From holtzhau at gmail.com  Mon Jul  4 11:10:59 2011
From: holtzhau at gmail.com (Pieter Holtzhausen)
Date: Mon, 4 Jul 2011 08:10:59 -0700
Subject: Pieter Holtzhausen wants to chat
Message-ID: <CAOA5xCxjxzUnDxrB6iKP-cRX269_gewVOOs_=BvKrbL0sG+aMA@mail.gmail.com>

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From stefan at sun.ac.za  Tue Jul  5 19:26:23 2011
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 5 Jul 2011 16:26:23 -0700
Subject: Help on updating website
Message-ID: <BANLkTikdxtS=G3rOcLzSU0o4MYktRG=hRg@mail.gmail.com>

Hi all

I examined the IPython website structure over the weekend, and think
we can borrow some ideas there.

1. Have a decent landing page--not the user guide.
2. Store the generated webpage in a separate repo, not to pollute the
code repo.  We should therefore have the following repos:
    - scikits.image (also contains user guide rst)
    - scikits.image-web (landing page rst)
    - scikits.image-web-html (generated web page)
    - scikits.image-doc-html (generated manuals)

Then, I'm also thinking of moving the project to a new entity on
github.  What would you suggest?  "scikits-image.github.com" or
"scikit-image.github.com" (the latter is the convention that
scikits.learn uses, but not sure whether that is the best form?).
Having the project move away from my name means that I can add other
administrators to the project, so that I am not the bottleneck in
applying patches.

If you know of a person who would be willing to help with the webpage
design, please let me know.

Thanks!
St?fan


From sccolbert at gmail.com  Tue Jul  5 19:33:05 2011
From: sccolbert at gmail.com (Chris Colbert)
Date: Tue, 5 Jul 2011 19:33:05 -0400
Subject: Help on updating website
In-Reply-To: <BANLkTikdxtS=G3rOcLzSU0o4MYktRG=hRg@mail.gmail.com>
References: <BANLkTikdxtS=G3rOcLzSU0o4MYktRG=hRg@mail.gmail.com>
Message-ID: <CAPc_zRVvFunc+uwE6BZfJ=B0w3JhhirVcmekKD6foch8OuR=xQ@mail.gmail.com>

I'm +1 for scikits-image.github.com

2011/7/5 St?fan van der Walt <stefan at sun.ac.za>

> Hi all
>
> I examined the IPython website structure over the weekend, and think
> we can borrow some ideas there.
>
> 1. Have a decent landing page--not the user guide.
> 2. Store the generated webpage in a separate repo, not to pollute the
> code repo.  We should therefore have the following repos:
>    - scikits.image (also contains user guide rst)
>    - scikits.image-web (landing page rst)
>    - scikits.image-web-html (generated web page)
>    - scikits.image-doc-html (generated manuals)
>
> Then, I'm also thinking of moving the project to a new entity on
> github.  What would you suggest?  "scikits-image.github.com" or
> "scikit-image.github.com" (the latter is the convention that
> scikits.learn uses, but not sure whether that is the best form?).
> Having the project move away from my name means that I can add other
> administrators to the project, so that I am not the bottleneck in
> applying patches.
>
> If you know of a person who would be willing to help with the webpage
> design, please let me know.
>
> Thanks!
> St?fan
>
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From stefan at sun.ac.za  Tue Jul  5 22:36:06 2011
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 5 Jul 2011 19:36:06 -0700
Subject: Help on updating website
In-Reply-To: <CAPc_zRVvFunc+uwE6BZfJ=B0w3JhhirVcmekKD6foch8OuR=xQ@mail.gmail.com>
References: <BANLkTikdxtS=G3rOcLzSU0o4MYktRG=hRg@mail.gmail.com> <CAPc_zRVvFunc+uwE6BZfJ=B0w3JhhirVcmekKD6foch8OuR=xQ@mail.gmail.com>
Message-ID: <BANLkTinzDkq+mVfM-3_-5y_=jbBAig5SfQ@mail.gmail.com>

On Tue, Jul 5, 2011 at 4:33 PM, Chris Colbert <sccolbert at gmail.com> wrote:
>
> I'm +1 for scikits-image.github.com

OK, I've gone ahead and registered the organization with myself, you
and Thouis as owners.  Over the next few days, I will transfer the
repo there and make a posting here when it is done.

St?fan


From stefan at sun.ac.za  Thu Jul  7 18:15:17 2011
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 7 Jul 2011 15:15:17 -0700
Subject: Repository moved
Message-ID: <CABDkGQm66NsyEtB9q30-8S2Q-5__C2ZeWPXyOESUpnBfdAo54g@mail.gmail.com>

Hi all,

The code repository now officially resides at

http://github.com/scikits-image/scikits.image.git

I'll be working on moving the web page over and registering our domain
over the next couple of days.

Please, if you know of a talented web designer who would like to get
involved in the project, let me know.

Regards
St?fan


From stefan at sun.ac.za  Thu Jul  7 20:01:17 2011
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 7 Jul 2011 17:01:17 -0700
Subject: Greyscale reconstruction and merging CellProfiler code
In-Reply-To: <CAEym_HqV5XGA0cG2b0JftrDh-LuQxu31RB07m0mYK9p33N5KpQ@mail.gmail.com>
References: <CAEym_HqV5XGA0cG2b0JftrDh-LuQxu31RB07m0mYK9p33N5KpQ@mail.gmail.com>
Message-ID: <CABDkGQnjamXNc6yzh=s84zJRinrhUzRKZb0XWdoN_Pvs=uhW-A@mail.gmail.com>

Hi Tony

On Thu, Jul 7, 2011 at 4:39 PM, Tony Yu <tsyu80 at gmail.com> wrote:
> The addition was added over a series of commits?with only minor changes to
> the original CellProfiler code (except for one large, unused chunk of code
> that I deleted). That brings me to my question: what are the suggested
> changes when merging CellProfiler code? Is it as simple as putting the
> chunks of code in the right place (i.e. putting the code in the correct
> module(s) and adding the tests)? There's a number of things that could be
> added/changed, but I'm uncertain about how much *needs* to be done in order
> to be "acceptable" for addition into the scikit.

There are some differences in our documentation and styles.  For
example, I like for the contributors.txt file to be updated, and for
the docs to be in the numpy docs format and highly descriptive.  In
this example, I cannot figure out what the function is meant to do, so
based on that I would be hesitant to commit.  Maybe add a longer
description, as well as a few references.  Also, an update to the docs
would be welcome, illustrating its use (this could also be done under
Examples in the docstring).

Cheers
St?fan


From stefan at sun.ac.za  Thu Jul  7 20:07:22 2011
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 7 Jul 2011 17:07:22 -0700
Subject: Repository moved
In-Reply-To: <CAEym_Hqr95Ln9TSyR6X8AQi-hxVqxpoKCz2kY2yxagR_CsNxSQ@mail.gmail.com>
References: <CABDkGQm66NsyEtB9q30-8S2Q-5__C2ZeWPXyOESUpnBfdAo54g@mail.gmail.com>
 <CAEym_Hqr95Ln9TSyR6X8AQi-hxVqxpoKCz2kY2yxagR_CsNxSQ@mail.gmail.com>
Message-ID: <CABDkGQnW+wo9=wqqEQA6K0Wqu2=cxo=8rm0QWN4qhq=KUyAMFA@mail.gmail.com>

On Thu, Jul 7, 2011 at 4:15 PM, Tony Yu <tsyu80 at gmail.com> wrote:
> That's great. In honor of the new repo. I added my previous pull request
> (for fixing TV denoise) to the new repo.

Thanks!  Does the stricted test now catch the bug introduced by the
invalid order of parameters?  If not, we should add a new test for
that.

> As a side note: I don't know if there's a "correct" way to change where your
> repo is forked from. I ended deleting my scikits-image repo on github and
> forking a new one from scikits-image (instead of stefanv). I was able to
> push my local branches to the new fork without any issues.

It should be fine to simply redefine the origin:

git remote rm origin
git remote add origin git at github.com:scikits-image/scikits.image.git

Cheers
St?fan


From tsyu80 at gmail.com  Thu Jul  7 19:15:34 2011
From: tsyu80 at gmail.com (Tony Yu)
Date: Thu, 7 Jul 2011 19:15:34 -0400
Subject: Repository moved
In-Reply-To: <CABDkGQm66NsyEtB9q30-8S2Q-5__C2ZeWPXyOESUpnBfdAo54g@mail.gmail.com>
References: <CABDkGQm66NsyEtB9q30-8S2Q-5__C2ZeWPXyOESUpnBfdAo54g@mail.gmail.com>
Message-ID: <CAEym_Hqr95Ln9TSyR6X8AQi-hxVqxpoKCz2kY2yxagR_CsNxSQ@mail.gmail.com>

2011/7/7 St?fan van der Walt <stefan at sun.ac.za>

> Hi all,
>
> The code repository now officially resides at
>
> http://github.com/scikits-image/scikits.image.git
>
> I'll be working on moving the web page over and registering our domain
> over the next couple of days.
>
> Please, if you know of a talented web designer who would like to get
> involved in the project, let me know.
>
> Regards
> St?fan
>

That's great. In honor of the new repo. I added my previous pull request
(for fixing TV denoise) to the new repo.

As a side note: I don't know if there's a "correct" way to change where your
repo is forked from. I ended deleting my scikits-image repo on github and
forking a new one from scikits-image (instead of stefanv). I was able to
push my local branches to the new fork without any issues.

Best,
-Tony
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From tsyu80 at gmail.com  Thu Jul  7 19:39:07 2011
From: tsyu80 at gmail.com (Tony Yu)
Date: Thu, 7 Jul 2011 19:39:07 -0400
Subject: Greyscale reconstruction and merging CellProfiler code
Message-ID: <CAEym_HqV5XGA0cG2b0JftrDh-LuQxu31RB07m0mYK9p33N5KpQ@mail.gmail.com>

Hi,

I recently had the need for a function to do greyscale reconstruction and
found out that the CellProfiler code has this available. I've added that
chunk of code from the CellProfiler code to a branch in my repo:

https://github.com/tonysyu/scikits.image/tree/reconstruction

The addition was added over a series of
commits<https://github.com/tonysyu/scikits.image/commits/reconstruction>
with
only minor changes to the original CellProfiler code (except for one large,
unused chunk of code that I deleted). That brings me to my question: what
are the suggested changes when merging CellProfiler code? Is it as simple as
putting the chunks of code in the right place (i.e. putting the code in the
correct module(s) and adding the tests)? There's a number of things that
could be added/changed, but I'm uncertain about how much *needs* to be done
in order to be "acceptable" for addition into the scikit.

