Issue

This Content is from Stack Overflow. Question asked by Vovin

I use BallTree structure from scikitlearn in order to find nearest points inside a radius. I have a geometry array consisting of 1203 points. It works well. For example, let’s find nearest points inside 100 km around an isolate from Fujisawa:

ball_tree = BallTree(
    geometry_array,
    metric="haversine",
)

isolate_index = foreign_AVP1.index.get_loc("LC035020.1")
near_indices = ball_tree.query_radius(
    geometry_array[isolate_index].reshape(1, -1), r=kmToRadians(100)
).item()

foreign_AVP1.iloc[near_indices].locale

The head of the output:

taxon	locale
LC037396.1	Japan Yokohama
LC035020.1	Japan Fujisawa
LC037395.1	Japan Yokohama
LC014787.1	Japan Tokyo
AB279734.1	Japan Tokyo

I was curious to look at the tree structure & used get_tree_stats method to know the leaves number. Unawares, I got zeros tuple: (0, 0, 0). This is strange as there are a default leaf size 40 & the number of samples 1203 that should result in about 16-30 leaves. When I used get_arrays method to get the raw data I saw a normal picture (this is just a part), there are 16 leaves:

array([(   0, 1203, 0, 3.0947303 ), (   0,  601, 0, 2.41933654),
        ( 601, 1203, 0, 0.58490656), (   0,  300, 0, 1.85505229),
        ( 300,  601, 0, 0.89693236), ( 601,  902, 0, 0.49983081),
        ( 902, 1203, 0, 0.40970688), (   0,  150, 0, 1.48087714),
        ( 150,  300, 0, 0.32291627), ( 300,  450, 0, 0.20494666),
        ( 450,  601, 0, 0.81787611), ( 601,  751, 0, 0.55418562),
        ( 751,  902, 0, 0.33448889), ( 902, 1052, 0, 0.01141954),
        (1052, 1203, 0, 0.39229974), (   0,   75, 1, 1.00467692),
        (  75,  150, 1, 1.07852748), ( 150,  225, 1, 0.25955598),
        ( 225,  300, 1, 0.24115038), ( 300,  375, 1, 0.12721095),
        ( 375,  450, 1, 0.1702189 ), ( 450,  525, 1, 0.78454107),
        ( 525,  601, 1, 0.09367431), ( 601,  676, 1, 0.0368483 ),
        ( 676,  751, 1, 0.4762352 ), ( 751,  826, 1, 0.2375712 ),
        ( 826,  902, 1, 0.17776855), ( 902,  977, 1, 0.01107241),
        ( 977, 1052, 1, 0.0118055 ), (1052, 1127, 1, 0.32023704),
        (1127, 1203, 1, 0.09146244)],
       dtype=[('idx_start', '<i8'), ('idx_end', '<i8'), ('is_leaf', '<i8'), ('radius', '<f8')]),

Why does the method get_tree_stats have the unexpected behavior?

Solution

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