3D_paths.py

"""
3D Paths
========

Display two vectors layers ontop of a 4-D image layer. One of the vectors
layers is 3D and "sliced" with a different set of vectors appearing on
different 3D slices. Another is 2D and "broadcast" with the same vectors
appearing on each slice.

.. tags:: visualization-advanced, layers
"""

import numpy as np
from skimage import data

import napari

blobs = data.binary_blobs(
            length=128, blob_size_fraction=0.05, n_dim=3, volume_fraction=0.05
        )

viewer = napari.Viewer(ndisplay=3)
viewer.add_image(blobs.astype(float))

# sample vector coord-like data
path = np.array([np.array([[0, 0, 0], [0, 10, 10], [0, 5, 15], [20, 5, 15],
    [56, 70, 21], [127, 127, 127]]),
    np.array([[0, 0, 0], [0, 10, 10], [0, 5, 15], [0, 5, 15],
        [0, 70, 21], [0, 127, 127]])])

print('Path', path.shape)
layer = viewer.add_shapes(
    path, shape_type='path', edge_width=4, edge_color=['red', 'blue']
)

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