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"""
Visualizing optical flow in napari
==================================
Adapted from the scikit-image gallery [1]_.
In napari, we can show the flowing vortex as an additional dimension in the
image, visible by moving the slider.
.. tags:: visualization-advanced, layers
.. [1] https://scikit-image.org/docs/stable/auto_examples/registration/plot_opticalflow.html
"""
import numpy as np
from skimage.data import vortex
from skimage.registration import optical_flow_ilk
import napari
#######################################################################
# First, we load the vortex image as a 3D array. (time, row, column)
vortex_im = np.asarray(vortex())
#######################################################################
# We compute the optical flow using scikit-image. (Note: as of
# scikit-image 0.21, there seems to be a transposition of the image in
# the output, which we account for later.)
u, v = optical_flow_ilk(vortex_im[0], vortex_im[1], radius=15)
#######################################################################
# Compute the flow magnitude, for visualization.
magnitude = np.sqrt(u ** 2 + v ** 2)
#######################################################################
# We subsample the vector field to display it — it's too
# messy otherwise! And we transpose the rows/columns axes to match the
# current scikit-image output.
nvec = 21
nr, nc = magnitude.shape
step = max(nr//nvec, nc//nvec)
offset = step // 2
usub = u[offset::step, offset::step]
vsub = v[offset::step, offset::step]
vectors_field = np.transpose( # transpose required — skimage bug?
np.stack([usub, vsub], axis=-1),
(1, 0, 2),
)
#######################################################################
# Finally, we create a viewer, and add the vortex frames, the flow
# magnitude, and the vector field.
viewer, vortex_layer = napari.imshow(vortex_im)
mag_layer = viewer.add_image(magnitude, colormap='magma', opacity=0.3)
flow_layer = viewer.add_vectors(
vectors_field,
name='optical flow',
scale=[step, step],
translate=[offset, offset],
edge_width=0.3,
length=0.3,
)
if __name__ == '__main__':
napari.run()
|
