Topostats filters plugin for playNano

[derollins]

Hi all, I've been developing a platform for high speed (time series/ video) AFM processing and analysis, playNano and have wrapped the TopoStats filters module so it can be used as a plugin for the playNano processing workflow. You can configure most of the settings, i.e. lines in the config file, from the function parameters which lets it interface with playNano's internals and CLI.

The TopoStats plugin is part of the playNano plugin library under processing: https://github.com/derollins/playNano-plugins/tree/d5d3c47685cbda735de18da99d6c170a1b7ecd55/src/playnano_plugins/processing

[ns-rse]

We've some breaking changes in the pipeline for you @derollins as #1284 completely overhauls how we handle data internally and pass things around, introducing dataclasses with type validation via Pydantic.

A cursory look and I think it might just be this call that will need changing but you'll also have to from topostats.classes import TopoStast and construct a TopoStats object to pass in to the call that instantiates an object of type Filters.

[derollins]

Thanks for the heads-up, I had spotted the big changes in the Issues list but I haven't had a chance to go in and see how they would work. I'll look here and I'll try and make a patch based on that PR ready for when it merges. I guess I just have to build the topostats_object and use that rather than the bare numpy array, I'll probably keep the filler vaules for pixel_to_nm_scaling and something arbitary for filename to keep the numpy array in- numpy array out API for playNano.

P.s. The dataclass approach looks really clean, I was thinking about something similar for the AFMImageStack within playNano which is functionally very similar but I just went with a standard class as that was more familiar. May look at refactoring it in the future.

[derollins]

UPDATE: I've updated the topostats_filters function to create a TopoStats object and feed that into Filters if topostats.classes is available. The previous behaviour is retained if topostats.classes can't be imported (in older versions of Topostats). It seems to work alright for version 2.4.0 and previous versions. I've made a PR and am just working on tidying and testing.

PR: derollins/playNano-plugins#2