From stefan at sun.ac.za  Thu Jun  3 16:25:26 2010
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 3 Jun 2010 13:25:26 -0700
Subject: License for parts of CellProfiler changed to BSD to allow 
	incorporation into SciPy
In-Reply-To: <AANLkTim9gfd3EluSykvuFFQ4Q2IbvoojRcjjJule7Bgy@mail.gmail.com>
References: <AANLkTim9gfd3EluSykvuFFQ4Q2IbvoojRcjjJule7Bgy@mail.gmail.com>
Message-ID: <AANLkTik3snBF0XYKS4zQOB79dg-K_xiVMxfC8wwPDrcc@mail.gmail.com>

2010/6/3 Vebjorn Ljosa <ljosa at broad.mit.edu>:
> We have changed the license of some parts of CellProfiler from GNU GPL
> to BSD. ?It has previously been proposed [1] that some of the image
> processing code in CellProfiler be merged into SciPy, and the license
> change makes this possible.

This is wonderful news, guys!  I hope to merge most of this code into
our codebase as part of the SciPy2010 sprint.  All hands welcome!

Regards
St?fan


From ljosa at broad.mit.edu  Thu Jun  3 16:15:30 2010
From: ljosa at broad.mit.edu (Vebjorn Ljosa)
Date: Thu, 3 Jun 2010 16:15:30 -0400
Subject: License for parts of CellProfiler changed to BSD to allow 
	incorporation into SciPy
Message-ID: <AANLkTim9gfd3EluSykvuFFQ4Q2IbvoojRcjjJule7Bgy@mail.gmail.com>

We have changed the license of some parts of CellProfiler from GNU GPL
to BSD.  It has previously been proposed [1] that some of the image
processing code in CellProfiler be merged into SciPy, and the license
change makes this possible.

The CellProfiler SVN repository is at
https://svn.broadinstitute.org/CellProfiler/trunk/CellProfiler/.  The
file LICENSE [2] contains a list of BSD-licensed subdirectories as
well as other license details.  The rest of CellProfiler continues to
be licensed under the GNU GPL.  The BSD-licensed subdirectories are:

 * CellProfiler/cpmath [3]: image processing algorithms
 * CellProfiler/utilities [4]: contains a Java bridge, making it
possible to call Java functions from Python
 * bioformats [5]: wrapper that uses the Java bridge to have
Bioformats [6] read or write an image file

Good luck with the upcoming scikits.image sprint.  I don't think
anyone from the CellProfiler team will be able to take part in the
sprint this time, but don't hesitate to ask on the
cellprofiler-dev at broadinstitute.org mailing list.

Thanks,
Vebjorn

[1] http://stefanv.github.com/scikits.image/contribute.html
[2] https://svn.broadinstitute.org/CellProfiler/trunk/CellProfiler/LICENSE
[3] https://svn.broadinstitute.org/CellProfiler/trunk/CellProfiler/cellprofiler/cpmath/
[4] https://svn.broadinstitute.org/CellProfiler/trunk/CellProfiler/cellprofiler/utilities/
[5] https://svn.broadinstitute.org/CellProfiler/trunk/CellProfiler/bioformats/
[6] http://www.loci.wisc.edu/software/bio-formats

-- 
Vebjorn Ljosa, PhD
Computational Biologist
Broad Institute of MIT and Harvard


From stefan at sun.ac.za  Tue Jun  8 18:00:54 2010
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 8 Jun 2010 16:00:54 -0600
Subject: Problems with PIL/imread
Message-ID: <AANLkTikvOmufTq5rDkfZcbUrVF_ByqFravctn6uEi8PV@mail.gmail.com>

Hi all,

Has anybody else seen the behaviour described in

http://github.com/stefanv/scikits.image/issues/#issue/2

?  I'd like to pin down the problem, but can't reproduce it on my machine.

Also, I've added 'imshow' to the PIL plugin, available for review/testing here:

http://github.com/stefanv/scikits.image/tree/io

Regards
St?fan


From stefan at sun.ac.za  Wed Jun  9 04:40:29 2010
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 9 Jun 2010 02:40:29 -0600
Subject: New build system
Message-ID: <AANLkTimP87ptZNYiRsJBp_Vzd1Rn8Q3VCduHE2A0hdg_@mail.gmail.com>

Hi all,

David Cournapeau's Bento build system (a replacement for distutils) is
maturing nicely.  I'd like to switch to it eventually, but for now
I've simply put all the necessary changes in the 'bento' branch.
Bento is entirely self-contained, so just check out the branch and do:

make bento

It keeps track of changes to C files, so incremental builds work.
Commands are provided for generating the docs, running tests, etc.

Let me know what you think.

Regards
St?fan


From sccolbert at gmail.com  Wed Jun  9 20:07:48 2010
From: sccolbert at gmail.com (S. Chris Colbert)
Date: Wed, 09 Jun 2010 20:07:48 -0400
Subject: New build system
In-Reply-To: <AANLkTimP87ptZNYiRsJBp_Vzd1Rn8Q3VCduHE2A0hdg_@mail.gmail.com>
References: <AANLkTimP87ptZNYiRsJBp_Vzd1Rn8Q3VCduHE2A0hdg_@mail.gmail.com>
Message-ID: <4C102CD4.90601@gmail.com>

Considering that we are vying for adoption, I would hold off adopting a 
new build system until it (or we) become more popular.

