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PreibischLab / BigStitcher

ImgLib2/BDV implementation of Stitching for large datasets
GNU General Public License v2.0
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Getting BigStitcher to work with pyimagej #74

Closed alam-shahul closed 4 years ago

alam-shahul commented 4 years ago

Hi! I'm trying to operate BigStitcher in headless mode via pyimagej. I made a post on forum.image.sc about my problem.

It works fine when I invoke the macro from the command line, but when I try to do it in pyimagej I get the following error:

0
Cannot add scrollbars, it's not a Container but a GenericDialogPlus

This seems like a GUI-related error, which makes me think BigStitcher isn't actually running in headless mode when I call it this way. Is there a way to get around this?

hoerldavid commented 4 years ago

It turns out this was caused by a typo in the input filename. We should not hang indefinitely in that case, but exit cleanly, I guess.

hoerldavid commented 4 years ago

Hi @alam-shahul,

There was indeed a bug that would cause the Automatic Loader to run into an infinite loop when an incorrect path is given to it. It should be fixed with https://github.com/PreibischLab/multiview-reconstruction/commit/c194a79aabdb7bf0671c8fcba7e34b3adec5d57f. Now, we show an error message in that case:

Screenshot 2020-07-29 at 14 34 20

I made a new release of BigStitcher in Fiji which includes the fix.

Best, David

alam-shahul commented 4 years ago

Oh, great! Thanks for looking into it.