Add points with features

Display a points layer on top of an image layer using the add_points and add_image APIs

Tags: visualization-basic

import numpy as np
from skimage import data
from skimage.color import rgb2gray

import napari

# add the image
viewer = napari.view_image(rgb2gray(data.astronaut()))
# add the points
points = np.array([[100, 100], [200, 200], [333, 111]])

# create features for each point
features = {
    'confidence': np.array([1, 0.5, 0]),
    'good_point': np.array([True, False, False])
}

# define the color cycle for the face_color annotation
face_color_cycle = ['blue', 'green']

# create a points layer where the face_color is set by the good_point feature
# and the border_color is set via a color map (grayscale) on the confidence
# feature.
points_layer = viewer.add_points(
    points,
    features=features,
    size=20,
    border_width=7,
    border_width_is_relative=False,
    border_color='confidence',
    border_colormap='gray',
    face_color='good_point',
    face_color_cycle=face_color_cycle
)

# set the border_color mode to colormap
points_layer.border_color_mode = 'colormap'


# bind a function to toggle the good_point annotation of the selected points
@viewer.bind_key('t')
def toggle_point_annotation(viewer):
    selected_points = list(points_layer.selected_data)
    if len(selected_points) > 0:
        good_point = points_layer.features['good_point']
        good_point[selected_points] = ~good_point[selected_points]
        points_layer.features['good_point'] = good_point

        # we need to manually refresh since we did not use the Points.features
        # setter to avoid changing the color map if all points get toggled to
        # the same class, we set update_colors=False (only re-colors the point
        # using the previously-determined color mapping).
        points_layer.refresh_colors(update_color_mapping=False)


if __name__ == '__main__':
    napari.run()