On 06/09/2010 04:40 AM, St??????fan van der Walt wrote:
> Hi all,
>
> David Cournapeau's Bento build system (a replacement for distutils) is
> maturing nicely.  I'd like to switch to it eventually, but for now
> I've simply put all the necessary changes in the 'bento' branch.
> Bento is entirely self-contained, so just check out the branch and do:
>
> make bento
>
> It keeps track of changes to C files, so incremental builds work.
> Commands are provided for generating the docs, running tests, etc.
>
> Let me know what you think.
>
> Regards
> St??????fan
>    



From stefan at sun.ac.za  Wed Jun  9 23:30:31 2010
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 9 Jun 2010 21:30:31 -0600
Subject: New build system
In-Reply-To: <4C102CD4.90601@gmail.com>
References: <AANLkTimP87ptZNYiRsJBp_Vzd1Rn8Q3VCduHE2A0hdg_@mail.gmail.com> 
	<4C102CD4.90601@gmail.com>
Message-ID: <AANLkTik-jjFKihtNpBDzUBFT3i2q5FwBbAsfzrC778Jg@mail.gmail.com>

On 9 June 2010 18:07, S. Chris Colbert <sccolbert at gmail.com> wrote:
> Considering that we are vying for adoption, I would hold off adopting a new
> build system until it (or we) become more popular.

Sure, it is optional (and also, Bento has the ability to generate
distutils compatible setup.py files if needed).  I would like to show
support for David's effort, which I think is by far the best and
cleanest design.  I'm sure our adoption will only strengthen his case.

Regards
St?fan


From stefan at sun.ac.za  Wed Jun 16 13:00:23 2010
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 16 Jun 2010 11:00:23 -0600
Subject: New build system
In-Reply-To: <AANLkTikQXDbTfETJVJIb48wGgrEytQfyfyx8ZLTrzqFF@mail.gmail.com>
References: <AANLkTimP87ptZNYiRsJBp_Vzd1Rn8Q3VCduHE2A0hdg_@mail.gmail.com>
	<4C102CD4.90601@gmail.com>
	<AANLkTik-jjFKihtNpBDzUBFT3i2q5FwBbAsfzrC778Jg@mail.gmail.com>
	<AANLkTin_We4LUWp7WBoNhV1a7dEFtT3-MjzTJheoruAI@mail.gmail.com>
	<AANLkTikQXDbTfETJVJIb48wGgrEytQfyfyx8ZLTrzqFF@mail.gmail.com>
Message-ID: <AANLkTikNUuJw_gDuToxnih5RaJXkeVc_T4wN08yTwBzB@mail.gmail.com>

The binary is a compressed script that gets unpacked upon execution. Quite
clever!

Regards
Stefan

On Jun 16, 2010 10:50 AM, "Ralf Gommers" <ralf.gommers at googlemail.com>
wrote:



2010/6/10 St?fan van der Walt <stefan at sun.ac.za>

> > On 9 June 2010 18:07, S. Chris Colbert <sccolbert at gmail.com> wrote: > >
Considering that we are...
Looks good, I really like the bento.info format. And the new name. I'm a bit
puzzled about the binary code inside the bentomaker file, what's going on
there?

It builds fine, so no reason to merge it into your master branch soon I
think.

Cheers,
Ralf
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From ralf.gommers at googlemail.com  Wed Jun 16 11:28:39 2010
From: ralf.gommers at googlemail.com (Ralf Gommers)
Date: Wed, 16 Jun 2010 23:28:39 +0800
Subject: New build system
In-Reply-To: <AANLkTik-jjFKihtNpBDzUBFT3i2q5FwBbAsfzrC778Jg@mail.gmail.com>
References: <AANLkTimP87ptZNYiRsJBp_Vzd1Rn8Q3VCduHE2A0hdg_@mail.gmail.com>
	<4C102CD4.90601@gmail.com>
	<AANLkTik-jjFKihtNpBDzUBFT3i2q5FwBbAsfzrC778Jg@mail.gmail.com>
Message-ID: <AANLkTin_We4LUWp7WBoNhV1a7dEFtT3-MjzTJheoruAI@mail.gmail.com>

2010/6/10 St?fan van der Walt <stefan at sun.ac.za>

> On 9 June 2010 18:07, S. Chris Colbert <sccolbert at gmail.com> wrote:
> > Considering that we are vying for adoption, I would hold off adopting a
> new
> > build system until it (or we) become more popular.
>
> Sure, it is optional (and also, Bento has the ability to generate
> distutils compatible setup.py files if needed).  I would like to show
> support for David's effort, which I think is by far the best and
> cleanest design.  I'm sure our adoption will only strengthen his case.
>
> Looks good, I really like the bento.info format. And the new name. I'm a
bit puzzled about the binary code inside the bentomaker file, what's going
on there?

It builds fine, so no reason to merge it into your master branch soon I
think.

Cheers,
Ralf
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From ceball at gmail.com  Wed Jun 30 08:00:27 2010
From: ceball at gmail.com (Chris Ball)
Date: Wed, 30 Jun 2010 05:00:27 -0700 (PDT)
Subject: Color spaces
Message-ID: <51d89270-10a3-4674-9ad0-2fae8b62b87f@r27g2000yqb.googlegroups.com>

Hi,

Some time ago, there was a thread about what color spaces to include
in scikits.image:
http://groups.google.com/group/scikits-image/browse_thread/thread/4b4e69fd0dbce9cc

I wonder if you would be interested in seeing more color space
conversions being added to the colorconv.py module, or if you are
deliberately keeping it simple? For instance, I would like to add
conversions to and from CIE LAB, and to allow alternative white
points.

I'm also interested in seeing conversions to and from human cone LMS
spaces available somewhere for SciPy users. I'm not sure whether or
not this kind of thing would be appropriate for scikits.image.

I thought I should first post a short message about this before
starting anything. I'm aware that the SciPy image sandbox used to
contain more conversions, probably in a slightly confusing way
(e.g.http://projects.scipy.org/scipy/browser/trunk/Lib/sandbox/image/
color.py?rev=1698). Anyway, please let me know what you think.

Thanks,
Chris