From simone at codeluppi.org  Thu Aug  7 11:23:42 2014
From: simone at codeluppi.org (Simone Codeluppi)
Date: Thu, 7 Aug 2014 08:23:42 -0700 (PDT)
Subject: blid deconvolution
Message-ID: <3f890543-e956-4cfe-9101-b6508a150c1c@googlegroups.com>



I am working on a pipeline to process microscopy images. Each image is a 
stack of tiff planes and I would like to run deconvolution on the stack 
however I don't have the information about the psf. So far I have been 
using the matlab function deconvblind 
<http://www.mathworks.se/help/images/deblurring-with-the-blind-deconvolution-algorithm.html>. 
I digged into the scikit-image restoration.modules and the one described 
works fine but all require the psf. The description of the deconvblind in 
matlab says

*The algorithm maximizes the likelihood that the resulting image, when 
convolved with the resulting PSF, is an instance of the blurred image, 
assuming Poisson noise statistics.*

Is there a way I can implement this algorithm in python then estimate the 
psf and use one of the restoration.modules provided by scikit-image?

Thanks
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From stefan at sun.ac.za  Thu Aug  7 11:38:10 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Thu, 7 Aug 2014 17:38:10 +0200
Subject: blid deconvolution
In-Reply-To: <3f890543-e956-4cfe-9101-b6508a150c1c@googlegroups.com>
References: <3f890543-e956-4cfe-9101-b6508a150c1c@googlegroups.com>
Message-ID: <CABDkGQ=e_6azWSuyBL0hFrWYVfcUNXOJzX7gDVdH2h-Q2VaCsw@mail.gmail.com>

Hi Simone

On Thu, Aug 7, 2014 at 5:23 PM, Simone Codeluppi <simone at codeluppi.org> wrote:
> The algorithm maximizes the likelihood that the resulting image, when
> convolved with the resulting PSF, is an instance of the blurred image,
> assuming Poisson noise statistics.
>
> Is there a way I can implement this algorithm in python then estimate the
> psf and use one of the restoration.modules provided by scikit-image?

We don't currently have any PSF estimation implemented, but would be
interested in such an addition.

Also, are you sure you need deconvolution?  How are your images
formed, and what is the effect that you are trying to rectify?  What
happens throughout the stack--does the focus vary?

St?fan


From matthew.brett at gmail.com  Thu Aug  7 21:55:52 2014
From: matthew.brett at gmail.com (Matthew Brett)
Date: Thu, 7 Aug 2014 18:55:52 -0700
Subject: We need help working on code coverage for Cython code
Message-ID: <CAH6Pt5qEvD6=QqSaxDXWY9+1fxcA4bRMGEb4MqbZQACtvuNX4Q@mail.gmail.com>

Hi,

Over on another mailing list, we've hit a big problem trying to work
out coverage on a large amount of Cython code.

As y'all probably know, there's no automated way of checking code
coverage on Cython code at the moment.

The Cython developers have done some work on this [1] but it is
currently stalled for lack of developer time to work on it.

We'd really like to get this working, and the Cython developers have
offered to help, to get this started.

Can anyone help us out by a) joining an interactive discussion for 15
minutes or so with the Cython developers to get us started b) helping
with a short burst of coding that will follow, we estimate a few days.

I think this is something many of us need, and it would also be a
thank you to the Cython team for their work, which we all use so much.

Cheers,

Matthew

[1] http://trac.cython.org/cython_trac/ticket/815


From jni.soma at gmail.com  Fri Aug  8 01:53:55 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Fri, 8 Aug 2014 15:53:55 +1000
Subject: We need help working on code coverage for Cython code
In-Reply-To: <CAH6Pt5qEvD6=QqSaxDXWY9+1fxcA4bRMGEb4MqbZQACtvuNX4Q@mail.gmail.com>
References: <CAH6Pt5qEvD6=QqSaxDXWY9+1fxcA4bRMGEb4MqbZQACtvuNX4Q@mail.gmail.com>
Message-ID: <CA+JHcKQYy8n+hXgmhgNcfRi7LkrJyvWNEsKF1R56AOYyLySf5w@mail.gmail.com>

A honking good idea!

... But I am very much flat out for the next 2-3 months, so I will have to
watch from the sidelines...

Thank you!

Juan.


