Posted by
Rex Kerr on
Dec 01, 2013; 2:19pm
URL: http://imagej.273.s1.nabble.com/Standalone-ImgLib2-usage-tp5005746p5005748.html
Hi Stephan,
Thanks for the swift reply!
That only partly helps; it takes care of dependencies, but requires me to
use Eclipse, which while almost essential for Java is more of an irritation
to me than useful when using Scala (which I am). But fine--I can use
Eclipse.
But the dependencies are only part of the issue. I know how to solve all
of those semi-manually and did (after realizing that the dependencies
listed on the examples page were incomplete). The bigger problem is that I
can't figure out how to do much of anything without looking at source code,
which usually means something in Fiji, which usually depends on more things
in Fiji.
My experience so far, trying to stick to ImgLib2 alone, has gone something
like this:
Tried to save an image file. There are zero examples of saving a file.
SCIFIO javadocs are not easily available. Trial and error revealed
something to do with images not being PlanarImg. Using the "universal
image copy" example didn't work to copy to a PlanarImg--the planar image
would stay blank. SCIFIO then throws exceptions on an Img without telling
you it wants an ImgPlus. No examples of copying an ImgPlus. Etc..
Another case study: I tried to take a histogram. No examples. Methods
look straightforward enough, but do nothing. Eventually I notice the
.process method. No documentation stating that you need to call it or you
will get zeros (rather than e.g. an exception).
Another: I try to take a threshold. No examples of thresholds. Classes
and methods that contain the word "threshold" are not documented. Forget
it and implement it myself.
It shouldn't be this hard, should it?
--Rex
On Sun, Dec 1, 2013 at 5:44 AM, Stephan Preibisch <
[hidden email]>wrote:
> Hi Rex,
>
> ImgLib2 can be developed and run independent of Fiji. The easiest way is to
>
> 1) check out the ImgLib2 repository using GIT
>
https://github.com/imagej/imglib> 2) Install & Run Eclipse
> 3) File > Import > Existing Maven Project (then select the directory and
> choose all the poms that you want, for example all of them)
>
> You are good to go, now add these projects as dependency of your project.
>
> To get started, try the examples:
http://fiji.sc/ImgLib2_Examples> You also find them in the submodule (ImgLib2-examples)
>
> Hope this helps,
> Stephan
> ---
>
> Dr. Stephan Preibisch
> HFSP Fellow
> Eugene Myers lab / Robert H. Singer
>
> MPI-CBG / Albert Einstein College of Medicine / HHMI Janelia Farm
>
> email:
[hidden email] /
[hidden email] /
>
[hidden email]
> web:
http://www.preibisch.net/>
>
> On Dec 1, 2013, at 14:23 , Rex Kerr wrote:
>
> > I've been attempting to use ImgLib2 in a quasi-standalone fashion to
> > automate some image processing tasks. So far this has been an exercise
> in
> > frustration due to a combination of underdocumented dependency on other
> > libraries for critical functionality (ImageJ/Fiji, SCIFIO, etc.) and lack
> > of documentation of ImgLib2 itself.
> >
> > This has been so difficult thus far that I have to wonder if I'm missing
> > some key resource. Before I ask specific questions: what is it that I
> was
> > supposed to do? Or is ImgLib2 not intended to be used apart from Fiji
> etc.
> > (and a good working knowledge of what ImageJ can do and how it does it)?
> >
> > --Rex
> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
> --
> ImageJ mailing list:
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