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Re: [fiji-devel] Fiji, the nrrd file format, and HandleExtraFileTypes

Posted by dscho on Apr 19, 2013; 8:42pm
URL: http://imagej.273.s1.nabble.com/Fiji-the-nrrd-file-format-and-HandleExtraFileTypes-tp5002602p5002724.html

Hi Curtis,

On Thu, 18 Apr 2013, Curtis Rueden wrote:

> > In many cases, the source can be found (as I pointed out in earlier
> > mails) via http://fiji.sc/(class-name.java). In this case:
> > http://fiji.sc/HandleExtraFileTypes.java
>
> Thanks for the reminder about this useful feature. However, I fear it
> may be broken at the moment due to the recent server migration.
> Accessing the link above tries to load a wiki page with that name and
> reports "There is currently no text in this page."

Yes, you're correct. I added a script to fiji.git which lets me check
whenever I have to make updates to fiji.sc's Apache configuration that all
the services work as expected: bin/verify-fiji.sc.sh.

Now, the convenient source code search should work again.

> > I agree that the way to go is ImageJ2 (in conjunction with SCIFIO).
> > With the work I will complete soon, Fiji will always have an ImageJ2
> > context available. After that, we can use ij-io in
> > HandleExtraFileTypes.
>
> Good idea! Doing that had not occurred to me.

Great, I will let you know as soon as I finished that work. FWIW I will
also post updates here: http://trac.imagej.net/ticket/1662

> > That will bring all the benefits of SCIFIO to ImageJ 1.x while
> > avoiding duplicate work when implementing format readers/writers (no
> > need to implement things twice, once for ImageJ 1.x and once for all
> > the users of SCIFIO such as KNIME, Icy, ITK etc).
>
> Indeed. However, as pointed out by Jay Unruh in another thread [1], it
> would still not be quite as powerful as HandleExtraFileTypes in that
> there is no obvious way to override the display of the image data after
> it is loaded. We will need a separate extensibility point for that.

Well, HandleExtraFileTypes is the class I would like to use for the ij-io
wrapper. So everything HandleExtraFileTypes can do, we will still be able
to do, just better.

For example, the major idea of ImageJ 1.x plugins implementing image
readers was that they extend ImagePlus. That way, the result could be
intercepted by the batch mode. And likewise, IJ.openImage() would still
return the ImagePlus (actually, the reader plugin instance).

But maybe I misunderstood what you meant by overriding the display?

Ciao,
Dscho

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