Raise warning and errors when np.nan provided to mne.stats.permutation_t_test().

mne/stats/permutations.py

@@ -9,7 +9,7 @@
 import numpy as np
 
 from ..parallel import parallel_func
-from ..utils import check_random_state, logger, verbose
+from ..utils import _check_if_nan, check_random_state, logger, verbose
 
 
 def _max_stat(X, X2, perms, dof_scaling):
@@ -77,6 +77,7 @@ def permutation_t_test(
     """
     from .cluster_level import _get_1samp_orders
 
+    _check_if_nan(X)
     n_samples, n_tests = X.shape
     X2 = np.mean(X**2, axis=0)  # precompute moments
     mu0 = np.mean(X, axis=0)

mne/utils/check.py

@@ -699,10 +699,14 @@ def _path_like(item):
         return False
 
 
-def _check_if_nan(data, msg=" to be plotted"):
+def _check_if_nan(data, on_nan="error", msg=" to be plotted"):
     """Raise if any of the values are NaN."""
+    _check_option("on_nan", on_nan, ("error", "warn"))
     if not np.isfinite(data).all():
-        raise ValueError(f"Some of the values {msg} are NaN.")
+        if on_nan == "error":
+            raise ValueError(f"Some of the values {msg} are NaN.")
+        elif on_nan == "warn":
+            warn(f"Some of the values {msg} are NaN")
 
 
 @verbose

mne/utils/tests/test_check.py

@@ -20,6 +20,7 @@
     Bunch,
     _check_ch_locs,
     _check_fname,
+    _check_if_nan,
     _check_info_inv,
     _check_option,
     _check_range,
@@ -206,6 +207,24 @@ def test_check_option():
         assert _check_option("option", "bad", ["valid"])
 
 
+def test_check_if_nan():
+    """Test NaN handling and option validation."""
+    msg = (
+        "Invalid value for the 'on_nan' parameter. "
+        "Allowed values are 'error' and 'warn', but got 'er' instead."
+    )
+    nan_error_msg = r"Some of the values\s+to be plotted are NaN\."
+    nan_warn_msg = r"Some of the values\s+to be plotted are NaN"
+    with pytest.raises(ValueError, match=msg):
+        _check_if_nan([0.0], on_nan="er")
+
+    with pytest.raises(ValueError, match=nan_error_msg):
+        _check_if_nan([0.0, np.nan], on_nan="error")
+
+    with pytest.warns(RuntimeWarning, match=nan_warn_msg):
+        _check_if_nan([0.0, np.nan], on_nan="warn")
+
+
 def test_path_like():
     """Test _path_like()."""
     str_path = str(base_dir)