Best,
-Tony
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From tsyu80 at gmail.com  Thu Jul  7 20:32:35 2011
From: tsyu80 at gmail.com (Tony Yu)
Date: Thu, 7 Jul 2011 20:32:35 -0400
Subject: Repository moved
In-Reply-To: <CABDkGQnW+wo9=wqqEQA6K0Wqu2=cxo=8rm0QWN4qhq=KUyAMFA@mail.gmail.com>
References: <CABDkGQm66NsyEtB9q30-8S2Q-5__C2ZeWPXyOESUpnBfdAo54g@mail.gmail.com>
	<CAEym_Hqr95Ln9TSyR6X8AQi-hxVqxpoKCz2kY2yxagR_CsNxSQ@mail.gmail.com>
	<CABDkGQnW+wo9=wqqEQA6K0Wqu2=cxo=8rm0QWN4qhq=KUyAMFA@mail.gmail.com>
Message-ID: <CAEym_HrXziajpxZJtpPkZgkPmzEZ2mGT-M=03gThgGy8hXr_TQ@mail.gmail.com>

2011/7/7 St?fan van der Walt <stefan at sun.ac.za>

> On Thu, Jul 7, 2011 at 4:15 PM, Tony Yu <tsyu80 at gmail.com> wrote:
> > That's great. In honor of the new repo. I added my previous pull request
> > (for fixing TV denoise) to the new repo.
>
> Thanks!  Does the stricted test now catch the bug introduced by the
> invalid order of parameters?  If not, we should add a new test for
> that.
>

Yes, the stricter test fails when the order of parameters is switched.


> > As a side note: I don't know if there's a "correct" way to change where
> your
> > repo is forked from. I ended deleting my scikits-image repo on github and
> > forking a new one from scikits-image (instead of stefanv). I was able to
> > push my local branches to the new fork without any issues.
>
> It should be fine to simply redefine the origin:
>
> git remote rm origin
> git remote add origin git at github.com:scikits-image/scikits.image.git
>

I knew I should have asked first ;)

Best,
-Tony


> Cheers
> St?fan
>
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From tsyu80 at gmail.com  Thu Jul  7 21:30:45 2011
From: tsyu80 at gmail.com (Tony Yu)
Date: Thu, 7 Jul 2011 21:30:45 -0400
Subject: Greyscale reconstruction and merging CellProfiler code
In-Reply-To: <CABDkGQnjamXNc6yzh=s84zJRinrhUzRKZb0XWdoN_Pvs=uhW-A@mail.gmail.com>
References: <CAEym_HqV5XGA0cG2b0JftrDh-LuQxu31RB07m0mYK9p33N5KpQ@mail.gmail.com>
	<CABDkGQnjamXNc6yzh=s84zJRinrhUzRKZb0XWdoN_Pvs=uhW-A@mail.gmail.com>
Message-ID: <CAEym_HrA+L1g3U9ACtVycD2pUd0p1KF4e5vxsYhyZasTBzfhUA@mail.gmail.com>

2011/7/7 St?fan van der Walt <stefan at sun.ac.za>

> Hi Tony
>
> On Thu, Jul 7, 2011 at 4:39 PM, Tony Yu <tsyu80 at gmail.com> wrote:
> > The addition was added over a series of commits with only minor changes
> to
> > the original CellProfiler code (except for one large, unused chunk of
> code
> > that I deleted). That brings me to my question: what are the suggested
> > changes when merging CellProfiler code? Is it as simple as putting the
> > chunks of code in the right place (i.e. putting the code in the correct
> > module(s) and adding the tests)? There's a number of things that could be
> > added/changed, but I'm uncertain about how much *needs* to be done in
> order
> > to be "acceptable" for addition into the scikit.
>
> There are some differences in our documentation and styles.  For
> example, I like for the contributors.txt file to be updated, and for
> the docs to be in the numpy docs format and highly descriptive.  In
> this example, I cannot figure out what the function is meant to do, so
> based on that I would be hesitant to commit.  Maybe add a longer
> description, as well as a few references.  Also, an update to the docs
> would be welcome, illustrating its use (this could also be done under
> Examples in the docstring).
>
>
I added a reference and tried to expand on the description, but the
description is still poor. Even in the papers I've read, the descriptions
are quite difficult for me to understand (the figures in those papers really
help). I've also added an example to the docstring, but it's quite ...
verbose<https://github.com/tonysyu/scikits.image/commit/c122b1dbba5d88db8cecd4fe0ce404d83410a6a3>
.

I'd like to add a longer example in the docs, but that will have to wait
until I have a bit more time. When I do add it, where should put it? I'd
like for it to be more like a tutorial than a function-specific example
(specifically, I'd like to compare reconstruction and top-hat for peak
detection).

Best,
-Tony
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From stefan at sun.ac.za  Sun Jul 10 14:21:47 2011
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 10 Jul 2011 11:21:47 -0700
Subject: New website
Message-ID: <CABDkGQmc4SXR9P4bApg2-8Q+pvU9zy2ieGu7uwyN2V2_EDcL=g@mail.gmail.com>

Hi all,

Our new webpage is now online at:

http://scikits-image.org

The documentation is not yet built, so those links are broken.  Feel
free to pitch in!

Regards
St?fan


From stefan at sun.ac.za  Sun Jul 10 16:46:47 2011
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 10 Jul 2011 13:46:47 -0700
Subject: New website
In-Reply-To: <CAEym_HqD1-852DoskS1SmzeLvdOeZP65hRsyZK=p6xfJgJSQwg@mail.gmail.com>
References: <CABDkGQmc4SXR9P4bApg2-8Q+pvU9zy2ieGu7uwyN2V2_EDcL=g@mail.gmail.com>
 <CAEym_HqD1-852DoskS1SmzeLvdOeZP65hRsyZK=p6xfJgJSQwg@mail.gmail.com>
Message-ID: <CABDkGQkcm3koW=u2qSEFMq=7ujrq-cSH0eGQ-Cz8XFPPw7DZCg@mail.gmail.com>

Hi Tony

On Sun, Jul 10, 2011 at 12:58 PM, Tony Yu <tsyu80 at gmail.com> wrote:
>> Our new webpage is now online at:
>>
>> http://scikits-image.org
>>
> Ooh, the new design looks nice.

You'll notice that is closely resembles http://ipython.org -- this is
not coincidence :)  I asked Fernando Perez whether we could use their
tools, and he agreed.

