Backport PR #13067 on branch maint/1.9 ([BUG] Fix taper weighting in …

…computation of TFR multitaper power) (#13072)

Co-authored-by: Eric Larson <[email protected]>

doc/changes/devel/13067.bugfix.rst

@@ -0,0 +1 @@
+Fix bug where taper weights were not correctly applied when computing multitaper power with :meth:`mne.Epochs.compute_tfr` and :func:`mne.time_frequency.tfr_array_multitaper`, by `Thomas Binns`_.

mne/export/_export.py

@@ -25,6 +25,14 @@ def export_raw(
 
     %(export_warning)s
 
+    .. warning::
+        When exporting ``Raw`` with annotations, ``raw.info["meas_date"]`` must be the
+        same as ``raw.annotations.orig_time``. This guarantees that the annotations are
+        in the same reference frame as the samples. When
+        :attr:`Raw.first_time <mne.io.Raw.first_time>` is not zero (e.g., after
+        cropping), the onsets are automatically corrected so that onsets are always
+        relative to the first sample.
+
     Parameters
     ----------
     %(fname_export_params)s
@@ -216,7 +224,6 @@ def _infer_check_export_fmt(fmt, fname, supported_formats):
 
         supported_str = ", ".join(supported)
         raise ValueError(
-            f"Format '{fmt}' is not supported. "
-            f"Supported formats are {supported_str}."
+            f"Format '{fmt}' is not supported. Supported formats are {supported_str}."
         )
     return fmt

mne/time_frequency/tests/test_tfr.py

@@ -255,22 +255,6 @@ def test_tfr_morlet():
     # computed within the method.
     assert_allclose(epochs_amplitude_2.data**2, epochs_power_picks.data)
 
-    # test that averaging power across tapers when multitaper with
-    # output='complex' gives the same as output='power'
-    epoch_data = epochs.get_data()
-    multitaper_power = tfr_array_multitaper(
-        epoch_data, epochs.info["sfreq"], freqs, n_cycles, output="power"
-    )
-    multitaper_complex = tfr_array_multitaper(
-        epoch_data, epochs.info["sfreq"], freqs, n_cycles, output="complex"
-    )
-
-    taper_dim = 2
-    power_from_complex = (multitaper_complex * multitaper_complex.conj()).real.mean(
-        axis=taper_dim
-    )
-    assert_allclose(power_from_complex, multitaper_power)
-
     print(itc)  # test repr
     print(itc.ch_names)  # test property
     itc += power  # test add

mne/time_frequency/tfr.py

@@ -266,6 +266,7 @@ def _make_dpss(
         The wavelets time series.
     """
     Ws = list()
+    Cs = list()
 
     freqs = np.array(freqs)
     if np.any(freqs <= 0):
@@ -281,6 +282,7 @@ def _make_dpss(
 
     for m in range(n_taps):
         Wm = list()
+        Cm = list()
         for k, f in enumerate(freqs):
             if len(n_cycles) != 1:
                 this_n_cycles = n_cycles[k]
@@ -302,12 +304,15 @@ def _make_dpss(
                 real_offset = Wk.mean()
                 Wk -= real_offset
             Wk /= np.sqrt(0.5) * np.linalg.norm(Wk.ravel())
+            Ck = np.sqrt(conc[m])
 
             Wm.append(Wk)
+            Cm.append(Ck)
 
         Ws.append(Wm)
+        Cs.append(Cm)
     if return_weights:
-        return Ws, conc
+        return Ws, Cs
     return Ws
 
 
@@ -529,15 +534,18 @@ def _compute_tfr(
     if method == "morlet":
         W = morlet(sfreq, freqs, n_cycles=n_cycles, zero_mean=zero_mean)
         Ws = [W]  # to have same dimensionality as the 'multitaper' case
+        weights = None  # no tapers for Morlet estimates
 
     elif method == "multitaper":
-        Ws = _make_dpss(
+        Ws, weights = _make_dpss(
             sfreq,
             freqs,
             n_cycles=n_cycles,
             time_bandwidth=time_bandwidth,
             zero_mean=zero_mean,
+            return_weights=True,  # required for converting complex → power
         )
+        weights = np.asarray(weights)
 
     # Check wavelets
     if len(Ws[0][0]) > epoch_data.shape[2]:
@@ -560,7 +568,7 @@ def _compute_tfr(
     if ("avg_" in output) or ("itc" in output):
         out = np.empty((n_chans, n_freqs, n_times), dtype)
     elif output in ["complex", "phase"] and method == "multitaper":
-        out = np.empty((n_chans, n_tapers, n_epochs, n_freqs, n_times), dtype)
+        out = np.empty((n_chans, n_epochs, n_tapers, n_freqs, n_times), dtype)
     else:
         out = np.empty((n_chans, n_epochs, n_freqs, n_times), dtype)
 
@@ -571,7 +579,7 @@ def _compute_tfr(
 
     # Parallelization is applied across channels.
     tfrs = parallel(
-        my_cwt(channel, Ws, output, use_fft, "same", decim, method)
+        my_cwt(channel, Ws, output, use_fft, "same", decim, weights)
         for channel in epoch_data.transpose(1, 0, 2)
     )
 
@@ -581,10 +589,8 @@ def _compute_tfr(
 
     if ("avg_" not in output) and ("itc" not in output):
         # This is to enforce that the first dimension is for epochs
-        if output in ["complex", "phase"] and method == "multitaper":
-            out = out.transpose(2, 0, 1, 3, 4)
-        else:
-            out = out.transpose(1, 0, 2, 3)
+        out = np.moveaxis(out, 1, 0)
+
     return out
 
 
@@ -658,7 +664,7 @@ def _check_tfr_param(
     return freqs, sfreq, zero_mean, n_cycles, time_bandwidth, decim
 
 
-def _time_frequency_loop(X, Ws, output, use_fft, mode, decim, method=None):
+def _time_frequency_loop(X, Ws, output, use_fft, mode, decim, weights=None):
     """Aux. function to _compute_tfr.
 