On Fri, Aug 8, 2014 at 11:55 AM, Matthew Brett <matthew.brett at gmail.com>
wrote:

> Hi,
>
> Over on another mailing list, we've hit a big problem trying to work
> out coverage on a large amount of Cython code.
>
> As y'all probably know, there's no automated way of checking code
> coverage on Cython code at the moment.
>
> The Cython developers have done some work on this [1] but it is
> currently stalled for lack of developer time to work on it.
>
> We'd really like to get this working, and the Cython developers have
> offered to help, to get this started.
>
> Can anyone help us out by a) joining an interactive discussion for 15
> minutes or so with the Cython developers to get us started b) helping
> with a short burst of coding that will follow, we estimate a few days.
>
> I think this is something many of us need, and it would also be a
> thank you to the Cython team for their work, which we all use so much.
>
> Cheers,
>
> Matthew
>
> [1] http://trac.cython.org/cython_trac/ticket/815
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From ralf.gommers at gmail.com  Tue Aug 12 15:19:09 2014
From: ralf.gommers at gmail.com (Ralf Gommers)
Date: Tue, 12 Aug 2014 21:19:09 +0200
Subject: We need help working on code coverage for Cython code
In-Reply-To: <CAH6Pt5qEvD6=QqSaxDXWY9+1fxcA4bRMGEb4MqbZQACtvuNX4Q@mail.gmail.com>
References: <CAH6Pt5qEvD6=QqSaxDXWY9+1fxcA4bRMGEb4MqbZQACtvuNX4Q@mail.gmail.com>
Message-ID: <CABL7CQjKHyRMvPKwdrd7-2VuD61qje84cLFt2zBQVaAX2DQoYg@mail.gmail.com>

Hi Matthew,

On Fri, Aug 8, 2014 at 3:55 AM, Matthew Brett <matthew.brett at gmail.com>
wrote:

> Hi,
>
> Over on another mailing list, we've hit a big problem trying to work
> out coverage on a large amount of Cython code.
>
> As y'all probably know, there's no automated way of checking code
> coverage on Cython code at the moment.
>
> The Cython developers have done some work on this [1] but it is
> currently stalled for lack of developer time to work on it.
>
> We'd really like to get this working, and the Cython developers have
> offered to help, to get this started.
>

Would be great to get this working.

Can anyone help us out by a) joining an interactive discussion for 15
> minutes or so with the Cython developers to get us started b) helping
> with a short burst of coding that will follow, we estimate a few days.
>

This request isn't scikit-image specific, is it? Maybe you can ask on the
numpy mailing list to get more responses?

Cheers,
Ralf


I think this is something many of us need, and it would also be a
> thank you to the Cython team for their work, which we all use so much.
>
> Cheers,
>
> Matthew
>
> [1] http://trac.cython.org/cython_trac/ticket/815
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From jsch at demuc.de  Thu Aug 14 07:38:19 2014
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=0F=F6nberger?=)
Date: Thu, 14 Aug 2014 07:38:19 -0400
Subject: Release notes
Message-ID: <766B7CF2-CE8D-4F1E-9DAA-3381EC7EF59C@demuc.de>

Hi everyone,

Just a reminder: before merging a PR in the future, we want to make sure, that the changes are documented in `doc/release/release_dev.txt`.

Johannes Sch?nberger



From njs at vorpus.org  Thu Aug 14 11:09:47 2014
From: njs at vorpus.org (njs at vorpus.org)
Date: Thu, 14 Aug 2014 08:09:47 -0700 (PDT)
Subject: FYI - implementation of CIECAM02 in Python
Message-ID: <5320c2d5-a9e2-4dad-9232-820491353f61@googlegroups.com>

Hi scikit-imageers,

I don't have time to prepare a PR, but just as a heads-up in case anyone 
else wants to do so -- I wrote a complete, tested implementation of the 
CIECAM02 forward and inverse transforms in Python (BSD-2), which might be a 
nice extension to skimage.color:
  https://github.com/njsmith/pycam02ucs/blob/master/pycam02ucs/ciecam02.py

I'm pretty confident in its correctness; the only place where it disagrees 
with Mark Fairchild's spreadsheet implementation, it turns out the 
spreadsheet is (was) wrong :-). It could probably be optimized further -- 
it is vectorized, but I didn't go to any great efforts to extract redundant 
temporaries or perform operations in-place. It's a pretty direct 
implementation of the equations.

The API may not be exactly the scikit-image's taste ATM either -- I forget 
whether you prefer to use the 0-1 or 0-100 scale for XYZ (this code uses 
0-100 b/c that's what the spec uses). And CIECAM02 is a weird space -- the 
forward transform spits out 7 named dimensions, and the inverse transform 
needs 3 of these, but is quite flexible about which 3, so I treat each 
dimension as a separate array instead of stacking them into one.

