Fix bug with ica.plot_properties

Author: larsoner

mne/viz/ica.py

@@ -238,13 +238,11 @@ def _plot_ica_properties(
 
     # image and erp
     # we create a new epoch with dropped rows
-    epoch_data = epochs_src.get_data(copy=False)
-    epoch_data = np.insert(
-        arr=epoch_data,
-        obj=(dropped_indices - np.arange(len(dropped_indices))).astype(int),
-        values=0.0,
-        axis=0,
-    )
+    src_data = epochs_src.get_data(copy=False)
+    n = len(src_data) + len(dropped_indices)
+    epoch_data = np.zeros((n,) + (src_data.shape[1:]), dtype=src_data.dtype)
+    use_idx = np.setdiff1d(np.arange(n), dropped_indices)
+    epoch_data[use_idx] = src_data
     from ..epochs import EpochsArray
 
     epochs_src = EpochsArray(
@@ -283,9 +281,11 @@ def _plot_ica_properties(
         range(len(epoch_var)), epoch_var, alpha=0.5, facecolor=[0, 0, 0], lw=0
     )
     # rejected epochs in red
+    # TODO: This can't be right as the variance is computed on the good/remaining
+    # epochs, so these are by necessity zero
     var_ax.scatter(
         dropped_indices,
-        epoch_var[dropped_indices],
+        0,
         alpha=1.0,
         facecolor=[1, 0, 0],
         lw=0,
@@ -610,7 +610,6 @@ def _fast_plot_ica_properties(
         )
     del reject
     ica_data = np.swapaxes(data[:, picks, :], 0, 1)
-    dropped_src = ica_data
 
     # spectrum
     Nyquist = inst.info["sfreq"] / 2.0
@@ -656,16 +655,6 @@ def set_title_and_labels(ax, title, xlab, ylab):
 
         # we reconstruct an epoch_variance with 0 where indexes where dropped
         epoch_var = np.var(ica_data[idx], axis=1)
-        drop_var = np.var(dropped_src[idx], axis=1)
-        drop_indices_corrected = (
-            dropped_indices - np.arange(len(dropped_indices))
-        ).astype(int)
-        epoch_var = np.insert(
-            arr=epoch_var,
-            obj=drop_indices_corrected,
-            values=drop_var[dropped_indices],
-            axis=0,
-        )
 
         # the actual plot
         fig = _plot_ica_properties(
@@ -772,7 +761,7 @@ def _prepare_data_ica_properties(inst, ica, reject_by_annotation=True, reject="a
                 )
         # getting dropped epochs indexes
         if drop_inds is not None:
-            dropped_indices = [(d[0] // len(epochs_src.times)) + 1 for d in drop_inds]
+            dropped_indices = [(d[0] // len(epochs_src.times)) for d in drop_inds]
         kind = "Segment"
     else:
         drop_inds = None

mne/viz/tests/test_ica.py

@@ -13,6 +13,7 @@
 from mne import (
     Annotations,
     Epochs,
+    create_info,
     make_fixed_length_events,
     pick_types,
     read_cov,
@@ -143,7 +144,7 @@ def test_plot_ica_components():
 
 
 @pytest.mark.slowtest
-def test_plot_ica_properties():
+def test_plot_ica_properties_basic():
     """Test plotting of ICA properties."""
     raw = _get_raw(preload=True).crop(0, 5)
     raw.add_proj([], remove_existing=True)
@@ -281,6 +282,33 @@ def test_plot_ica_properties():
     plt.close("all")
 
 
+@pytest.mark.parametrize("kind", ["first", "last"])
+def test_plot_ica_properties_reject(kind):
+    """Check for gh-13879."""
+    sfreq, duration = 100.0, 10.0
+    n_samples = int(sfreq * duration)
+    rng = np.random.default_rng(0)
+    n_channels = 3
+    data = rng.uniform(-3e-6, 3e-6, size=(n_channels, n_samples))
+    assert kind in ("first", "last")
+    idx = 0 if kind == "first" else -1
+    data[0, idx] = 1000e-6
+    info = create_info(["Fz", "Cz", "C2"], sfreq, "eeg")
+    raw = RawArray(data, info)
+    raw.set_montage("standard_1020")
+    ica = ICA(
+        n_components=2,
+        method="picard",
+        random_state=0,
+        fit_params=dict(ortho=False, extended=True),
+    )
+    with pytest.warns(RuntimeWarning, match="filtered"), catch_logging(True) as log:
+        ica.fit(raw, reject=dict(eeg=500e-6))
+    log = log.getvalue()
+    assert log.count("Artifact detected") == 1  # dropped one epoch
+    ica.plot_properties(raw, picks=[0], show=False)
+
+
 def test_plot_ica_sources(raw_orig, browser_backend, monkeypatch):
     """Test plotting of ICA panel."""
     raw = raw_orig.copy().crop(0, 1)

tutorials/preprocessing/40_artifact_correction_ica.py

@@ -320,7 +320,6 @@
 
 # %%
 # .. note::
-#
 #     `~mne.preprocessing.ICA.plot_components` (which plots the scalp
 #     field topographies for each component) has an optional ``inst`` parameter
 #     that takes an instance of `~mne.io.Raw` or `~mne.Epochs`.