lowe-lab-ucl / arboretum

Track and lineage visualization with btrack and Napari :evergreen_tree:

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testing script

alessandrofelder opened this issue · comments

For testing purposes it would save a lot of time to have a python script that:

Adds some sample data to napari
Opens a napari window
Opens and runs arboretum

Analogous to brainglobe/cellfinder#325 but wouldn't suffer from https://github.com/brainglobe/cellfinder-napari/issues/#71 as we (at least for now) run everything in the same thread.

###Pseudo-code sketch (untested and likely wrong!)

import napari
from pathlib import Path

viewer = napari.Viewer()
file_path = Path() # any images needing opening
viewer.open(file_path)

# call script
from arboretum import what_you_want_test

what_you_want_to_test() # this may change depending on what the dev wants to test?```