     Loops time-frequency transform across wavelets and epochs.
@@ -685,9 +691,8 @@ def _time_frequency_loop(X, Ws, output, use_fft, mode, decim, method=None):
         See numpy.convolve.
     decim : slice
         The decimation slice: e.g. power[:, decim]
-    method : str | None
-        Used only for multitapering to create tapers dimension in the output
-        if ``output in ['complex', 'phase']``.
+    weights : array, shape (n_tapers, n_wavelets) | None
+        Concentration weights for each taper in the wavelets, if present.
     """
     # Set output type
     dtype = np.float64
@@ -701,10 +706,12 @@ def _time_frequency_loop(X, Ws, output, use_fft, mode, decim, method=None):
     n_freqs = len(Ws[0])
     if ("avg_" in output) or ("itc" in output):
         tfrs = np.zeros((n_freqs, n_times), dtype=dtype)
-    elif output in ["complex", "phase"] and method == "multitaper":
-        tfrs = np.zeros((n_tapers, n_epochs, n_freqs, n_times), dtype=dtype)
+    elif output in ["complex", "phase"] and weights is not None:
+        tfrs = np.zeros((n_epochs, n_tapers, n_freqs, n_times), dtype=dtype)
     else:
         tfrs = np.zeros((n_epochs, n_freqs, n_times), dtype=dtype)
+    if weights is not None:
+        weights = np.expand_dims(weights, axis=-1)  # add singleton time dimension
 
     # Loops across tapers.
     for taper_idx, W in enumerate(Ws):
@@ -719,6 +726,8 @@ def _time_frequency_loop(X, Ws, output, use_fft, mode, decim, method=None):
         # Loop across epochs
         for epoch_idx, tfr in enumerate(coefs):
             # Transform complex values
+            if output not in ["complex", "phase"] and weights is not None:
+                tfr = weights[taper_idx] * tfr  # weight each taper estimate
             if output in ["power", "avg_power"]:
                 tfr = (tfr * tfr.conj()).real  # power
             elif output == "phase":
@@ -734,8 +743,8 @@ def _time_frequency_loop(X, Ws, output, use_fft, mode, decim, method=None):
             # Stack or add
             if ("avg_" in output) or ("itc" in output):
                 tfrs += tfr
-            elif output in ["complex", "phase"] and method == "multitaper":
-                tfrs[taper_idx, epoch_idx] += tfr
+            elif output in ["complex", "phase"] and weights is not None:
+                tfrs[epoch_idx, taper_idx] += tfr
             else:
                 tfrs[epoch_idx] += tfr
 
@@ -749,9 +758,14 @@ def _time_frequency_loop(X, Ws, output, use_fft, mode, decim, method=None):
     if ("avg_" in output) or ("itc" in output):
         tfrs /= n_epochs
 
-    # Normalization by number of taper
-    if n_tapers > 1 and output not in ["complex", "phase"]:
-        tfrs /= n_tapers
+    # Normalization by taper weights
+    if n_tapers > 1 and output not in ["complex", "phase", "itc"]:
+        if "avg_" not in output:  # add singleton epochs dimension to weights
+            weights = np.expand_dims(weights, axis=0)
+        tfrs.real *= 2 / (weights * weights.conj()).real.sum(axis=-3)
+        if output == "avg_power_itc":  # weight itc by the number of tapers
+            tfrs.imag = tfrs.imag / n_tapers
+
     return tfrs
 
 

mne/utils/docs.py

@@ -1494,19 +1494,22 @@ def _reflow_param_docstring(docstring, has_first_line=True, width=75):
 
 docdict["export_fmt_support_epochs"] = """\
 Supported formats:
-    - EEGLAB (``.set``, uses :mod:`eeglabio`)
+
+- EEGLAB (``.set``, uses :mod:`eeglabio`)
 """
 
 docdict["export_fmt_support_evoked"] = """\
 Supported formats:
-    - MFF (``.mff``, uses :func:`mne.export.export_evokeds_mff`)
+
+- MFF (``.mff``, uses :func:`mne.export.export_evokeds_mff`)
 """
 
 docdict["export_fmt_support_raw"] = """\
 Supported formats:
-    - BrainVision (``.vhdr``, ``.vmrk``, ``.eeg``, uses `pybv <https://github.com/bids-standard/pybv>`_)
-    - EEGLAB (``.set``, uses :mod:`eeglabio`)
-    - EDF (``.edf``, uses `edfio <https://github.com/the-siesta-group/edfio>`_)
+
+- BrainVision (``.vhdr``, ``.vmrk``, ``.eeg``, uses `pybv <https://github.com/bids-standard/pybv>`_)
+- EEGLAB (``.set``, uses :mod:`eeglabio`)
+- EDF (``.edf``, uses `edfio <https://github.com/the-siesta-group/edfio>`_)
 """  # noqa: E501
 
 docdict["export_warning"] = """\