During work on this PR <a class="issue-link js-issue-link" data-error-text="Failed to

A preliminary approach is in <a class="issue-link js-issue-link" data-error-text="Fail

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Always treat bars with infinite death as essential bars about giotto-ph HOT 4 CLOSED

giotto-ai commented on May 20, 2024

Always treat bars with infinite death as essential bars

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Comments (4)

ulupo commented on May 20, 2024

A preliminary approach is in ulupo#1

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MonkeyBreaker commented on May 20, 2024

Maybe we could add the diamond example and the output when running in sparse and dense, where we can observe an unexpected difference ?

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ulupo commented on May 20, 2024

@MonkeyBreaker indeed. Here goes:

import numpy as np
from gph.python import ripser_parallel

diamond_dm = np.array(
    [[0,      1,      np.inf, 1,      1,      1],
     [0,      0,      1,      np.inf, 1,      1],
     [0,      0,      0,      1,      1,      1],
     [0,      0,      0,      0,      1,      1],
     [0,      0,      0,      0,      0,      np.inf],
     [0,      0,      0,      0,      0,      0]],
    dtype=np.float64
)
diamond_dm += diamond_dm.T

res = ripser_parallel(diamond_dm, metric="precomputed", maxdim=2, return_generators=True)

yields the correct barcode

[array([[ 0.,  1.],
        [ 0.,  1.],
        [ 0.,  1.],
        [ 0.,  1.],
        [ 0.,  1.],
        [ 0., inf]]),
 array([], shape=(0, 2), dtype=float64),
 array([[ 1., inf]])]

but the incorrect generators

(array([[5, 5, 3],
       [3, 5, 2],
       [2, 5, 1],
       [1, 5, 0],
       [4, 4, 3]], dtype=int64),
 [array([], shape=(0, 4), dtype=int64), array([[1, 0, 5, 4]], dtype=int64)],
 array([0], dtype=int64),
 [array([], shape=(0, 2), dtype=int64), array([], shape=(0, 2), dtype=int64)])

The sparse version

from scipy.sparse import coo_matrix

diamond_dm = np.where(diamond_dm == np.inf, 0, diamond_dm)
diamond_dm = coo_matrix(diamond_dm)

gives the correct

(array([[5, 5, 3],
       [3, 5, 2],
       [2, 5, 1],
       [1, 5, 0],
       [4, 4, 3]], dtype=int64),
 [array([], shape=(0, 4), dtype=int64), array([], shape=(0, 4), dtype=int64)],
 array([0], dtype=int64),
 [array([], shape=(0, 2), dtype=int64), array([[1, 0]], dtype=int64)])