> Speaking of building the documentation (sorry to hijack the thread), I've
> run into a number of problems:

Thanks for having a look at the documentation.  There are currently a
number of problems that need to be addressed (including the ones you
mention).  Foremost is that we should have a look at the way IPython
puts multiple versions of the docs online at a given time--this seems
like a very handy feature.

Also, the current script that pushes the docs is a mess, and should be fixed.

> plot_directive.py (see?http://projects.scipy.org/numpy/ticket/1489). As a
> fix, I changed conf.py to import plot_directive from matplotlib.sphinxext.
> I'm assuming that this isn't ideal since plot_directive must have been
> forked from matplotlib by numpy to fix-issues and/or add features, but it
> seems to work for me.

If the copy in ext is outdated, we should simply replace it with the
latest version from matplotlib.

> * Auto docs don't work properly (at least on my system) when other scikits
> are on the python path. Basically, the call to __import__('scikits.image')
> in apigen.py returns the path to *a different scikit*. A work around is to
> use the import function shown
> here:?http://stackoverflow.com/questions/211100/pythons-import-doesnt-work-as-expected/211101#211101
> * Also, it *might* be a good idea to remove auto-generated API docs when
> running "make clean". I got a number of Sphinx warnings because of dead
> links to old classes/functions.

Glad you caught all of these!  Would you please file a pull request
with your changes?

Thanks
St?fan


From stefan at sun.ac.za  Sun Jul 10 17:06:24 2011
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 10 Jul 2011 14:06:24 -0700
Subject: Repository moved
In-Reply-To: <CAEym_Hqr95Ln9TSyR6X8AQi-hxVqxpoKCz2kY2yxagR_CsNxSQ@mail.gmail.com>
References: <CABDkGQm66NsyEtB9q30-8S2Q-5__C2ZeWPXyOESUpnBfdAo54g@mail.gmail.com>
 <CAEym_Hqr95Ln9TSyR6X8AQi-hxVqxpoKCz2kY2yxagR_CsNxSQ@mail.gmail.com>
Message-ID: <CABDkGQ=n6u0+YqzV0t1rh9y4k-sWhZpb3bG6bb5xtU29eoydJw@mail.gmail.com>

On Thu, Jul 7, 2011 at 4:15 PM, Tony Yu <tsyu80 at gmail.com> wrote:
> That's great. In honor of the new repo. I added my previous pull request
> (for fixing TV denoise) to the new repo.

Thanks!  Merged.

Cheers
St?fan


From stefan at sun.ac.za  Sun Jul 10 17:38:50 2011
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 10 Jul 2011 14:38:50 -0700
Subject: Greyscale reconstruction and merging CellProfiler code
In-Reply-To: <CAEym_HrA+L1g3U9ACtVycD2pUd0p1KF4e5vxsYhyZasTBzfhUA@mail.gmail.com>
References: <CAEym_HqV5XGA0cG2b0JftrDh-LuQxu31RB07m0mYK9p33N5KpQ@mail.gmail.com>
 <CABDkGQnjamXNc6yzh=s84zJRinrhUzRKZb0XWdoN_Pvs=uhW-A@mail.gmail.com> <CAEym_HrA+L1g3U9ACtVycD2pUd0p1KF4e5vxsYhyZasTBzfhUA@mail.gmail.com>
Message-ID: <CABDkGQmZ+np9LVx0qjDk639LkqwvJ2svpMsMANDUWPcC=MaVcA@mail.gmail.com>

On Thu, Jul 7, 2011 at 6:30 PM, Tony Yu <tsyu80 at gmail.com> wrote:
> I added a reference and tried to expand on the description, but the
> description is still poor. Even in the papers I've read, the descriptions
> are quite difficult for me to understand (the figures in those papers really
> help). I've also added an example to the docstring, but it's quite ...
> verbose.

I guess the question then becomes whether such a specialised algorithm
is of enough common interest to include it.  In the end, every piece
of code requires maintenance, and our aim is to provide a fairly
generic set of tools that can be used to construct image processing
experiments.

I don't know this algorithm specifically, so I can't say, but it is an
aspect worth considering.

> I'd like to add a longer example in the docs, but that will have to wait
> until I have a bit more time. When I do add it, where should put it? I'd
> like for it to be more like a tutorial than a function-specific example
> (specifically, I'd like to compare reconstruction and top-hat for peak
> detection).

We are eagerly awaiting tutorial contributions for the docs, but no
one's volunteered so far :)  I'd love to have more of these, as it
shows common patterns (such as how to use io, displaying images,
etc.).

Regards
St?fan


From tsyu80 at gmail.com  Sun Jul 10 15:58:09 2011
From: tsyu80 at gmail.com (Tony Yu)
Date: Sun, 10 Jul 2011 15:58:09 -0400
Subject: New website
In-Reply-To: <CABDkGQmc4SXR9P4bApg2-8Q+pvU9zy2ieGu7uwyN2V2_EDcL=g@mail.gmail.com>
References: <CABDkGQmc4SXR9P4bApg2-8Q+pvU9zy2ieGu7uwyN2V2_EDcL=g@mail.gmail.com>
Message-ID: <CAEym_HqD1-852DoskS1SmzeLvdOeZP65hRsyZK=p6xfJgJSQwg@mail.gmail.com>

2011/7/10 St?fan van der Walt <stefan at sun.ac.za>

> Hi all,
>
> Our new webpage is now online at:
>
> http://scikits-image.org
>
> The documentation is not yet built, so those links are broken.  Feel
> free to pitch in!
>
> Regards
> St?fan
>

Ooh, the new design looks nice.

