From stefan at sun.ac.za  Tue Nov  1 21:13:10 2011
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 1 Nov 2011 18:13:10 -0700
Subject: Renaming / 0.4 timeline
In-Reply-To: <CABDkGQ=4gsArXEzhhK8KbT62VGCwM1Y+5F=j55iivOiVqiVxvA@mail.gmail.com>
References: <CABDkGQ=b2t7gya=Ns_M3HZNfS8XH+4tUrJKe878HzZAKhUWkFg@mail.gmail.com>
 <20111018193227.GB26732@phare.normalesup.org> <CABDkGQ=4gsArXEzhhK8KbT62VGCwM1Y+5F=j55iivOiVqiVxvA@mail.gmail.com>
Message-ID: <CABDkGQmJ1QBe2_DHYUxJ0poomeNQ=f0nJh6O5CErm+qj6EMV0Q@mail.gmail.com>

Hi all,

2011/10/18 St?fan van der Walt <stefan at sun.ac.za>:
> Tue Oct 18th to Sat Oct 22nd : File and merge PRs of work-in-progress
> made against the current repo
> Sun Oct 23rd : Rename the repository, update documentation, test
> Mon Oct 24th to Fri Oct 28th : Apply bugfixes, add features, etc.
> required for 0.4, including polishing the Debian package
> Oct 29th to 30th : Release v0.4

Is everybody ready for the 0.4 release?  Any last minute patches you
want to get in?

Regards
St?fan


From stefan at sun.ac.za  Wed Nov  2 15:24:33 2011
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 2 Nov 2011 12:24:33 -0700
Subject: documentation marathon :-)
In-Reply-To: <20111025202023.GA25495@phare.normalesup.org>
References: <20111025202023.GA25495@phare.normalesup.org>
Message-ID: <CABDkGQ=4=nmR43wmesUcViXfDW7kniRR9b1Ki0NJ20N1Mypi2A@mail.gmail.com>

On Tue, Oct 25, 2011 at 1:20 PM, Emmanuelle Gouillart
<emmanuelle.gouillart at nsup.org> wrote:
> feature: hog

Brian did write a little visualisation snippet, that you can access by
passing some keyword to HoG.  Maybe we should grab that for an
example?

St?fan


From stefan at sun.ac.za  Tue Nov  8 18:27:22 2011
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 8 Nov 2011 15:27:22 -0800
Subject: [JOB] junior developer position
In-Reply-To: <20111108223612.GA18336@phare.normalesup.org>
References: <20111108223612.GA18336@phare.normalesup.org>
Message-ID: <CABDkGQn8t3DsOmo5t1_-R+rqfpanq98EuRw+b1nN7YK9-87M2w@mail.gmail.com>

On Tue, Nov 8, 2011 at 2:36 PM, Emmanuelle Gouillart
<emmanuelle.gouillart at nsup.org> wrote:
> handling of different file formats). The package will consist of a Python
> package and a set of ImageJ routines. For easier maintenance, some
> algorithms of general interest will be contributed instead to the
> open-source Python scikits-image ``skimage``.

Wonderful!  I'll also send this on to the labs and Python groups back
home.  I plan to organise another funded position on the project,
starting around 2013, so then we should be able to sustain good
momentum.

Cheers
St?fan


From emmanuelle.gouillart at nsup.org  Tue Nov  8 17:36:12 2011
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Tue, 8 Nov 2011 23:36:12 +0100
Subject: [JOB] junior developer position
Message-ID: <20111108223612.GA18336@phare.normalesup.org>

	Dear all,

	a 1-year Python (and ImageJ) developer position on 3-D image
processing is available in my team, hopefully involving some
contributions to skimage! See the description below, and also
http://www.svi.cnrs-bellevue.fr/wikimedia/index.php/EDDAM_developer_position

	Please spread the word!

	Cheers,

	Emmanuelle

*****************

Hiring a junior developer on 3-D image processing in the joint lab
CNRS/Saint-Gobain (Paris)


Description of the position
---------------------------

The goal of this 1-year project is to build a user-friendly and
good-quality 3-D image processing package from the miscellaneous
codebases written by different research teams working together on X-ray
tomography. In a first phase, you will strongly interact with the
researchers of the different teams in order to list and collect the
different algorithms used by the teams (including a few state-of-the-art
algorithms used by specialists on image processing collaborating with the
teams). You will integrate these algorithms (starting with those of most
common interest) into a common package, taking special care of usability
(documentation, installation, ...) and robustness of the code (testing,
handling of different file formats). The package will consist of a Python
package and a set of ImageJ routines. For easier maintenance, some
algorithms of general interest will be contributed instead to the
open-source Python scikits-image ``skimage``.