That tree also has an implementation of forward and inverse transforms to 
the CAM02-UCS perceptually uniform space (Luo et al, 2006):
  https://github.com/njsmith/pycam02ucs/blob/master/pycam02ucs/cam02ucs.py

-n
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From hannesschoenberger at gmail.com  Thu Aug 14 11:14:25 2014
From: hannesschoenberger at gmail.com (=?UTF-8?Q?Johannes_Sch=C3=B6nberger?=)
Date: Thu, 14 Aug 2014 08:14:25 -0700 (PDT)
Subject: We need help working on code coverage for Cython code
In-Reply-To: <CAH6Pt5qEvD6=QqSaxDXWY9+1fxcA4bRMGEb4MqbZQACtvuNX4Q@mail.gmail.com>
References: <CAH6Pt5qEvD6=QqSaxDXWY9+1fxcA4bRMGEb4MqbZQACtvuNX4Q@mail.gmail.com>
Message-ID: <37806e72-decf-4349-b88f-2f56331f7ec0@googlegroups.com>

Hi,

This would indeed be a great feature, but unfortunately I am lacking the 
time to contribute to it at the moment and foreseeable future.

Johannes

On Thursday, August 7, 2014 9:56:14 PM UTC-4, Matthew Brett wrote:
>
> Hi, 
>
> Over on another mailing list, we've hit a big problem trying to work 
> out coverage on a large amount of Cython code. 
>
> As y'all probably know, there's no automated way of checking code 
> coverage on Cython code at the moment. 
>
> The Cython developers have done some work on this [1] but it is 
> currently stalled for lack of developer time to work on it. 
>
> We'd really like to get this working, and the Cython developers have 
> offered to help, to get this started. 
>
> Can anyone help us out by a) joining an interactive discussion for 15 
> minutes or so with the Cython developers to get us started b) helping 
> with a short burst of coding that will follow, we estimate a few days. 
>
> I think this is something many of us need, and it would also be a 
> thank you to the Cython team for their work, which we all use so much. 
>
> Cheers, 
>
> Matthew 
>
> [1] http://trac.cython.org/cython_trac/ticket/815 
>
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From tcaswell at gmail.com  Thu Aug 14 14:12:42 2014
From: tcaswell at gmail.com (Thomas Caswell)
Date: Thu, 14 Aug 2014 14:12:42 -0400
Subject: Release notes
In-Reply-To: <CABDkGQnZO9x0et5p=GsXbm8B0LSq3XM8oDfzd9HXvBJx9qGcbg@mail.gmail.com>
References: <766B7CF2-CE8D-4F1E-9DAA-3381EC7EF59C@demuc.de>
	<CABDkGQnZO9x0et5p=GsXbm8B0LSq3XM8oDfzd9HXvBJx9qGcbg@mail.gmail.com>
Message-ID: <CAA48SF-WkW1oOv=U0itOrN8neqdVHVwpf-W+qdZM8ESEeEUq_Q@mail.gmail.com>

As a side note, mpl has been doing something similar and having
everyone work on the same file leads to a stupendous amount of
conflicts.  We are moving to having a folder to create files in and
then re-assembling them at release time.

Tom

On Thu, Aug 14, 2014 at 12:21 PM, St?fan van der Walt <stefan at sun.ac.za> wrote:
> On Thu, Aug 14, 2014 at 1:38 PM, Johannes Sch ?nberger <jsch at demuc.de> wrote:
>> Just a reminder: before merging a PR in the future, we want to make sure, that the changes are documented in `doc/release/release_dev.txt`.
>
> Ouch, good point--thanks for the reminder.
>
> St?fan
>
> --
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.



-- 
Thomas Caswell
tcaswell at gmail.com


From silvertrumpet999 at gmail.com  Thu Aug 14 19:09:26 2014
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Thu, 14 Aug 2014 16:09:26 -0700 (PDT)
Subject: Release notes
In-Reply-To: <B98A67E5-ABE6-473E-8BA5-4AB4956D4FF0@demuc.de>
References: <766B7CF2-CE8D-4F1E-9DAA-3381EC7EF59C@demuc.de> <CABDkGQnZO9x0et5p=GsXbm8B0LSq3XM8oDfzd9HXvBJx9qGcbg@mail.gmail.com> <CAA48SF-WkW1oOv=U0itOrN8neqdVHVwpf-W+qdZM8ESEeEUq_Q@mail.gmail.com>
 <B98A67E5-ABE6-473E-8BA5-4AB4956D4FF0@demuc.de>
Message-ID: <4433053c-3540-41b8-9341-875c08e29c58@googlegroups.com>

+1 from me, avoiding rebases is always positive (and greatly helps those new to Git).

