Choose a threshold value using a magicgui widget in napari.

napari_threshold_segmentation.py

"""Choose a threshold value using a magicgui widget in napari.

Based on the magicgui excample script napari_parameter_sweep.py
https://github.com/napari/magicgui/blob/main/examples/napari_param_sweep.py
"""
import napari
import skimage.data
import skimage.filters
from napari.layers import Image
from napari.types import LabelsData

from magicgui import magicgui

# create a viewer and add some images
viewer = napari.Viewer()
viewer.add_image(skimage.data.astronaut().mean(-1), name="astronaut")
viewer.add_image(skimage.data.grass().astype("float"), name="grass")

# turn the gaussian blur function into a magicgui
# for details on why the `-> ImageData` return annotation works:
# https://napari.org/guides/magicgui.html#return-annotations
@magicgui(
    # tells magicgui to call the function whenever a parameter changes
    auto_call=True,
    # `widget_type` to override the default (spinbox) "float" widget
    thresh={"widget_type": "IntSlider", "max": 255},
    layout="horizontal",
)
def threshold(layer: Image, thresh: int = 10, dark_background: bool = False) -> LabelsData:
    """Choose a threshold value for the ``layer``."""
    if layer:
        if dark_background is False:
            return layer.data > thresh
        else:
            return layer.data < thresh


# Add it to the napari viewer
viewer.window.add_dock_widget(threshold, area="bottom")

napari.run()