Feat smartspim zarr compression #2
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jtyoung84
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May 30, 2024
| # Construct settings from env vars | ||
| job_settings = SmartspimJobSettings( | ||
| input_source="/data/SmartSPIM_714635_2024-03-18_10-47-48", | ||
| output_directory="/scratch/", |
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Should output_directory and input_source be hardcoded? Pydantic BaseSettings classes have a neat feature where they'll automatically search for env vars if not set. So if you did something like export INPUT_SOURCE="/data/SmartSPIM_714635_2024-03-18_10-47-48" and export output_directory="/scartch/", then job_settings = SmartspimJobSettings() will pick them up.
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You're right, I was using that for testing. Thanks Jon!
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Adding SmartSPIM raw PNG to Zarr compression for all the stacks of tiles per channel using parallel computing.