From jsch at demuc.de  Thu Aug 14 17:22:41 2014
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=0F=F6nberger?=)
Date: Thu, 14 Aug 2014 17:22:41 -0400
Subject: Release notes
In-Reply-To: <CAA48SF-WkW1oOv=U0itOrN8neqdVHVwpf-W+qdZM8ESEeEUq_Q@mail.gmail.com>
References: <766B7CF2-CE8D-4F1E-9DAA-3381EC7EF59C@demuc.de> <CABDkGQnZO9x0et5p=GsXbm8B0LSq3XM8oDfzd9HXvBJx9qGcbg@mail.gmail.com> <CAA48SF-WkW1oOv=U0itOrN8neqdVHVwpf-W+qdZM8ESEeEUq_Q@mail.gmail.com>
Message-ID: <B98A67E5-ABE6-473E-8BA5-4AB4956D4FF0@demuc.de>

Thanks for letting us know. I have not thought of this, but I can definitely see this happening in our case as well. Separate files in a subdirectory sound as a good workaround. What do the other think?

Johannes Sch?nberger

On Aug 14, 2014, at 2:12 PM, Thomas Caswell <tcaswell at gmail.com> wrote:

> As a side note, mpl has been doing something similar and having
> everyone work on the same file leads to a stupendous amount of
> conflicts.  We are moving to having a folder to create files in and
> then re-assembling them at release time.
> 
> Tom
> 
> On Thu, Aug 14, 2014 at 12:21 PM, St?fan van der Walt <stefan at sun.ac.za> wrote:
>> On Thu, Aug 14, 2014 at 1:38 PM, Johannes Sch ?nberger <jsch at demuc.de> wrote:
>>> Just a reminder: before merging a PR in the future, we want to make sure, that the changes are documented in `doc/release/release_dev.txt`.
>> 
>> Ouch, good point--thanks for the reminder.
>> 
>> St?fan
>> 
>> --
>> You received this message because you are subscribed to the Google Groups "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
> 
> 
> 
> -- 
> Thomas Caswell
> tcaswell at gmail.com
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.



From stefan at sun.ac.za  Thu Aug 14 12:21:14 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Thu, 14 Aug 2014 18:21:14 +0200
Subject: Release notes
In-Reply-To: <766B7CF2-CE8D-4F1E-9DAA-3381EC7EF59C@demuc.de>
References: <766B7CF2-CE8D-4F1E-9DAA-3381EC7EF59C@demuc.de>
Message-ID: <CABDkGQnZO9x0et5p=GsXbm8B0LSq3XM8oDfzd9HXvBJx9qGcbg@mail.gmail.com>

On Thu, Aug 14, 2014 at 1:38 PM, Johannes Sch ?nberger <jsch at demuc.de> wrote:
> Just a reminder: before merging a PR in the future, we want to make sure, that the changes are documented in `doc/release/release_dev.txt`.

Ouch, good point--thanks for the reminder.

St?fan


From stefan at sun.ac.za  Fri Aug 15 03:15:05 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Fri, 15 Aug 2014 09:15:05 +0200
Subject: Release notes
In-Reply-To: <B98A67E5-ABE6-473E-8BA5-4AB4956D4FF0@demuc.de>
References: <766B7CF2-CE8D-4F1E-9DAA-3381EC7EF59C@demuc.de>
 <CABDkGQnZO9x0et5p=GsXbm8B0LSq3XM8oDfzd9HXvBJx9qGcbg@mail.gmail.com>
 <CAA48SF-WkW1oOv=U0itOrN8neqdVHVwpf-W+qdZM8ESEeEUq_Q@mail.gmail.com> <B98A67E5-ABE6-473E-8BA5-4AB4956D4FF0@demuc.de>
Message-ID: <CABDkGQmm1hMMrucipS+iN=mFX7BrwS73fEp2MK--V02yb9-TUw@mail.gmail.com>

On Thu, Aug 14, 2014 at 11:22 PM, Johannes Sch ?nberger <jsch at demuc.de> wrote:
> Thanks for letting us know. I have not thought of this, but I can definitely see this happening in our case as well. Separate files in a subdirectory sound as a good workaround. What do the other think?

