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Re: interested in "image IO" for GSoC 2015


From: Daniel
Subject: Re: interested in "image IO" for GSoC 2015
Date: Tue, 17 Mar 2015 09:57:27 -0400



On Mon, Mar 16, 2015 at 11:01 AM, Carnë Draug <address@hidden> wrote:
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

Hi,

Thanks a lot for the links. That (converting Bioformat from Java to a library in C++/Octave 4.0.0)could be an interesting GSoC project, if possible; but I am not sure how much work/effort it would need.

I am trying to come up some my own thought, but I really love the idea about imglib2 package accessing plugins of ImageJ. I think many people in biomedical or  microscopy area use ImageJ heavily and they also have Bioformats as you mentioned. I would definitely like to look into this. About myself with Java, I am not proficient with Java; I am taking a Java programming course right now this semester at my university. It would be a great opportunity to challenge myself. 

I can access Mac OS when I work in the university and my own laptop runs Ubuntu. I have been trying to build from source with my laptop. Just as an update, a latest piece of excerpt of the configure output was pasted in the end showing many dependencies were missing, which I will be working on to resolve them today.

For the rest days of this week, I will take a look at previous GSoC Octave projects to get a sense how much work can put into a project and I had better have something written down as a draft of the project proposal. Meanwhile, any suggestion/comments are highly appreciated.

Thanks,

Daniel
//------------part of ./configure output 
configure: WARNING: 

I didn't find rsvg-convert, but it's only a problem if you need to
reconstruct octave-logo-*.png, which is the case if you're building
from VCS sources.

configure: WARNING: UNEXPECTED: found nth_element working in g++ 4.8.2.  Has it been patched on your system?
configure: WARNING: Qhull library not found.  This will result in loss of functionality of some geometry functions.
configure: WARNING: GLPK library not found.  The glpk function for solving linear programs will be disabled.
configure: WARNING: cURL library not found.  The ftp objects, urlread and urlwrite functions will be disabled.
configure: WARNING: Xft library not found.  Native graphics will be disabled.
configure: WARNING: FLTK config script not found.  Native graphics will be disabled.
configure: WARNING: OSMesa library not found.  Offscreen rendering with OpenGL will be disabled.
configure: WARNING: qrupdate not found.  The QR & Cholesky updating functions will be slow.
configure: WARNING: AMD library not found.  This will result in some lack of functionality for sparse matrices.
configure: WARNING: CAMD library not found.  This will result in some lack of functionality for sparse matrices.
configure: WARNING: COLAMD library not found.  This will result in some lack of functionality for sparse matrices.
configure: WARNING: CCOLAMD library not found.  This will result in some lack of functionality for sparse matrices.
configure: WARNING: CHOLMOD library not found.  This will result in some lack of functionality for sparse matrices.
configure: WARNING: CXSparse library not found.  This will result in some lack of functionality for sparse matrices.
configure: WARNING: UMFPACK not found.  This will result in some lack of functionality for sparse matrices.
configure: WARNING: ARPACK not found.  The eigs function will be disabled.
configure: WARNING: JAVA_HOME environment variable not initialized.  Auto-detection will proceed but is unreliable.
configure: WARNING: Qt libraries not found -- disabling GUI
configure: WARNING: 
configure: WARNING: I didn't find the necessary libraries to compile native
configure: WARNING: graphics.  It isn't necessary to have native graphics,
configure: WARNING: but you will need to have gnuplot installed or you won't
configure: WARNING: be able to use any of Octave's plotting commands
configure: WARNING: 
configure: 
configure: NOTE: Libraries or auxiliary programs may be skipped if they are
configure: NOTE: not found OR if they are missing required features on your
configure: NOTE: system. 

//-------EOF 


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