Speaking of building the documentation (sorry to hijack the thread), I've
run into a number of problems:

* Building docs gives the following error (Sphinx >= 1.0):

    Exception occurred:
       File "/Library/Python/2.6/site-packages/docutils/statemachine.py",
line 1193, in __radd__
        raise TypeError('adding ViewList to a non-ViewList')
    TypeError: adding ViewList to a non-ViewList

    This turns out to be a problem in the Sphinx extension,
plot_directive.py (see http://projects.scipy.org/numpy/ticket/1489). As a
fix, I changed conf.py<https://github.com/tonysyu/scikits.image/commit/ed95691924461f02352467f48d8332ce9b43eee9>to
import plot_directive from matplotlib.sphinxext. I'm assuming that
this
isn't ideal since plot_directive must have been forked from matplotlib by
numpy to fix-issues and/or add features, but it seems to work for me.

* Auto docs don't work properly (at least on my system) when other scikits
are on the python path. Basically, the call to __import__('scikits.image')
in apigen.py returns the path to *a different scikit*. A work
around<https://github.com/tonysyu/scikits.image/commit/1965297cfc59cc522daab6adc366003481b019ec>is
to use the import function shown here:
http://stackoverflow.com/questions/211100/pythons-import-doesnt-work-as-expected/211101#211101

* Also, it *might* be a good idea to remove auto-generated API
docs<https://github.com/tonysyu/scikits.image/commit/6ae5008e1f449510188c25d7d32b83703f1bf21c>when
running "make clean". I got a number of Sphinx warnings because of
dead
links to old classes/functions.

I'm also getting a lot of Sphinx warnings, but it'll take me some time to
track them down.

Cheers,
-Tony
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From stefan at sun.ac.za  Sun Jul 10 21:15:24 2011
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 10 Jul 2011 18:15:24 -0700
Subject: New website
In-Reply-To: <CAEym_HrT_30nfrGEz50=vgKa=T9niXhjTo7h6P-EqF4u-3p+Nw@mail.gmail.com>
References: <CABDkGQmc4SXR9P4bApg2-8Q+pvU9zy2ieGu7uwyN2V2_EDcL=g@mail.gmail.com>
 <CAEym_HqD1-852DoskS1SmzeLvdOeZP65hRsyZK=p6xfJgJSQwg@mail.gmail.com>
 <CABDkGQkcm3koW=u2qSEFMq=7ujrq-cSH0eGQ-Cz8XFPPw7DZCg@mail.gmail.com> <CAEym_HrT_30nfrGEz50=vgKa=T9niXhjTo7h6P-EqF4u-3p+Nw@mail.gmail.com>
Message-ID: <CABDkGQmdASF0yr2oX-LbeHLz2hKeGaPSWAPkgR3pq+eGCZGEsw@mail.gmail.com>

On Sun, Jul 10, 2011 at 5:52 PM, Tony Yu <tsyu80 at gmail.com> wrote:
> That sounds good. Should I copy the file from matplotlib or numpy? (I think
> original was copied from numpy.)

My guess would be that the matplotlib directive is more up to date.

> ?I'll definitely file a pull request with the updated copy of
> plot_directive.py

Great, thank you!

St?fan


From tsyu80 at gmail.com  Sun Jul 10 20:52:54 2011
From: tsyu80 at gmail.com (Tony Yu)
Date: Sun, 10 Jul 2011 20:52:54 -0400
Subject: New website
In-Reply-To: <CABDkGQkcm3koW=u2qSEFMq=7ujrq-cSH0eGQ-Cz8XFPPw7DZCg@mail.gmail.com>
References: <CABDkGQmc4SXR9P4bApg2-8Q+pvU9zy2ieGu7uwyN2V2_EDcL=g@mail.gmail.com>
	<CAEym_HqD1-852DoskS1SmzeLvdOeZP65hRsyZK=p6xfJgJSQwg@mail.gmail.com>
	<CABDkGQkcm3koW=u2qSEFMq=7ujrq-cSH0eGQ-Cz8XFPPw7DZCg@mail.gmail.com>
Message-ID: <CAEym_HrT_30nfrGEz50=vgKa=T9niXhjTo7h6P-EqF4u-3p+Nw@mail.gmail.com>

2011/7/10 St?fan van der Walt <stefan at sun.ac.za>
>
> > plot_directive.py (see http://projects.scipy.org/numpy/ticket/1489). As
> a
> > fix, I changed conf.py to import plot_directive from
> matplotlib.sphinxext.
> > I'm assuming that this isn't ideal since plot_directive must have been
> > forked from matplotlib by numpy to fix-issues and/or add features, but it
> > seems to work for me.
>
> If the copy in ext is outdated, we should simply replace it with the
> latest version from matplotlib.
>

That sounds good. Should I copy the file from matplotlib or numpy? (I think
original was copied from numpy.)

> * Auto docs don't work properly (at least on my system) when other scikits
> > are on the python path. Basically, the call to
> __import__('scikits.image')
> > in apigen.py returns the path to *a different scikit*. A work around is
> to
> > use the import function shown
> > here:
> http://stackoverflow.com/questions/211100/pythons-import-doesnt-work-as-expected/211101#211101
> > * Also, it *might* be a good idea to remove auto-generated API docs when
> > running "make clean". I got a number of Sphinx warnings because of dead
> > links to old classes/functions.
>
> Glad you caught all of these!  Would you please file a pull request
> with your changes?
>
 I'll definitely file a pull request with the updated copy of
plot_directive.py

