add group to permutation

pyriemann/stats.py

@@ -100,6 +100,17 @@ def _initial_transform(self, X):
         """Initial transformation. By default return X."""
         return X
 
+    def _shuffle(self, y, groups, rs):
+        """Return a shuffled copy of y eventually shuffle among same groups."""
+        if groups is None:
+            indices = rs.permutation(len(y))
+        else:
+            indices = numpy.arange(len(groups))
+            for group in numpy.unique(groups):
+                this_mask = (groups == group)
+                indices[this_mask] = rs.permutation(indices[this_mask])
+        return y[indices]
+
     def plot(self, nbins=10, range=None, axes=None):
         """Plot results of the permutation test.
 

tests/test_stats.py

@@ -19,10 +19,13 @@ def test_permutation_distance():
     """Test one way permutation test"""
     covset = generate_cov(10, 5)
     labels = np.array([0, 1]).repeat(5)
+    groups = np.array([0] * 5 + [1] * 5)
     assert_raises(ValueError, PermutationDistance, mode='badmode')
     # pairwise
     p = PermutationDistance(100, mode='pairwise')
     p.test(covset, labels)
+    # with group
+    p.test(covset, labels, groups=groups)
     # t-test
     p = PermutationDistance(100, mode='ttest')
     p.test(covset, labels)