Output particles in "intermediates" mode of 3D-variability display?

3D Variability Analysis
6

Here’s what I did, in your case you can just use idx = (x > lo) & (x < hi) to index the cs and pt array instead of the whole KNN thing I’m doing.

import numpy as np
cs = np.load("P16/J205/cryosparc_P16_J205_particles.cs")
pt = np.load("P16/J205/P16_J205_passthrough_particles.cs")
x, y, z = cs['components_mode_0/value'], cs['components_mode_1/value'], cs['components_mode_2/value']
X = np.array([x, y, z])
mu = np.mean(X, axis=1)
vsmu = sp.spatial.distance.cdist(np.atleast_2d(mu), X.T)
knn_2p18 = np.argsort(vsmu)[0, :2**18]
np.save("P16_J205_particles_muknn_2p18.cs", cs[knn_2p18], allow_pickle=True, fix_imports=True)
np.save("P16_J205_passthrough_particles_muknn_2p18.cs", pt[knn_2p18], allow_pickle=True, fix_imports=True)

Then cp P16_J205_particles.csg P16_J205_particles_muknn_2p18.csg and edit the new file to point to your new .cs files. You can now import this .csg file as a results group.

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