Cheers,
-Tony
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From tsyu80 at gmail.com  Mon Jul 11 10:18:52 2011
From: tsyu80 at gmail.com (Tony Yu)
Date: Mon, 11 Jul 2011 10:18:52 -0400
Subject: New website
In-Reply-To: <CABDkGQmdASF0yr2oX-LbeHLz2hKeGaPSWAPkgR3pq+eGCZGEsw@mail.gmail.com>
References: <CABDkGQmc4SXR9P4bApg2-8Q+pvU9zy2ieGu7uwyN2V2_EDcL=g@mail.gmail.com>
	<CAEym_HqD1-852DoskS1SmzeLvdOeZP65hRsyZK=p6xfJgJSQwg@mail.gmail.com>
	<CABDkGQkcm3koW=u2qSEFMq=7ujrq-cSH0eGQ-Cz8XFPPw7DZCg@mail.gmail.com>
	<CAEym_HrT_30nfrGEz50=vgKa=T9niXhjTo7h6P-EqF4u-3p+Nw@mail.gmail.com>
	<CABDkGQmdASF0yr2oX-LbeHLz2hKeGaPSWAPkgR3pq+eGCZGEsw@mail.gmail.com>
Message-ID: <CAEym_Hr2x1DEwKxPSAMXab88BWYa0Tuw=pmqCN06TC8bUgt2uQ@mail.gmail.com>

2011/7/10 St?fan van der Walt <stefan at sun.ac.za>

> On Sun, Jul 10, 2011 at 5:52 PM, Tony Yu <tsyu80 at gmail.com> wrote:
> >  I'll definitely file a pull request with the updated copy of
> > plot_directive.py
>
> Great, thank you!


I just sent a pull request. Note that I haven't committed any changes to the
API docs because I don't have a compatible version of OpenCV installed.
Running "make clean; make html" should update a couple of those docs so that
they can be committed. Unfortunately, there's still a number of warnings
that I haven't had time to track down.

Best,
-Tony
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From thouis at gmail.com  Mon Jul 11 08:43:51 2011
From: thouis at gmail.com (Thouis (Ray) Jones)
Date: Mon, 11 Jul 2011 14:43:51 +0200
Subject: Post-doctoral position in image & data analysis for image-based
 high-content screening
Message-ID: <CAHGWWxHvK6LcbSPnnjVWjsJbdzipc3OKUH1u22wuC3QsrQWsdA@mail.gmail.com>

Short summary:
A funded post-doctoral position in data analysis, machine-learning,
and statistics applied to biological image-based high-content
screening is available at the BioPhenics platform of the Curie
Institute (Paris, France).

The position involves development and maintenance of tools in Python,
Matlab, or R that will be used both to analyze current screens and as
a contribution to a larger community. Expertise in machine learning or
statistical analysis with large biological datasets is desirable, good
knowledge of image processing tools is an asset.

Full details at:
http://dl.dropbox.com/u/16028921/PostDocApp_MachineLearning_BFX.pdf

Thouis Jones
Institut Curie


From stefan at sun.ac.za  Sat Jul 16 18:47:48 2011
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sat, 16 Jul 2011 17:47:48 -0500
Subject: Package rename
Message-ID: <CABDkGQk51UhJupPmBgzWs9Ld4x-X6ppr=XyRsVdaW5tv16Xg=A@mail.gmail.com>

Hi all,

I'd like to make you aware of the discussion on the scikits learn
website regarding package renames:

http://j.mp/pt9bcg

The problem is that the "scikits" namespace causes numerous problems
during package installation, and that we may need to consider renaming
the package.

Since we recently moved over to

http://scikits-image.org
http://github.com/scikits-image

I suggest that we maintain this branding, and consider renaming the
package itself to "skimage", so that you'll do

import skimage

instead of

import scikits.image

Feel free to discuss name suggestions etc. (but do read Ga?l's post first).

Thanks!
St?fan


From stefan at sun.ac.za  Sat Jul 16 19:22:21 2011
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sat, 16 Jul 2011 18:22:21 -0500
Subject: Sprint report
Message-ID: <CABDkGQnj+Kq9cJtf7XBq+MgGAECiNOur6oz+bEMz=tzxDd+xTw@mail.gmail.com>

Hi everyone,

The SciPy2011 sprints are over... here's a short summary of what we worked on:

- Completed the move over to the new webpage, improving documentation
build infrastructure along the way [Pieter Holtzhausen, Stefan]
- Python 3 compatibility [Neil Muller]
- New Qt-based imread [Neil Muller]
- Comparison chart to show how we stack up to MATLAB [Kyle Mandli]
- Improved FITS plugin to support multiple images and meta-data [James Turner]

Check out http://github.com/scikits-image/scikits.image.git for a
detailed changelog.

Regards
St?fan


From stefan at sun.ac.za  Sun Jul 17 09:17:10 2011
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 17 Jul 2011 08:17:10 -0500
Subject: Package rename
In-Reply-To: <CAOA5xCwMhjky1tMunjnsovt7qO3bFcROWqyevuX_RDNZAw_pPg@mail.gmail.com>
References: <CABDkGQk51UhJupPmBgzWs9Ld4x-X6ppr=XyRsVdaW5tv16Xg=A@mail.gmail.com>
	<CAOA5xCwMhjky1tMunjnsovt7qO3bFcROWqyevuX_RDNZAw_pPg@mail.gmail.com>
Message-ID: <CABDkGQk4D=NbqQJoVO2rYUqEC+zGWqSLB4pv551Gxk_JKFnXEQ@mail.gmail.com>

Hi,

On Jul 17, 2011 5:55 AM, "Pieter Holtzhausen" <holtzhau at gmail.com> wrote:
>
> Sounds reasonable.
>
> What about scyimage or skyimage?
> Then one can pronounce the import without without entering consonant
> mode i.e. esskayimage.

I think there needs to be a clear link between the project name and the
package, otherwise we may as well rebrand completely with some catchy name.

> What is the policy on scikit vs scikits?
> http://scikit-learn.sourceforge.net/ while scikits on the website text
> for example. If one builds a brand one should standardize on one or
> the other.

Their domain name struck me as slightly odd. What do you think about the
singular? If that seems more natural we can make a plan.

