FIX: Selecting correct position information from layout in plot_joint (#5765)

* FIX: issue #5764. Position information from layout restricted to channels that actually exist in info.

* Bugfix for issue #5764. Position information from layout restricted to channels that actually exist in info.

* Update tfr.py

* FIX: Issue #5764.

* FIX: Issue #5764.

* FIX: Issue #5764.

* FIX: Issue #5764.

* style

* style

* Update tfr.py

* pep8

* pep8

* Update whats_new.rst

* Update whats_new.rst

Author: davidhaslacher

doc/whats_new.rst

@@ -48,6 +48,8 @@ Bug
 
 - Fix path bugs in :func:`mne.bem.make_flash_bem` and :ref:`gen_mne_flash_bem` by `Eric Larson`_
 
+- Fixed a bug where :meth:`mne.time_frequency.AverageTFR.plot_joint` would mishandle bad channels, by `David Haslacher`_ and `Jona Sassenhagen`_
+
 API
 ~~~
 
@@ -3118,3 +3120,5 @@ of commits):
 .. _Sara Sommariva: http://www.dima.unige.it/~sommariva/
 
 .. _Cristóbal Moënne-Loccoz: https://github.com/cmmoenne
+
+.. _David Haslacher: https://github.com/davidhaslacher

mne/time_frequency/tests/test_tfr.py

@@ -521,8 +521,12 @@ def test_plot_joint():
                    topomap_args=topomap_args)
     plt.close('all')
     assert_array_equal(tfr.data, tfr_orig.data)
-    assert (set(tfr.ch_names) == set(tfr_orig.ch_names))
-    assert (set(tfr.times) == set(tfr_orig.times))
+    assert set(tfr.ch_names) == set(tfr_orig.ch_names)
+    assert set(tfr.times) == set(tfr_orig.times)
+
+    # test tfr with picked channels
+    tfr.pick_channels(tfr.ch_names[:-1])
+    tfr.plot_joint(title='auto', colorbar=True, topomap_args=topomap_args)
 
 
 def test_add_channels():
@@ -633,8 +637,8 @@ def test_compute_tfr():
 
     # Inter-trial coherence tests
     out = _compute_tfr(data, freqs, sfreq, output='itc', n_cycles=2.)
-    assert (np.sum(out >= 1) == 0)
-    assert (np.sum(out <= 0) == 0)
+    assert np.sum(out >= 1) == 0
+    assert np.sum(out <= 0) == 0
 
     # Check decim shapes
     # 2: multiple of len(times) even

mne/time_frequency/tfr.py

@@ -1524,7 +1524,14 @@ def plot_joint(self, timefreqs=None, picks=None, baseline=None,
 
             data = tfr.data
 
-            pos = find_layout(tfr.info).pos if layout is None else layout.pos
+            if layout is None:
+                loaded_layout = find_layout(tfr.info)
+
+            # only use position information for channels from layout
+            # whose names appear as a substring in tfr.ch_names
+            idx = [any(ch_name in ch_name_tfr for ch_name_tfr in tfr.ch_names)
+                   for ch_name in loaded_layout.names]
+            pos = loaded_layout.pos[np.array(idx)]
 
             # merging grads here before rescaling makes ERDs visible
             if ch_type == 'grad':