[med-svn] [python-mne] 47/52: ENH : add support for ND-array in FDR + Bonferroni

[Yaroslav Halchenko]

This is an automated email from the git hooks/post-receive script.

yoh pushed a commit to annotated tag v0.2
in repository python-mne.

commit 683de5c563018b82cb62f347f5c99f539a157391
Author: Alexandre Gramfort <alexandre.gramfort at inria.fr>
Date:   Tue Nov 8 10:58:23 2011 -0500

    ENH : add support for ND-array in FDR + Bonferroni
---
 mne/stats/multi_comp.py            |  8 ++++++--
 mne/stats/tests/test_multi_comp.py | 11 ++++++++---
 2 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/mne/stats/multi_comp.py b/mne/stats/multi_comp.py
index 3e508c6..60d810a 100644
--- a/mne/stats/multi_comp.py
+++ b/mne/stats/multi_comp.py
@@ -48,6 +48,8 @@ def fdr_correction(pvals, alpha=0.05, method='indep'):
     discovery rate. Neuroimage. 2002 Apr;15(4):870-8.
     """
     pvals = np.asarray(pvals)
+    shape_init = pvals.shape
+    pvals = pvals.ravel()
 
     pvals_sortind = np.argsort(pvals)
     pvals_sorted = pvals[pvals_sortind]
@@ -61,7 +63,7 @@ def fdr_correction(pvals, alpha=0.05, method='indep'):
     else:
         raise ValueError("Method should be 'indep' and 'negcorr'")
 
-    reject = pvals_sorted < ecdffactor * alpha
+    reject = pvals_sorted < (ecdffactor * alpha)
     if reject.any():
         rejectmax = max(np.nonzero(reject)[0])
     else:
@@ -71,7 +73,9 @@ def fdr_correction(pvals, alpha=0.05, method='indep'):
     pvals_corrected_raw = pvals_sorted / ecdffactor
     pvals_corrected = np.minimum.accumulate(pvals_corrected_raw[::-1])[::-1]
     pvals_corrected[pvals_corrected > 1.0] = 1.0
-    return reject[sortrevind], pvals_corrected[sortrevind]
+    pvals_corrected = pvals_corrected[sortrevind].reshape(shape_init)
+    reject = reject[sortrevind].reshape(shape_init)
+    return reject, pvals_corrected
 
 
 def bonferroni_correction(pval, alpha=0.05):
diff --git a/mne/stats/tests/test_multi_comp.py b/mne/stats/tests/test_multi_comp.py
index 34eb1b5..cd2ee77 100644
--- a/mne/stats/tests/test_multi_comp.py
+++ b/mne/stats/tests/test_multi_comp.py
@@ -10,22 +10,27 @@ def test_multi_pval_correction():
     """Test pval correction for multi comparison (FDR and Bonferroni)
     """
     rng = np.random.RandomState(0)
-    X = rng.randn(10, 10000)
-    X[:, :50] += 4.0  # 50 significant tests
+    X = rng.randn(10, 1000, 10)
+    X[:, :50, 0] += 4.0  # 50 significant tests
     alpha = 0.05
 
     T, pval = stats.ttest_1samp(X, 0)
 
-    n_samples, n_tests = X.shape
+    n_samples = X.shape[0]
+    n_tests = X.size / n_samples
     thresh_uncorrected = stats.t.ppf(1.0 - alpha, n_samples - 1)
 
     reject_bonferroni, pval_bonferroni = bonferroni_correction(pval, alpha)
     thresh_bonferroni = stats.t.ppf(1.0 - alpha / n_tests, n_samples - 1)
+    assert_true(pval_bonferroni.ndim == 2)
+    assert_true(reject_bonferroni.ndim == 2)
 
     fwer = np.mean(reject_bonferroni)
     assert_almost_equal(fwer, alpha, 1)
 
     reject_fdr, pval_fdr = fdr_correction(pval, alpha=alpha, method='indep')
+    assert_true(pval_fdr.ndim == 2)
+    assert_true(reject_fdr.ndim == 2)
     thresh_fdr = np.min(np.abs(T)[reject_fdr])
     assert_true(0 <= (reject_fdr.sum() - 50) <= 50 * 1.05)
     assert_true(thresh_uncorrected <= thresh_fdr <= thresh_bonferroni)

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-mne.git