pass None for default preprocessing config - #178
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alessandrofelder
marked this pull request as ready for review
March 26, 2026 17:03
PolarBean
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May 15, 2026
| """ | ||
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| if isinstance(config, Path): | ||
| if not config: |
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This assumes config is truthy. its fine but it would be safer to say if config is None
PolarBean
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May 15, 2026
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| logger.info(f"Csv file path: {standardised_csv}") | ||
| logger.info(f"Config: {config}") |
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maybe you should now log preproc_config so that its not None
PolarBean
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May 15, 2026
| if not config: | ||
| # use default mask and padding, and default to outputting | ||
| # into sibling folder of `standardised/` | ||
| preproc_config = PreprocConfig( |
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why not just define MaskConfig() as the default argument for PreprocConfig simplify.
PolarBean
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May 15, 2026
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Some small suggestions but overall looks good :) |
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Description
What is this PR
Why is this PR needed?
Following group meeting discussion, we decided that it should be possible to run
preprocesswithout needing any configuration object. This simplifies the code that people need to understand when working through a basic template-building guide.What does this PR do?
Allows
preprocessfunction to take aNoneconfig (now the default), and handles this by instantiating a defaultPreprocConfigandMaskConfigin the sibling folder ofstandardised.Also ignores read time-outs to biorxiv for link checker.
References
Related to internal discussion of brainglobe/brainglobe.github.io#465
How has this PR been tested?
Added a parameter to an existing unit test
Is this a breaking change?
Nope
Does this PR require an update to the documentation?
Docstrings updated.
Part of simplifying API to enable better documentation in brainglobe/brainglobe.github.io#465
Checklist: