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Configure btrack run from napari #26
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This reverts commit 753b40e.
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Looking good! I had a play with this and have a little bit of feedback while this is still in development:
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improve docstrings and function signature Co-authored-by: David Stansby <[email protected]>
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Thanks for some great review comments, @dstansby @paddyroddy @quantumjot ! |
quantumjot
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…figs (#64) Fixes #63 - handle arbitrary user configs - when the plugin starts, the example `cell_config` and `particle_config` files are loaded, and users can load more of their own This ended up being a bigger refactor than I planned - I need to refactor quite a few of the functions because they assume there are two modes ('cell' and 'particle'). And at the same time I moved toward a more modular structure as has been suggested #26. **refactor `napari_btrack.track` into various sub-packages and modules** - `napari_btrack.track`: - renamed to `napari_btrack.main` - contains only code for launching the plugin, defining callback functions, and running the analysis - `napari_btrack.config`: - a new module with classes to handle converting between scaled and unscaled matrices in `MotionModel`s - removed `Matrices` class (which hardcoded values for `cell` or `particle`modes) and replaced with `UnscaledTrackerConfig` to handle arbitrary user configs - `napari_btrack.widgets`: - a new sub-package for creating the widgets for the plugin - `napari_btrack.sync`: - a new module to handle updating a config from widget values or vice versa **other changes** - added per-file-ignores for some linting rules (allow `assert` in test files, allow unused imports in `__init__.py` files) - some classes / functions were being imported only for type checking - move these imports in a check `if TYPE_CHECKING:` so that they're not imported at runtime - renamed the function that launches the plugin from `napari_btrack.track.track` to `napari_btrack.main.create_btrack_widget` - explicitly set the expected `widget_type` when using `magicgui.widgets.create_widget` - knowing the widgets we're using should make it easier to move to using `qt` directly at some point, which would allow us to have separate tabs for each section - add tooltips for every widget - they're based on the `btrack` api docs --------- Co-authored-by: Patrick Roddy <[email protected]>
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This PR adds
This PR represents the fallback option if we don't manage to address the related issues quantumjot/btrack#268 quantumjot/btrack#267 , so I'd suggest to merge this once we're happy the functionality is correct (although the code and the aesthetic are rough around the edges).
The code behind this could definitely do with some modularisation (~all in one file currently 😱 ) and other tidying.
I suggest we address the modularisation and tidying as part of quantumjot/btrack#266 (the next priority) as the tabifying should naturally enforce some modularisation.