlay and
underlying image, where I just want the overlay.
2) The file > save as dialog actually crashes when the underlying image is
RGB! (PR forthcoming)
3) But most of all, I don't actually want to save the overlay, I just want
to return it to the calling process. How would one go about this? Here's my
code now:

v = viewer.ImageViewer(rgbs[0])
v += CentroPlugin()
v.show()


which works as expected. I'd like something like:

v = viewer.ImageViewer(rgbs[0])
v += CentroPlugin()
overlay = v.show()

Is this possible?

Thanks,

Juan.
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From tsyu80 at gmail.com  Tue Oct 29 00:07:10 2013
From: tsyu80 at gmail.com (Tony Yu)
Date: Mon, 28 Oct 2013 23:07:10 -0500
Subject: Returning an image from the viewer
In-Reply-To: <e825243b-5db6-405c-a4dd-409c54efe37f@googlegroups.com>
References: <CA+JHcKTfpiC8ADpquU6TfH0vjX1YSaDQR69SO34HbZXHd41UCA@mail.gmail.com>
 <e825243b-5db6-405c-a4dd-409c54efe37f@googlegroups.com>
Message-ID: <CAEym_HoQZDpBXDJh_FKD8hY6E8xm5hjNAVx86zDWL3Z08zpfGg@mail.gmail.com>

On Mon, Oct 28, 2013 at 6:25 PM, Josh Warner <silvertrumpet999 at gmail.com>wrote:

> There was some discussion about the save functionality in the original PR.
> I admit, I advocated to change "File -> Save As" from saving the overlay to
> saving the actual image the user sees... so feel free to send some blame
> for the present behavior my way.
>
> There should be an option to add a Save Overlay *button* which should
> allow you to grab the overlay specifically. As to your second question: I
> think you can send data either to a file, or to a buffer which can be read
> out using `skimage.io.pop`. I've used this before, but my memory is a bit
> fuzzy on it now. If this isn't currently available for scripting like your
> hoped-for functionality example, I'm sure it could be implemented.
>
> Thanks for the PR fixing the save dialog if it's RGB!
>
>
> On Monday, October 28, 2013 2:19:03 AM UTC-5, Juan Nunez-Iglesias wrote:
>>
>> Hi all, but especially @tonysyu:
>>
>> I'm using the viewer for the first time to add some interactivity to my
>> work. Please forgive the noobish-ness: I've only ever worked on
>> command-line stuff. (Thanks btw to @tonysyu for his awesome SciPy lightning
>> talk, which inspired me to even dip my toes in this!)
>>
>> I'm running an RGB image through a bunch of thresholding and
>> morphological operations, and I want to fiddle with the parameters before
>> getting back the filter output. I'm running into the following problems:
>>
>> 1) The file > save as dialog saves a composite image of the overlay and
>> underlying image, where I just want the overlay.
>> 2) The file > save as dialog actually crashes when the underlying image
>> is RGB! (PR forthcoming)
>> 3) But most of all, I don't actually want to save the overlay, I just
>> want to return it to the calling process. How would one go about this?
>> Here's my code now:
>>
>> v = viewer.ImageViewer(rgbs[0])
>> v += CentroPlugin()
>> v.show()
>>
>>
>> which works as expected. I'd like something like:
>>
>> v = viewer.ImageViewer(rgbs[0])
>> v += CentroPlugin()
>> overlay = v.show()
>>
>> Is this possible?
>>
>
I'm sure this is possible, but I'd have to think a bit about the right way
to implement this. Currently, the viewer knows very little about the
plugins, and overlays are drawn in a different layer than the image. It's
definitely possible to retrieve the overlay from the viewer object, but I'm
not sure how to do it cleanly.

That said, I don't know why I didn't think to return an image from the
viewer. Thanks for the idea:

https://github.com/scikit-image/scikit-image/pull/805

-T


>
>> Thanks,
>>
>> Juan.
>>
>  --
> You received this message because you are subscribed to the Google Groups
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From jni.soma at gmail.com  Tue Oct 29 00:05:59 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Tue, 29 Oct 2013 15:05:59 +1100
Subject: Returning an image from the viewer
In-Reply-To: <e825243b-5db6-405c-a4dd-409c54efe37f@googlegroups.com>
References: <CA+JHcKTfpiC8ADpquU6TfH0vjX1YSaDQR69SO34HbZXHd41UCA@mail.gmail.com>
 <e825243b-5db6-405c-a4dd-409c54efe37f@googlegroups.com>
Message-ID: <CA+JHcKQNjnDmW1V-6Fr+Hgr7GVhSduBgx0hvFGWsOg9kF1gUyg@mail.gmail.com>

Thanks Josh!

On Tue, Oct 29, 2013 at 10:25 AM, Josh Warner <silvertrumpet999 at gmail.com>wrote:

> There was some discussion about the save functionality in the original PR.
> I admit, I advocated to change "File -> Save As" from saving the overlay to
> saving the actual image the user sees... so feel free to send some blame
> for the present behavior my way.
>

I can see both use cases. The solution, imho, is to have two menu items,
"save displayed as" and "save overlay as". I'll make a separate PR for that
function. =)

There should be an option to add a Save Overlay *button* which should allow
> you to grab the overlay specifically.
>

I thought about that but wasn't able to wrap my head around how to do that
before asking for help here. =)


>  As to your second question: I think you can send data either to a file,
> or to a buffer which can be read out using `skimage.io.pop`. I've used this
> before, but my memory is a bit fuzzy on it now. If this isn't currently
> available for scripting like your hoped-for functionality example, I'm sure
> it could be implemented.
>

I saw a comment in the code saying something similar to "this doesn't work
for interactive sessions", which scared me off it a little bit. But I'll
look into that option, which seems most suited to my needs.

Thanks for the PR fixing the save dialog if it's RGB!
>

No worries! Hopefully it'll get reviewed soon... ;)
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