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Catch json decoding error from incomplete NDTIFF#298

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ziw-liu merged 1 commit into
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ndtiff-skip-broken-json
May 8, 2025
Merged

Catch json decoding error from incomplete NDTIFF#298
ziw-liu merged 1 commit into
mainfrom
ndtiff-skip-broken-json

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@ziw-liu ziw-liu commented May 7, 2025

Allows conversion of:

/hpc/instruments/jacobo.isim/Notch/20250501_cldnb-lyn-mScar_myo6b-bactin-gfp_she-h2b-gfp_Notch_LY40nM_timelapse/50_hpf_1

@ziw-liu ziw-liu marked this pull request as ready for review May 7, 2025 16:25
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✅ Looks good to me!
Very rarely, but iSIM acquisitions can end unexpectedly. The default iohub behavior was to quit on such datasets, so this fix is very helpful. The warning message is clear and informative, and it’s great that the rest of the processing can continue even when metadata is incomplete.

Tested on my end with a partially written dataset - works as expected.

Nice and clean fix - thanks, Ziwen!

@akila-14 akila-14 self-requested a review May 8, 2025 16:34
@ziw-liu ziw-liu merged commit 0348acd into main May 8, 2025
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@ziw-liu ziw-liu deleted the ndtiff-skip-broken-json branch May 8, 2025 18:36
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2 participants