Scientific context
------------------

The French EDDAM project
(http://www.svi.cnrs-bellevue.fr/wikimedia/index.php/EDDAM) focusses on
the ultrafast 3-D X-ray imaging of amorphous materials under mechanical
load or thermal treatment. Thanks to state-of-the-art developements of
synchrotron X-ray tomography, it is now possible to image the evolution
of materials at timescales below 1s, giving unprecendented insights into
the transformation of materials. Such experiments typically produce huge
datasets, for which efficient automated image processing methods are
required.

Requirements
------------

* Good abilities for team working. Objective-driven mindset.

* Knowledge of a programming language and some scientific computing.
  Knowledge of one of the languages/sotfwares used by the team (Python,
  ImageJ + Java, Matlab) is a plus.

* Interest for quality assurance and best practices in software
  development: documentation, testing, version control.

* Interest and curiosity on image processing. A previous experience on
  image processing or a mathematical-oriented mindset is a plus.


Practical aspects
-----------------

The position is available from February 2012.

The salary depends on the level of experience of the candidate, from 1650
euros (net salary) per month (master's degree) to 1930 euros per month
(PhD degree). If you are finishing a master's degree and you are looking
for an internship, it is also possible to start with an internship before
taking the 1-year position.

Your employer will be the CNRS (French National Research Center), and you
will be located at the joint unit CNRS/Saint-Gobain
(http://www.svi.cnrs-bellevue.fr), in Aubervilliers, close to Paris
(France).

Candidates should send a CV with cover letter to Emmanuelle Gouillart at
emmanuelle.gouillart at nsup.org.




From stefan at sun.ac.za  Wed Nov  9 02:51:41 2011
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 8 Nov 2011 23:51:41 -0800
Subject: [JOB] junior developer position
In-Reply-To: <20111109080128.4bc5a88d117bb4b9b4a729cd@terre-adelie.org>
References: <20111108223612.GA18336@phare.normalesup.org>
	<CABDkGQn8t3DsOmo5t1_-R+rqfpanq98EuRw+b1nN7YK9-87M2w@mail.gmail.com>
	<20111109080128.4bc5a88d117bb4b9b4a729cd@terre-adelie.org>
Message-ID: <CABDkGQkA=LdL-iicofwsedZdHkQ3e-mtynhVyYp6kEph-v8kwQ@mail.gmail.com>

On Nov 8, 2011 11:10 PM, "J?r?me Kieffer" <google at terre-adelie.org> wrote:
> I would like to advertise another position (fixed term, 3 years max) on
experiment control (using python/Qt).

I can't read French, so I'll have to ask: does this project also provide
the opportunity to contribute back to an open source project?

Regards
St?fan
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From google at terre-adelie.org  Wed Nov  9 02:01:28 2011
From: google at terre-adelie.org (=?ISO-8859-1?Q?J=E9r=F4me?= Kieffer)
Date: Wed, 9 Nov 2011 08:01:28 +0100
Subject: [JOB] junior developer position
In-Reply-To: <CABDkGQn8t3DsOmo5t1_-R+rqfpanq98EuRw+b1nN7YK9-87M2w@mail.gmail.com>
References: <20111108223612.GA18336@phare.normalesup.org>
	<CABDkGQn8t3DsOmo5t1_-R+rqfpanq98EuRw+b1nN7YK9-87M2w@mail.gmail.com>
Message-ID: <20111109080128.4bc5a88d117bb4b9b4a729cd@terre-adelie.org>

Hi all,

I would like to advertise another position (fixed term, 3 years max) on experiment control (using python/Qt).

http://esrf.profilsearch.com/recrute/fo_annonce_voir.php?id=72

-- 
J?r?me Kieffer 


From google at terre-adelie.org  Wed Nov  9 03:32:44 2011
From: google at terre-adelie.org (Jerome Kieffer)
Date: Wed, 9 Nov 2011 09:32:44 +0100
Subject: [JOB] junior developer position
In-Reply-To: <CABDkGQkA=LdL-iicofwsedZdHkQ3e-mtynhVyYp6kEph-v8kwQ@mail.gmail.com>
References: <20111108223612.GA18336@phare.normalesup.org>
	<CABDkGQn8t3DsOmo5t1_-R+rqfpanq98EuRw+b1nN7YK9-87M2w@mail.gmail.com>
	<20111109080128.4bc5a88d117bb4b9b4a729cd@terre-adelie.org>
	<CABDkGQkA=LdL-iicofwsedZdHkQ3e-mtynhVyYp6kEph-v8kwQ@mail.gmail.com>
Message-ID: <20111109093244.e0b6dd23.google@terre-adelie.org>

On Tue, 8 Nov 2011 23:51:41 -0800
St?fan van der Walt <stefan at sun.ac.za> wrote:

> On Nov 8, 2011 11:10 PM, "J?r?me Kieffer" <google at terre-adelie.org> wrote:
> > I would like to advertise another position (fixed term, 3 years max) on
> experiment control (using python/Qt).
> 
> I can't read French, 

Weird ... sometimes the page is in french, sometimes in english with the same URL :/
Going through the portal is easier: http://www.esrf.fr/Jobs/english

> so I'll have to ask: does this project also provide
> the opportunity to contribute back to an open source project?

