Posted by
Paul van Schayck on
Jun 12, 2014; 6:51am
URL: http://imagej.273.s1.nabble.com/Headless-ImageJ2-rc2-Analyze-Particles-returns-no-result-tp5008127p5008154.html
Hey Johannes and Curtis,
Thank you for your quick responses.
On Thu, Jun 12, 2014 at 1:22 AM, Johannes Schindelin
<
[hidden email]> wrote:
> Thank you for that reproducer script, it really saved me *a lot* of time.
>
> What it uncovered, however, are two problems, not one. That's why it took
> so long: in headless mode, we would not register legacy images properly,
> and also -- a really, really longstanding bug! -- the headless generic
> dialog never parsed numbers properly. It always returned 0. Therefore,
> your circularity filter was converted into circularity=0.0-0.0.
>
> I fear this bug goes way back into our first headless support days in
> ImageJA, so it is really embarrassing, but all the better that you
> uncovered it!
>
> Unfortunately, I ran out of time today to clean up the fixes and upload
> new file versions, but I promise to do that tomorrow.
I figured it was a longer standing bug (and should have mentioned
that) as I could only get the particle analyzer headless working on
rather old version of Fiji. I'll keep an eye on Jenkins and Github for
the fixes. I'm also trying to rewrite the macro to js, still
struggling a bit with that, should the bug also be visible there?
Regarding the SCIFIO file opening. Your fix fixed the
NullPointerException. However, now when running with SCIFIO enabled
the following error is shown "There are no images open.". This
regardless of whether I run headless or not, but only occurs when
passing the macro through "-macro" as it does not happen when running
from the script editor. Also adding a wait(4000); fixes the problem.
I fully agree on making SCIFIO default, I was very surprised when I
first discovered a few months a go it was not implemented like this
yet. It will add a lot of nice features.
Regarding the command line options. I'm interested in running in true
headless mode making -batch not directly interesting. So, if I
understand correctly, that while "-macro" is a ImageJ1 option it is
also the preferred way of starting the new ImageJ2 scripts (in js,
bsh, etc). And how exactly does this all relate to the "--ij1" and
"--ij2" flags.
Thank you,
Paul
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