I saw this in the IPython project as well--should have thought of the
merge conflicts.  +1 for adopting a similar approach.

St?fan


From vighneshbirodkar at gmail.com  Sun Aug 17 15:21:11 2014
From: vighneshbirodkar at gmail.com (Vighnesh Birodkar)
Date: Sun, 17 Aug 2014 12:21:11 -0700 (PDT)
Subject: GSoC Recap Post
Message-ID: <fe22a4b1-3cf6-40eb-8cce-16785fc9a860@googlegroups.com>

Hello

I just wrote a post giving a quick recap of this years GSoC.
http://vcansimplify.wordpress.com/2014/08/17/gsoc-2014-signing-off/

I would like to have the link to the homepages of Johannes Sch?nberger and 
Guillaume Gay, so that I can link them in my post.

Thanks
Vighnesh
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From jsch at demuc.de  Sat Aug 23 10:00:19 2014
From: jsch at demuc.de (=?windows-1252?Q?Johannes_Sch=0F=F6nberger?=)
Date: Sat, 23 Aug 2014 10:00:19 -0400
Subject: GSoC 2014: Congratulations!
In-Reply-To: <87fvgnbak4.fsf@sun.ac.za>
References: <87fvgnbak4.fsf@sun.ac.za>
Message-ID: <61012C6E-B883-4664-BD3E-60C8F2CC54CF@demuc.de>

Congratulations to our students!

But also, many thanks for the hard work @Juan and @St?fan. Unfortunately, I have not had too much time to assist you two?

What do you think about releasing a new version in the coming future (including some of the remaining, open PRs)?

Johannes Sch?nberger

On Aug 23, 2014, at 9:27 AM, Stefan van der Walt <stefan at sun.ac.za> wrote:

> Hi everyone
> 
> I'd like to congratulate Vighnesh and Rishabh who just successfully
> completed the 2014 Google Summer of Code with scikit-image.  We have a
> whole lot to show for it!  Thank you, guys, for all your hard work and
> dedication.
> 
> For those of you who haven't been following, Vighnesh has been building
> Region Adjacency Graph infrastructure and algorithms under the very
> thorough mentorship of Juan.  Catering to my nitpicking was Rishabh, who
> developed a remote, sandboxed execution framework that gives us an
> interactive gallery (preview at [0]).
> 
> This was fun, and I look forward as much to our future collaboration!
> 
> Regards
> St?fan
> 
> 
> [0] http://sharky93.github.io/docs/gallery/auto_examples/
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.



From stefan at sun.ac.za  Sat Aug 23 09:27:39 2014
From: stefan at sun.ac.za (Stefan van der Walt)
Date: Sat, 23 Aug 2014 15:27:39 +0200
Subject: GSoC 2014: Congratulations!
Message-ID: <87fvgnbak4.fsf@sun.ac.za>

Hi everyone

I'd like to congratulate Vighnesh and Rishabh who just successfully
completed the 2014 Google Summer of Code with scikit-image.  We have a
whole lot to show for it!  Thank you, guys, for all your hard work and
dedication.

For those of you who haven't been following, Vighnesh has been building
Region Adjacency Graph infrastructure and algorithms under the very
thorough mentorship of Juan.  Catering to my nitpicking was Rishabh, who
developed a remote, sandboxed execution framework that gives us an
interactive gallery (preview at [0]).

This was fun, and I look forward as much to our future collaboration!

Regards
St?fan


[0] http://sharky93.github.io/docs/gallery/auto_examples/


From stefan at sun.ac.za  Sat Aug 23 10:17:10 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Sat, 23 Aug 2014 16:17:10 +0200
Subject: GSoC 2014: Congratulations!
In-Reply-To: <61012C6E-B883-4664-BD3E-60C8F2CC54CF@demuc.de>
References: <87fvgnbak4.fsf@sun.ac.za>
	<61012C6E-B883-4664-BD3E-60C8F2CC54CF@demuc.de>
Message-ID: <CABDkGQn_ceRHwb7wB_wofoQS=89rvuXxhL1qU99p2OsZsNCtFQ@mail.gmail.com>

On Aug 23, 2014 4:00 PM, "Johannes Sch ?nberger" <jsch at demuc.de> wrote:
> What do you think about releasing a new version in the coming future
(including some of the remaining, open PRs)?

I would love to see a new release ASAP, but the interpolation and
downsampling issue is currently a blocker. I'm trying to find time to work
on it without much success.

St?fan
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