By default all code ESRF produced should be available for our share-holders (mostly European countries). Making it open-source in GPL is the easiest way we found to meet this requirement (true for 95% of our projects).
Some projects:
https://forge.epn-campus.eu/projects/mxcube/repository
http://www.tango-controls.org/

Nevertheless this contract is very peculiar (french COD, fixed term contract related to a project) is targeting at the migration from Qt3 to Qt4 of a piece of code controlling many beamlines (7 at ESRF, but also in some other places)

So contributing back to open-source projects is possible (within this COD) only for closely related open-source project on which MXCube depends like PyQt, PyQwt, Qwt, Tango, PyMca, ...

Sorry, that's probably not the answer you expected :-/

-- 
Jerome Kieffer

PS: 
Software Engineer (m/f), short-term contract of 18 months minimum and 36 months maximum

time-limited contract
THE FUNCTION

As part of the general ESRF beamline portfolio renewal, the Structural Biology Group will create a new suite of state of the art beamlines for Macromolecular Crystallography (MASSIF). The facility will be built on ID30 and will comprise three beamlines, one with micro-focus capability. All beamlines will be equipped with automated sample changers and advanced sample evaluation instrumentation and software. You will participate in the enhancement of our Python/Qt based beamline control application, mxCuBE required for the implementation of advanced sample evaluation, in two distinct phases : 
? Adaptation of the current product to the latest developments of our sample evaluation and diffraction data processing platform (EDNA) as well as the development of the communication bothways to our laboratory information system (ISPYB) via webservices and implementation of more complicated sample characterisation and data collection strategies 
? Migration of mxCuBE to the new ESRF platform for beamline control applications The mission also involves deployment, support and maintenance tasks to allow a continuous usage of the software by our users during their experiments. Together with the opportunity to extend your knowledge of data acquisition you will work as a member of a team of scientists and developers dedicated to bringing the most advanced sample evaluation and data collection techniques to the European Macromolecular Crystallography Community. mxCuBE is also used by other synchrotrons within Europe and you?ll have therefore to enlarge your interactions to developers outside ESRF. 
This mission will be considered as finished when the migration of MxCuBE to the new platform is completed and all functionality is tested and stable.

 
QUALIFICATIONS AND EXPERIENCE

You should have a higher university degree (MSc, DESS, Master, Diploma, Licenciado, Laurea or equivalent) in Software Engineering. Professional skills with Python programming and the Qt graphical toolkit (PyQt) are mandatory. Knowledge of Javacript and web application development would be an asset. Working experience with git or a similar revision control system would be appreciated. Ideally, you should have a genuine interest in distributed systems, scientific instrumentation software and associated techniques. You should be highly motivated and capable of integrating into the ESRF's multidisciplinary and international staff; ability to work within a dynamic international collaboration is essential.

 

Ref. COD/MXCUBE - Deadline for returning application forms: 18/11/2011


From emmanuelle.gouillart at nsup.org  Sun Nov 13 18:06:05 2011
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Mon, 14 Nov 2011 00:06:05 +0100
Subject: skimage @scipy India
Message-ID: <20111113230605.GA30834@phare.normalesup.org>

	Dear all, 

	I'm going to the conference Scipy India this year, which takes
place from December 4th to 7th. I'll give a tutorial on image processing
similar to the one that I gave at euroscipy 2011
(http://scipy-lectures.github.com/advanced/image_processing/index.html),
Compared to my earlier tutorial, I'll probably include more examples from
skimage as we had a recent release with more goodies, more documentation,
etc. and it's worth advertising the scikit :-D. I will also give a talk
at the main conference where I plan to speak about skimage. 

	Speaking of releases, I'd love to mention/use the new name
`skimage` of the scikit during my talks. St??????fan, any chance that 0.4
could be released before Scipy India?

	There is also the possibility to have sprints at scipy india on
December 6th, I'll see if some people are interested at the conference in
participating to a skimage sprint.

