Usage instructions in readme #28
Conversation
|
NB: as noted by @manics and discussed with @pwalczysko, the behaviour of Just added more info about renaming of Well -> Well Name etc. |
will-moore
force-pushed
the
usage_instructions_in_README
branch
from
04d2acd to
c3b28f3
Compare
README.rst
Outdated
| - ``original``: Print the original metadata in ini format | ||
| - ``pixelsize``: Set physical pixel size | ||
| - ``populate``: Add metadata (bulk-annotations) to an object (see below) | ||
| - ``populateroi``: Add ROIs to an object |
There was a problem hiding this comment.
I think this feature is largely a legacy feature which came together with the decoupling of the metadata plugin:
- the ROI population API is still in upstream OMERO.py -see omero.util.populate_roi
- the
omero_metadataplugin currently simply imports this API and exposes it as a subcommand - in terms of functionality, the current version of
populate_roiprimarily supports ROIs generated by a few proprietary HCS file formats (Flex, MIAS, InCell)
Open for discussion but my feeling is we should rather keep this plugin focused its annotation functionalities (tables, maps, original metadata). As part of the IDR work, @manics started work on https://github.com/ome/omero-rois which might be a much more appropriate location for this particular API.
There was a problem hiding this comment.
How about deprecate populateroi (I've never figured out how it works or where it gets the ROIs from) and avoid mentioning it anywhere?
There was a problem hiding this comment.
I'll remove populateroi. There's also the rois command. Not sure what that does either.
There was a problem hiding this comment.
@will-moore the rois command enables to delete rois in that container and list them in form ROI:ID. I think it is useful
|
reads fine now. Ready to merge FMPOV |
Added usage instructions to the README, particularly for
populatecommand.See it staged at https://github.com/will-moore/omero-metadata/tree/usage_instructions_in_README