Regards
St?fan
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From holtzhau at gmail.com  Sun Jul 17 06:07:13 2011
From: holtzhau at gmail.com (Pieter Holtzhausen)
Date: Sun, 17 Jul 2011 12:07:13 +0200
Subject: Package rename
In-Reply-To: <CABDkGQk51UhJupPmBgzWs9Ld4x-X6ppr=XyRsVdaW5tv16Xg=A@mail.gmail.com>
References: <CABDkGQk51UhJupPmBgzWs9Ld4x-X6ppr=XyRsVdaW5tv16Xg=A@mail.gmail.com>
Message-ID: <CAOA5xCwMhjky1tMunjnsovt7qO3bFcROWqyevuX_RDNZAw_pPg@mail.gmail.com>

Sounds reasonable.

What about scyimage or skyimage?
Then one can pronounce the import without without entering consonant
mode i.e. esskayimage.

What is the policy on scikit vs scikits?
http://scikit-learn.sourceforge.net/ while scikits on the website text
for example. If one builds a brand one should standardize on one or
the other.

2011/7/17 St?fan van der Walt <stefan at sun.ac.za>:
> Hi all,
>
> I'd like to make you aware of the discussion on the scikits learn
> website regarding package renames:
>
> http://j.mp/pt9bcg
>
> The problem is that the "scikits" namespace causes numerous problems
> during package installation, and that we may need to consider renaming
> the package.
>
> Since we recently moved over to
>
> http://scikits-image.org
> http://github.com/scikits-image
>
> I suggest that we maintain this branding, and consider renaming the
> package itself to "skimage", so that you'll do
>
> import skimage
>
> instead of
>
> import scikits.image
>
> Feel free to discuss name suggestions etc. (but do read Ga?l's post first).
>
> Thanks!
> St?fan
>


From drnlmuller at gmail.com  Sun Jul 17 10:33:09 2011
From: drnlmuller at gmail.com (Neil Muller)
Date: Sun, 17 Jul 2011 16:33:09 +0200
Subject: Package rename
In-Reply-To: <CAOA5xCwMhjky1tMunjnsovt7qO3bFcROWqyevuX_RDNZAw_pPg@mail.gmail.com>
References: <CABDkGQk51UhJupPmBgzWs9Ld4x-X6ppr=XyRsVdaW5tv16Xg=A@mail.gmail.com>
	<CAOA5xCwMhjky1tMunjnsovt7qO3bFcROWqyevuX_RDNZAw_pPg@mail.gmail.com>
Message-ID: <CAPzz3hYZ1vWrSK+vchS4RBQJJfAwqmynBLuuZ2rAduzj-tDyPQ@mail.gmail.com>

On 17 July 2011 12:07, Pieter Holtzhausen <holtzhau at gmail.com> wrote:
> Sounds reasonable.
>
> What about scyimage or skyimage?

I'm opposed to skyimage, as that will be hard to search for easily,
but scyimage could work.

-- 
Neil Muller
drnlmuller at gmail.com

I've got a gmail account. Why haven't I become cool?


From stefan at sun.ac.za  Mon Jul 18 06:08:33 2011
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 18 Jul 2011 05:08:33 -0500
Subject: Package rename
In-Reply-To: <CAOA5xCycC8Rpegj3YEEDmU1eAoFHdBVb4NXvZ+EjB4153kL+og@mail.gmail.com>
References: <CABDkGQk51UhJupPmBgzWs9Ld4x-X6ppr=XyRsVdaW5tv16Xg=A@mail.gmail.com>
 <CAOA5xCwMhjky1tMunjnsovt7qO3bFcROWqyevuX_RDNZAw_pPg@mail.gmail.com>
 <CABDkGQk4D=NbqQJoVO2rYUqEC+zGWqSLB4pv551Gxk_JKFnXEQ@mail.gmail.com> <CAOA5xCycC8Rpegj3YEEDmU1eAoFHdBVb4NXvZ+EjB4153kL+og@mail.gmail.com>
Message-ID: <CABDkGQmqeWu11=OvobXbB0Ad4kEK1uQBXKq+6UYxTjuEEF-yHQ@mail.gmail.com>

On Mon, Jul 18, 2011 at 3:47 AM, Pieter Holtzhausen <holtzhau at gmail.com> wrote:
> For me the jump from sk -> scikits in our name would be similar to
> that from scy. The y is evocative of scipy and python in a way which
> could be good?
> But yeah either way would be good, just a suggestion.

I think I'm going to hold off onto the name change until the
discussions in the other groups have been finalised.  I don't think
waiting is going to make the choice easier, but it does make it easier
right now :)

Cheers
St?fan


From stefan at sun.ac.za  Mon Jul 18 06:20:47 2011
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 18 Jul 2011 05:20:47 -0500
Subject: New website
In-Reply-To: <CAEym_Hr2x1DEwKxPSAMXab88BWYa0Tuw=pmqCN06TC8bUgt2uQ@mail.gmail.com>
References: <CABDkGQmc4SXR9P4bApg2-8Q+pvU9zy2ieGu7uwyN2V2_EDcL=g@mail.gmail.com>
 <CAEym_HqD1-852DoskS1SmzeLvdOeZP65hRsyZK=p6xfJgJSQwg@mail.gmail.com>
 <CABDkGQkcm3koW=u2qSEFMq=7ujrq-cSH0eGQ-Cz8XFPPw7DZCg@mail.gmail.com>
 <CAEym_HrT_30nfrGEz50=vgKa=T9niXhjTo7h6P-EqF4u-3p+Nw@mail.gmail.com>
 <CABDkGQmdASF0yr2oX-LbeHLz2hKeGaPSWAPkgR3pq+eGCZGEsw@mail.gmail.com> <CAEym_Hr2x1DEwKxPSAMXab88BWYa0Tuw=pmqCN06TC8bUgt2uQ@mail.gmail.com>
Message-ID: <CABDkGQ=b3RiCdJscamBJWP0yJ7uoFGD4FuQGR_enNaEm2mD2qg@mail.gmail.com>

Hi Tony

On Mon, Jul 11, 2011 at 9:18 AM, Tony Yu <tsyu80 at gmail.com> wrote:
> I just sent a pull request. Note that I haven't committed any changes to the
> API docs because I don't have a compatible version of OpenCV installed.
> Running "make clean; make html" should update a couple of those docs so that
> they can be committed. Unfortunately, there's still a number of warnings
> that I haven't had time to track down.

