point in masked region (for Shen Han)

point_in_masked_region.py

import numpy as np
import napari
from skimage import data

# fake tomogram
tomogram = np.random.random((300, 300, 300))

# fake mask
mask = data.binary_blobs(
    length=300, n_dim=3, blob_size_fraction=0.3, volume_fraction=0.1
)

# random particle positions
positions = np.random.uniform(low=0, high=300, size=(100, 3))
idx = positions.astype(int)  # integer positions

# check if integer particle position is in a masked region
in_mask = mask[idx[:, 0], idx[:, 1], idx[:, 2]] == 1

# visualise in napari
viewer = napari.Viewer(ndisplay=3)
viewer.add_labels(mask, blending='translucent_no_depth')
viewer.add_points(
    positions,
    features={'in_mask': in_mask},
    face_color='in_mask',
    face_color_cycle=['white', 'green']
)
napari.run()