Fwd: interested in "image IO" for GSoC 2015

[Carnë Draug]

On 16 March 2015 at 13:42, Daniel <address@hidden> wrote:
> Hi everyone,
>
> I have been watching the list for many years and now I am a PhD student in
> the US studying graph-theory-based  molecular network topology prediction,
> primarily using C++.
>
> I am interested in Image Processing because  several of my previous
> microscopy projects; I was attempting to use Octave to do the image
> processing/analysis, but loading some formats of the images was not
> possible.

Have you ever heard of bioformats?  That will probably read all the formats
you need for microscopy.  They have a Matlab package which I started to port
to Octave last year.  However, it is still dependent on the upcoming 4.0.0
release [1].  I kinda regret how I did it, and will do it again once 4.0.0
is released but it may be useful for you.

> Therefore I found both the topics listed in the "Image Analysis"
> section in the webpage "http://wiki.octave.org/SoC_Project_Ideas"; very
> interesting and relevant to my data analysis work. I am planning to start
> contributing to Octave community in a relative intensive manner driven by my
> own interest and also some external pressure and guidance, by joining the
> GSoC project.
>
> I learnt C++ programming several years ago and currently my daily work is
> using C++ for my PhD project. During this summer, I would like to spend time
> on the GSoC. I am aware of the general procedures listed in the wiki and I
> also know there are several mailing lists, ICR and the content on the Octave
> wiki. Just to be sure, I still want to ask, what would you suggest me to do
> in the first place? Built it on my computer? And how can I get started for
> the GSoC application?

Being able to build Octave from sources is a must if you want to contribute
for Octave.  This is really easy if you are using Linux.

If your plan is to contribute to image processing, implementing imtranslate
for the image package is probably among the easiest short-projects.  If you
do image analysis, you have probably faced against a function that exists in
Matlab but not in Octave yet.  Such missing functions are nice because you
are developing them for you.  For example, imadjust only works for images
of class double with values in the [0 1] interval.  There is also a more
detailed list of missing functions [2].

> By the way, I am not sure if the image processing projects and its mentor
> are still available. If not, I may want to and I am also very happy to do
> something else, maybe related to my PhD thesis work.

Yes, I am still available to mentor any of those projects.  But feel free
to come up with your own projects.  Another idea, would be an imglib2 package
that converts Octave Arrays into net.imglib2.img in order to access the
many ImageJ plugins (this would require knowledge of Java as well).

Carnë

[1] https://github.com/carandraug/bioformats/tree/octave
[2] http://wiki.octave.org/Image_package#Missing_functions