Thanks for your work on the docs!  Your changes were incorporated into
those made by Pieter, and have been merged.

Regards
St?fan


From holtzhau at gmail.com  Mon Jul 18 04:47:56 2011
From: holtzhau at gmail.com (Pieter Holtzhausen)
Date: Mon, 18 Jul 2011 10:47:56 +0200
Subject: Package rename
In-Reply-To: <CABDkGQk4D=NbqQJoVO2rYUqEC+zGWqSLB4pv551Gxk_JKFnXEQ@mail.gmail.com>
References: <CABDkGQk51UhJupPmBgzWs9Ld4x-X6ppr=XyRsVdaW5tv16Xg=A@mail.gmail.com>
	<CAOA5xCwMhjky1tMunjnsovt7qO3bFcROWqyevuX_RDNZAw_pPg@mail.gmail.com>
	<CABDkGQk4D=NbqQJoVO2rYUqEC+zGWqSLB4pv551Gxk_JKFnXEQ@mail.gmail.com>
Message-ID: <CAOA5xCycC8Rpegj3YEEDmU1eAoFHdBVb4NXvZ+EjB4153kL+og@mail.gmail.com>

2011/7/17 St?fan van der Walt <stefan at sun.ac.za>:
> Hi,
>
> On Jul 17, 2011 5:55 AM, "Pieter Holtzhausen" <holtzhau at gmail.com> wrote:
>>
>> Sounds reasonable.
>>
>> What about scyimage or skyimage?
>> Then one can pronounce the import without without entering consonant
>> mode i.e. esskayimage.
>
> I think there needs to be a clear link between the project name and the
> package, otherwise we may as well rebrand completely with some catchy name.

For me the jump from sk -> scikits in our name would be similar to
that from scy. The y is evocative of scipy and python in a way which
could be good?
But yeah either way would be good, just a suggestion.

>
>> What is the policy on scikit vs scikits?
>> http://scikit-learn.sourceforge.net/ while scikits on the website text
>> for example. If one builds a brand one should standardize on one or
>> the other.
>
> Their domain name struck me as slightly odd. What do you think about the
> singular? If that seems more natural we can make a plan.

I feel the plural works better.


From tsyu80 at gmail.com  Mon Jul 18 11:45:29 2011
From: tsyu80 at gmail.com (Tony Yu)
Date: Mon, 18 Jul 2011 11:45:29 -0400
Subject: New website
In-Reply-To: <CABDkGQ=b3RiCdJscamBJWP0yJ7uoFGD4FuQGR_enNaEm2mD2qg@mail.gmail.com>
References: <CABDkGQmc4SXR9P4bApg2-8Q+pvU9zy2ieGu7uwyN2V2_EDcL=g@mail.gmail.com>
	<CAEym_HqD1-852DoskS1SmzeLvdOeZP65hRsyZK=p6xfJgJSQwg@mail.gmail.com>
	<CABDkGQkcm3koW=u2qSEFMq=7ujrq-cSH0eGQ-Cz8XFPPw7DZCg@mail.gmail.com>
	<CAEym_HrT_30nfrGEz50=vgKa=T9niXhjTo7h6P-EqF4u-3p+Nw@mail.gmail.com>
	<CABDkGQmdASF0yr2oX-LbeHLz2hKeGaPSWAPkgR3pq+eGCZGEsw@mail.gmail.com>
	<CAEym_Hr2x1DEwKxPSAMXab88BWYa0Tuw=pmqCN06TC8bUgt2uQ@mail.gmail.com>
	<CABDkGQ=b3RiCdJscamBJWP0yJ7uoFGD4FuQGR_enNaEm2mD2qg@mail.gmail.com>
Message-ID: <CAEym_Ho6SLtVfaz5cBz8CBkQembcNS+UjMAMwwr0V=DfnzVNhg@mail.gmail.com>

2011/7/18 St?fan van der Walt <stefan at sun.ac.za>

> Hi Tony
>
> On Mon, Jul 11, 2011 at 9:18 AM, Tony Yu <tsyu80 at gmail.com> wrote:
> > I just sent a pull request. Note that I haven't committed any changes to
> the
> > API docs because I don't have a compatible version of OpenCV installed.
> > Running "make clean; make html" should update a couple of those docs so
> that
> > they can be committed. Unfortunately, there's still a number of warnings
> > that I haven't had time to track down.
>
> Thanks for your work on the docs!  Your changes were incorporated into
> those made by Pieter, and have been merged.
>
> Regards
> St?fan
>

Well, if you keep responding to my requests, I'm just going to keep bugging
you with more. ;)
I've added a pull
request<https://github.com/scikits-image/scikits.image/pull/9> for
changing the way the front page is created.

Cheers,
-Tony
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From stefan at sun.ac.za  Mon Jul 18 21:32:59 2011
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 18 Jul 2011 20:32:59 -0500
Subject: New website
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On Mon, Jul 18, 2011 at 10:45 AM, Tony Yu <tsyu80 at gmail.com> wrote:
> Well, if you keep responding to my requests, I'm just going to keep bugging
> you with more. ;)

Excellent :)  Thanks for the pull request; I've merged your changes
into master.  A made a minor tweak that made the table fit in (at
least on my browser).

Cheers
St?fan