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Fiji, the nrrd file format, and HandleExtraFileTypes

Posted by Colin Poczatek on Apr 10, 2013; 4:45pm
URL: http://imagej.273.s1.nabble.com/Fiji-the-nrrd-file-format-and-HandleExtraFileTypes-tp5002602.html

Hi all,

I've been trying to wrap my head around Fiji and I'm a little stuck on
the best way to handle this.  This is my train of thought.

- We have 2 image file formats, .im and .nrrd and a plugin that can open
both.

- At the OS level I'd like to be able to associate these file types with
Fiji to take advantage of consistency across platforms and avoid shell
script / classpath sillyness.

- In Fiji the HandleExtraFileTypes class is inside
IO_-2.0.0-SNAPSHOT.jar as opposed to having the .java and .class in
plugins/Input-Output/ where you could edit the java.

- Also I am most likely blind because I can't find the source for Fiji's
HandleExtraFileTypes.  It's not in the jar itself and it's not in fiji.git?

* Because of the above I'm not exactly sure what class is actually
opening .nrrd files.  In the case of a simple .nrrd (eg blobs.gif saved
as a nrrd, which has a bug I think but that's another email) it looks
like io.Nrrd_Reader.  In the case of one of my nrrds it's passed to loci...

- This makes me think that editing HandleExtraFileTypes is maybe not the
way to go.  Is there a better (or any?) way to associate a given file
type with a specific plugin?  Is there a reason HandleExtraFileTypes is
"hidden" in a jar?

Thoughts?

Thanks
Collin


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