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commit da8526e8456159b6a57b0cc23f956ffbbb1c11cc Author: Alexandre Gramfort <[email protected]> Date: Sun Jun 5 21:46:08 2011 -0400 FIX : bug fix in cluster_level with connectivity + FIX in pval computation --- mne/stats/cluster_level.py | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/mne/stats/cluster_level.py b/mne/stats/cluster_level.py index 5bd3e49..e95a42a 100644 --- a/mne/stats/cluster_level.py +++ b/mne/stats/cluster_level.py @@ -68,9 +68,16 @@ def _find_clusters(x, threshold, tail=0, connectivity=None): mask = np.logical_and(x_in[connectivity.row], x_in[connectivity.col]) if np.sum(mask) == 0: return [], np.empty(0) + mask = np.logical_and(x_in[connectivity.row], x_in[connectivity.col]) connectivity = sparse.coo_matrix((connectivity.data[mask], (connectivity.row[mask], - connectivity.col[mask]))) + connectivity.col[mask])), + shape=connectivity.shape) + idx = np.where(x_in)[0] + data = np.ones(len(idx), dtype=connectivity.data.dtype) + connectivity.row = np.concatenate((connectivity.row, idx)) + connectivity.col = np.concatenate((connectivity.col, idx)) + connectivity.data = np.concatenate((connectivity.data, data)) _, components = cs_graph_components(connectivity) labels = np.unique(components) clusters = list() @@ -95,13 +102,14 @@ def _pval_from_histogram(T, H0, tail): # from pct to fraction if tail == -1: # up tail - pval = np.array([np.mean(H0 <= t) for t in T]) + pval = np.array([np.sum(H0 <= t) for t in T]) elif tail == 1: # low tail - pval = np.array([np.mean(H0 >= t) for t in T]) + pval = np.array([np.sum(H0 >= t) for t in T]) elif tail == 0: # both tails - pval = np.array([np.mean(H0 >= abs(t)) for t in T]) - pval += np.array([np.mean(H0 <= -abs(t)) for t in T]) + pval = np.array([np.sum(H0 >= abs(t)) for t in T]) + pval += np.array([np.sum(H0 <= -abs(t)) for t in T]) + pval = (pval + 1.0) / (H0.size + 1.0) # the init data is one resampling return pval -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-mne.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
