how to specify scale, translation, units
Closed this issue · 2 comments
How can I define the scaling, translation, and units of the data?
Transferred from NGFF-Converter to bioformats2raw, as NGFF-Converter uses bioformats2raw internally to perform conversion.
bioformats2raw doesn't have a way to specify scaling/translation metadata outside of what is parsed from the original input file. See:
- https://github.com/glencoesoftware/bioformats2raw/blob/master/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java#L2314
- https://github.com/glencoesoftware/bioformats2raw/blob/master/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java#L2353
We're very unlikely to add this capability in the foreseeable future; the best approach at the moment would be to insert this metadata after conversion.
Closing as wontfix, but feel free to re-open if there is a concrete use case where adding metadata post-conversion is not possible.
The decision to silently insert default values with no options for overrides is an invitation for confused users and potentially broken data. If this is the course you want to take, then this tool should visibly warn users that the scaling, translation, and unit metadata were not found in the source data and will be set to some defaults.