These are chat archives for fiji/fiji

16th
Nov 2016
Feivel92
@Feivel92
Nov 16 2016 15:12
Hi there! I am trying to run a macro including the bUnwarpJ plugin. When I record the macro, everything works just fine - but when I do the same image processing again, this time by running the macro, the bUnwarpJ step stops too early (approx after 2 sec vs 15 secs when doing it manually). I'm now trying to to figure out if it's a problem with ImageJ, the plugin, or me.. My best guess would be that in the macro processing, there's some kind of timer which kicks in when one step is taking too long, but I couldn't find any information on that. Have you heard of this before?
John Bogovic
@bogovicj
Nov 16 2016 15:19
@Feivel92 There is a parameter called "Stop Threshold" that determines how long the algorithm will run. But the particular images that are input will also play some part in how long the algorithm runs.
I would recommend trying to lower the stop threshold
Feivel92
@Feivel92
Nov 16 2016 15:27
@bogovicj When I do all the steps by hand, the whole thing works like a charm, only in the macro the step involving bUnwarpJ stops way too early - with the same threshold value as I used when doing it manually.
John Bogovic
@bogovicj
Nov 16 2016 15:27
@Feivel92 Are you also using the same images as input?
Feivel92
@Feivel92
Nov 16 2016 15:30
@bogovicj Yeah, I recorded the steps when I did them by hand and used the macro on the same data. (Also checked the recording afterwards)
John Bogovic
@bogovicj
Nov 16 2016 15:34
That is strange indeed, I take it the results are different as well?
Could you post the resulting macro?
Feivel92
@Feivel92
Nov 16 2016 15:36
@bogovicj Ah, I just compared the faulty results with some by-hand results where I leave out steps on purpose and I could reproduce them. It seems like it isn't a problem with FiJi, but with bUnwarpJ itself.. (He just ignores the landmarks file I feed him). Thank you for your help!
John Bogovic
@bogovicj
Nov 16 2016 15:38
I didn't do much, but glad to talk you through it - perhaps you can try contacting the author of the plugin
Curtis Rueden
@ctrueden
Nov 16 2016 17:53
The maintainer of bUnwarpJ is @iarganda, who is very responsive and helpful. Maybe he sees this? If not, post on forum.imagej.net and mention him there. Or open a GitHub issue in the fiji/bUnwarpJ repository. :smile: