|
| From: | Daniel |
| Subject: | Re: interested in "image IO" for GSoC 2015 |
| Date: | Fri, 27 Mar 2015 15:41:22 -0400 |
On Thu, Mar 26, 2015 at 8:03 AM, Carnë Draug <address@hidden> wrote:Again, please keep maintainers mailing list on CC, and write your
reply at the bottom.
On 26 March 2015 at 08:57, Daniel <address@hidden> wrote:
> Morning,> On Wed, Mar 25, 2015 at 8:46 AM, Carnë Draug <address@hidden> wrote:
>>
>> 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.
>> >
>
>
> I did some more research about with octave. There are some issues that I did
> not expect. Also I am afraid it is difficult to find an available mentor in
> that area.
>
> I am generally interested in the suggested project ImageIO, and if possible,
> if no else take it, I am also interested in the N-d image processing. I
> would like to start with you specifically. But I am sorry it might be late
> to prove myself given the limited time recently.
If you don't even submit a patch, then we you will not be selected. The
application deadline is tomorrow. We then have until 13 of April to rank
and select students.I have been working on imtranslate and imadjust, I mentioned the progress in my wiki @octave, http://wiki.octave.org/User:DanielI will continue working on it during the time and submit the patches. That is on my TODO list.
> I just want to avoid any
> conflict, I would like to write the template application before the deadline
> about the ImageIO project, (or also N-d image processing project), if so far
> no other student works on it.
As far as I am aware, no one else is applying for those projects. But
please, do not think that there's a slot for every project, or that we
will select a student just because there's no one else.
> And I will also reply this email regarding to
> this, in the list, after your confirmation.
Carnë
I really appreciate the comments and suggestion, this is *exactly* what I want. I would like to improve myself and give back to the community; I have been using Octave since 2007. Please find my wiki template here: http://wiki.octave.org/User:DanielI will update it when I can and also submit the form on google as soon as possible.Thanks a lot! Any comments are more than welcome!Daniel
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