	Cheers,
	Emmanuelle


From stefan at sun.ac.za  Mon Nov 14 23:41:51 2011
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 14 Nov 2011 20:41:51 -0800
Subject: skimage @scipy India
In-Reply-To: <20111113230605.GA30834@phare.normalesup.org>
References: <20111113230605.GA30834@phare.normalesup.org>
Message-ID: <CABDkGQk8ehGUnbhFW3haPRSHqOmprUFa77kDOvZZqbqndrj7mw@mail.gmail.com>

Hi all,

On Sun, Nov 13, 2011 at 3:06 PM, Emmanuelle Gouillart
<emmanuelle.gouillart at nsup.org> wrote:
> Compared to my earlier tutorial, I'll probably include more examples from
> skimage as we had a recent release with more goodies, more documentation,
> etc. and it's worth advertising the scikit :-D. I will also give a talk
> at the main conference where I plan to speak about skimage.

Excellent!  Let me know if you need help putting examples together.
You are also welcome to use any material I prepared for EuroScipy, of
course.

> ? ? ? ?Speaking of releases, I'd love to mention/use the new name
> `skimage` of the scikit during my talks. St?fan, any chance that 0.4
> could be released before Scipy India?

Absolutely!  I was meaning to push out a release a week or so ago, but
I still need some help updating the Debian package (specifically the
license file, and renaming from scikits-image to skimage).  Any
volunteers?

> ? ? ? ?There is also the possibility to have sprints at scipy india on
> December 6th, I'll see if some people are interested at the conference in
> participating to a skimage sprint.

Examples may be a great way to get people started.  I also want to
have a docs sprint sometime soon, because our user guide is in a
rather sorry (non-existent) state.

St?fan


From stefan at sun.ac.za  Fri Nov 25 22:23:13 2011
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Fri, 25 Nov 2011 19:23:13 -0800
Subject: "marching squares" contribution?
In-Reply-To: <424571F6-2155-45AE-8D97-60A326291800@yale.edu>
References: <424571F6-2155-45AE-8D97-60A326291800@yale.edu>
Message-ID: <CABDkGQn2w2Vw3EW-5a3uio_eOmdzsTzYWHtDGfRf5Y=8_7-2rA@mail.gmail.com>

Hi Zach

On Nov 25, 2011 6:56 PM, "Zachary Pincus" <zachary.pincus at yale.edu> wrote:
>
> I while ago I wrote some code to extract isocontours from 2d arrays using
a "marching-squares" type algorithm, with linear interpolation to get
subpixel precision. (It returns a list of numpy arrays containing the
coordinates of each contour...) The inner loop is in c, and it's pretty
fast. Occasionally people ask me for this code, as I've mentioned making it
available from time to time.
>
> Would it be a useful addition to skimage? Or a little too specific?

This item is long overdue on our todo list and would make a very welcome
addition.

Regards
St?fan
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From zachary.pincus at yale.edu  Fri Nov 25 21:44:27 2011
From: zachary.pincus at yale.edu (Zachary Pincus)
Date: Fri, 25 Nov 2011 21:44:27 -0500
Subject: "marching squares" contribution?
Message-ID: <424571F6-2155-45AE-8D97-60A326291800@yale.edu>

Hello,

I while ago I wrote some code to extract isocontours from 2d arrays using a "marching-squares" type algorithm, with linear interpolation to get subpixel precision. (It returns a list of numpy arrays containing the coordinates of each contour...) The inner loop is in c, and it's pretty fast. Occasionally people ask me for this code, as I've mentioned making it available from time to time.

Would it be a useful addition to skimage? Or a little too specific?

Zach


From zachary.pincus at yale.edu  Sat Nov 26 00:39:12 2011
From: zachary.pincus at yale.edu (Zachary Pincus)
Date: Sat, 26 Nov 2011 00:39:12 -0500
Subject: "marching squares" contribution?
In-Reply-To: <CABDkGQn2w2Vw3EW-5a3uio_eOmdzsTzYWHtDGfRf5Y=8_7-2rA@mail.gmail.com>
References: <424571F6-2155-45AE-8D97-60A326291800@yale.edu> <CABDkGQn2w2Vw3EW-5a3uio_eOmdzsTzYWHtDGfRf5Y=8_7-2rA@mail.gmail.com>
Message-ID: <A6AA3084-0B14-49BE-B74D-5107FC9949BE@yale.edu>

https://github.com/scikits-image/scikits-image/pull/82

On Nov 25, 2011, at 10:23 PM, St?fan van der Walt wrote:

> Hi Zach
> 
> On Nov 25, 2011 6:56 PM, "Zachary Pincus" <zachary.pincus at yale.edu> wrote:
> >
> > I while ago I wrote some code to extract isocontours from 2d arrays using a "marching-squares" type algorithm, with linear interpolation to get subpixel precision. (It returns a list of numpy arrays containing the coordinates of each contour...) The inner loop is in c, and it's pretty fast. Occasionally people ask me for this code, as I've mentioned making it available from time to time.
> >
> > Would it be a useful addition to skimage? Or a little too specific?
> 
> This item is long overdue on our todo list and would make a very welcome addition.
> 
> Regards
> St?fan