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[Fix] cell assembly detection #576

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merged 4 commits into from
Jul 12, 2023
Merged

[Fix] cell assembly detection #576

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b13d354
keep input alpha as "alph" to be coherent with the MATLAB implementat…
Dec 2, 2022
18e5f70
replace np.int with int, since np.int is deprecated
Dec 2, 2022
549f89f
add comment on changes, reference to issue #443
Dec 2, 2022
0830333
Merge branch 'master' into fix/cell_assembly_detection
Jul 12, 2023
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9 changes: 7 additions & 2 deletions elephant/cell_assembly_detection.py
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Original file line number Diff line number Diff line change
Expand Up @@ -255,7 +255,12 @@ def cell_assembly_detection(binned_spiketrain, max_lag, reference_lag=2,
# divide alpha by the number of tests performed in the first
# pairwise testing loop
number_test_performed = n_neurons * (n_neurons - 1) * (2 * max_lag + 1)
alpha = alpha * 2 / float(number_test_performed)
# Fix Issue #443
# keep alph as the original input for alpha, this was done following
# the MATLAB implementation by Eleonora Russo, see:
# https://github.com/DurstewitzLab/Cell-Assembly-Detection
alph = alpha
alpha = alph * 2 / float(number_test_performed)
if verbose:
print('actual significance_level', alpha)

Expand Down Expand Up @@ -363,7 +368,7 @@ def cell_assembly_detection(binned_spiketrain, max_lag, reference_lag=2,
if w2_to_test:

# bonferroni correction only for the tests actually performed
alpha = alpha / float(len(w2_to_test) * n_as * (2 * max_lag + 1))
alpha = alph / float(len(w2_to_test) * n_as * (2 * max_lag + 1))

# testing for the element in w2_to_test
for ww2 in range(len(w2_to_test)):
Expand Down