Re: kawa script using mpicbg_-1.0.2.jar -> ERROR

Posted by David Pirotte on Oct 18, 2015; 6:23am
URL: http://imagej.273.s1.nabble.com/kawa-script-using-mpicbg-1-0-2-jar-ERROR-tp5014635p5014673.html

Hello Stephan,

> You need mpicbg-1.0.2.jar and mpicbg_-1.0.2.jar, the latter contains
> ImageJ related classes (plugins and such, therefore the _) and has the
> first as dependency which does all the work.

Thanks, that solved the above. Now I have 2 other problems:

(1) "Linear Stack Alignment with SIFT" now works, _but_, iff I display images on
the screen, which is required to call "Images to Stack":

        (a) I want to open images in memory only and built the stack myself,
                example(s) [preferably kawa/clojure of course since I use kawa]
                welcome;

        (b) "Linear Stack Alignment with SIFT" does not expect/accept a stack
                argument, I would need, if possible, that you implement a version
                that accept a stack instead of 'magically' grab the one fiji creates
                when calling "Images to Stack" time:

        would that be possible?

(2) The following should be easier to solve, especially after I solve (1.a), but for
the record:

        (a) when using fiji, "Images to Stack" closes all image windows and
                reopen a new 1 which appears to be the stack displaying the first
                image;

                when scripting this re-opening does not happen

        (b) because of the above, which seems mandatory, "Stack to Images"
                fails when scripting, but even if it did, that would still not be
                sufficient for us, since I want to save the stack as new images
                on disk:  how do I get the new iplus of all images '...aligned...' on
                the stack?

As you understood already, it is extremely important for us, I should say mandatory
actually, that absolutely everything happens in memory and no windows  is/needs to
be opened during the execution of the script.

Thanks,
David

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