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fmi-faim / faim-ipa

A collection of Image Processing and Analysis (IPA) functions used at the Facility for Advanced Imaging and Microscopy (FAIM)
BSD 3-Clause "New" or "Revised" License
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z adjustment: be more tolerant with missing z positions #100

Closed imagejan closed 7 months ago

imagejan commented 8 months ago

We currently raise a ValueError here:

https://github.com/fmi-faim/faim-hcs/blob/79effcaceebd0596fad6030d475402b6f3ee5838/src/faim_hcs/hcs/cellvoyager/ZAdjustedStackAcquisition.py#L76-L77

This leads to disruption of processing when the trace log files contain data from acquisitions without SearchFirst mode.

Let's instead just log a warning, and either skip the current file or return null as its z position, so we can handle it later in the process.

imagejan commented 7 months ago

Addressed by https://github.com/fmi-faim/faim-hcs/pull/103.