Re: interested in "image IO" for GSoC 2015

[Carnë Draug]

Better to keep the maintainers mailing list on CC.  Also, on the Octave
mailing list, etiquete is to do interleaved or bottom posting which makes
conversations easier to follow:

  https://en.wikipedia.org/wiki/Posting_style#Bottom-posting

On 25 March 2015 at 03:08, Daniel <address@hidden> wrote:
> On Tue, Mar 24, 2015 at 6:31 PM, Carnë Draug <address@hidden> wrote:
>>
>> On 23 March 2015 at 18:45, Daniel <address@hidden> wrote:
>> >
>> > I decided to work on imglib2, if you agree for GSoC. Shall I fill in the
>> > public and private form from Octave wiki? If so, I will do it send you a
>> > draft for preview and finish the from as soon as possible.
>> >
>>
>> I would be happy to mentor such project, but please consider the
>> following:
>>
>>   1 - we will only accept applications from users that have already
>>   contributed to the project.  It is all good to tell us what you can
>>   do but you will also have to show us.  I already provided you with
>>   some easy projects.  You haven't submitted a single patch yet.
>>
>>   2 - for your specific project, would be better to have a proof of
>>   concept.  Are you sure Octave has what it needs to do it?  If it
>>   doesn't, then the project would turn into improving Octave's java
>>   interface which is a very different thing and would probably require
>>   a mentor other than me.
>>
>>   3 - I believe that most of ImageJ plugins and functions do not use
>>   imglib2, instead use the original ImageJ classes.  There may be more
>>   value on using that instead.  It should at least make distribution
>>   easier for downstream packagers since ImageJ2 seems like a pain and
>>   is packaged by no one.
>>
>>   4 - we expect GSoC students to take it as full-time job.  I don't know
>>   the details of your PhD studies, but please be aware of what we will
>>   expect from you time-wise.
>>
>> Carnë
>
>
> Hi Carnë,
>
>     Thank you very much for your guidance.
>
>     I have been trying to see different possibilities and do some planning
> in my mind, have not done real work yet. (It'd be better if I could start
> much earlier). I hope I can get something done lately.
>
>     Just for discussion, I did a bit research on the internet just now. I
> think the idea of an interface for importing imagej plugin so as to
> naturally involving packaging/managing system is really good. I found some
> projects/topics analogous or in relation to this.
>
>     0. There was discussion about image output format from Octave differs
> from ImageJ, [1][2]. The solution to this should be either simple (a
> converter) or complicate (maybe rewrite some library functions)
>
>     1. Matlab accesses Java, and provides Java-compatible compiler SDK.
> [3][4][5]
>
>     2. on Project Kenai, "GNU OCTAVE IMAGEJ BINDINGS",[6] . According to
> their webpage, they started this project in 2009 with three people. I have
> not found any further information about their progress. Maybe it is just
> identical to one of the followings.

I have seen this before.  They do this by writing temporary files and then
reading it on the other side.  Let us not do this.

>     3. MIJ, A Java package for running ImageJ and Fiji within Matlab, [7].
>
>     4. Miji,[8]
>
>     5. GigHub, imagej-matlab [9],  MATLAB integration with ImageJ data
> structures and runtime.
>
>
>     To sum up, we may have two different topics here. One is that the image
> output format is currently not compatible with ImageJ. Maybe this is related
> to the one of the suggestions in your first email to me --- convert octave
> array such that imagej/plugin can be used. The second one is that there
> might do not exist a Octave JVM that can be readily used to call Java
> routines, even load ImageJ plugin/macro directly. In the latter case, I am
> curious to know how you would think the usefulness to implement such JVM.
> Imagine, it may be able to use imagej plugin directly --- effectively,
> together with the prospective packaging system, it would or it has the
> potential to become an "enhanced" ImageJ that can readily do any image
> processing / post processing/ numerical analysis. Meanwhile, more Java
> components would be introduced. I am not sure if this could be in line with
> the big picture of the development of Octave. But of course, we only add
> what we really need to do; some balance can be made, just towards yet
> another Matlab, enhanced one. Anyway, I personally think this is fantastic.
> My question would be, in which way it is more performance-wise and/or
> effort-wise efficient or more manageable to write plugins/packages, using
> java, macro, or C++ or .m? I have not done further investigation. I only
> find several java source files in Octave. I will study it further.

macros? There's no macros in Octave.  Other than that, an Octave package
can have C++ and m files intermixed.  I have never written java code for
Octave but take a look at how the old Octave java package did it.

Again, I am unsure we have mentors for this project, so you better have
something sightly working and a good plan so we get an idea of what the
project encompasses if you want it to be accepted.

>     Lastly, I am fully aware of the fact that the summer project requires
> full-time commitment. That's not an issue for me. The nature of my current
> work at NYU determines my flexible working schedule, especially in the
> summer, I can focus on the summer project for sure. Personally, I also want
> to take this opportunity to push myself in programming and software design.
> Contributing to the open source community is a great way to go.
>
>     I will let you know my progress when I have something can show you.
>
>     Thanks,
>
>     Daniel
>
> [1] http://permalink.gmane.org/gmane.comp.java.imagej/35079
> [2]
> http://imagej.1557.x6.nabble.com/ImageJ-reads-reversed-bits-from-unsigned-16-bit-TIFF-saved-by-imwrite-from-GNU-Octave-td5010285.html
> [3] http://www.mathworks.com/products/matlab-compiler-sdk/index.html
> [4]
> http://blogs.mathworks.com/community/2009/07/06/calling-java-from-matlab/
> [5] http://www.mathworks.com/matlabcentral/newsreader/view_thread/290176
> [6] https://kenai.com/projects/octave-imagej
> [7] http://bigwww.epfl.ch/sage/soft/mij/
> [8] http://fiji.sc/Miji
> [9] https://github.com/imagej/imagej-matlab.
>