MRG, ENH: Add method to project onto max power ori

doc/changes/latest.inc

@@ -27,6 +27,8 @@ Changelog
 
 - Add :meth:`mne.MixedSourceEstimate.surface` and :meth:`mne.MixedSourceEstimate.volume` methods to allow surface and volume extraction by `Eric Larson`_
 
+- Add :meth:`mne.VectorSourceEstimate.project` to project vector source estimates onto the direction of maximum source power by `Eric Larson`_
+
 - Add support to :func:`mne.extract_label_time_course` for vector-valued and volumetric source estimates by `Eric Larson`_
 
 - Add method :meth:`mne.VolSourceEstimate.in_label` by `Eric Larson`_
@@ -233,6 +235,8 @@ API
 
 - The method ``stc_mixed.plot_surface`` for a :class:`mne.MixedSourceEstimate` has been deprecated in favor of :meth:`stc.surface().plot(...) <mne.MixedSourceEstimate.surface>` by `Eric Larson`_
 
+- The method ``stc.normal`` for :class:`mne.VectorSourceEstimate` has been deprecated in favor of :meth:`stc.project('nn', src) <mne.VectorSourceEstimate.project>` by `Eric Larson`_
+
 - Add ``use_dev_head_trans`` parameter to :func:`mne.preprocessing.annotate_movement` to allow choosing the device to head transform is used to define the fixed cHPI coordinates by `Luke Bloy`_
 
 - The function ``mne.channels.read_dig_captrack`` will be deprecated in version 0.22 in favor of :func:`mne.channels.read_dig_captrak` to correct the spelling error: "captraCK" -> "captraK", by `Stefan Appelhoff`_

examples/inverse/plot_vector_mne_solution.py

@@ -21,6 +21,7 @@
 #
 # License: BSD (3-clause)
 
+import numpy as np
 import mne
 from mne.datasets import sample
 from mne.minimum_norm import read_inverse_operator, apply_inverse
@@ -52,6 +53,21 @@
 brain = stc.plot(
     initial_time=peak_time, hemi='lh', subjects_dir=subjects_dir)
 
+###############################################################################
+# Plot the activation in the direction of maximal power for this data:
+
+stc_max, directions = stc.project('pca', src=inv['src'])
+# These directions must by design be close to the normals because this
+# inverse was computed with loose=0.2:
+print('Absolute cosine similarity between source normals and directions: '
+      f'{np.abs(np.sum(directions * inv["source_nn"][2::3], axis=-1)).mean()}')
+brain_max = stc_max.plot(
+    initial_time=peak_time, hemi='lh', subjects_dir=subjects_dir,
+    time_label='Max power')
+brain_normal = stc.project('normal', inv['src'])[0].plot(
+    initial_time=peak_time, hemi='lh', subjects_dir=subjects_dir,
+    time_label='Normal')
+
 ###############################################################################
 # You can also do this with a fixed-orientation inverse. It looks a lot like
 # the result above because the ``loose=0.2`` orientation constraint keeps

mne/minimum_norm/tests/test_inverse.py

@@ -335,15 +335,28 @@ def test_localization_bias_fixed(bias_params_fixed, method, lower, upper,
     ('eLORETA', 99, 100, 0.8, 0.2),
     ('eLORETA', 99, 100, 0.8, 0.001),
 ])
+@pytest.mark.parametrize('pick_ori', (None, 'vector'))
 def test_localization_bias_loose(bias_params_fixed, method, lower, upper,
-                                 depth, loose):
+                                 depth, loose, pick_ori):
     """Test inverse localization bias for loose minimum-norm solvers."""
+    if pick_ori == 'vector' and method == 'eLORETA':  # works, but save cycles
+        return
     evoked, fwd, noise_cov, _, want = bias_params_fixed
     fwd = convert_forward_solution(fwd, surf_ori=False, force_fixed=False)
     assert not is_fixed_orient(fwd)
     inv_loose = make_inverse_operator(evoked.info, fwd, noise_cov, loose=loose,
                                       depth=depth)
-    loc = apply_inverse(evoked, inv_loose, lambda2, method).data
+    loc = apply_inverse(
+        evoked, inv_loose, lambda2, method, pick_ori=pick_ori)
+    if pick_ori is not None:
+        assert loc.data.ndim == 3
+        loc, directions = loc.project('pca', src=fwd['src'])
+        abs_cos_sim = np.abs(np.sum(
+            directions * inv_loose['source_nn'][2::3], axis=1))
+        assert np.percentile(abs_cos_sim, 10) > 0.9  # most very aligned
+        loc = abs(loc).data
+    else:
+        loc = loc.data
     assert (loc >= 0).all()
     # Compute the percentage of sources for which there is no loc bias:
     perc = (want == np.argmax(loc, axis=0)).mean() * 100
@@ -535,7 +548,7 @@ def test_orientation_prior(bias_params_free, method, looses, vmin, vmax,
         [_get_src_nn(s) for s in inv['src']]))
     vec_stc_surf = np.matmul(rot, vec_stc.data)
     if 0. in looses:
-        vec_stc_normal = vec_stc.normal(inv['src'])
+        vec_stc_normal, _ = vec_stc.project('normal', inv['src'])
         assert_allclose(stcs[1].data, vec_stc_normal.data)
         del vec_stc
         assert_allclose(vec_stc_normal.data, vec_stc_surf[:, 2])
@@ -1065,8 +1078,9 @@ def test_inverse_mixed(all_src_types_inv_evoked):
                         stcs[kind].magnitude().data)
         assert_allclose(getattr(stcs['mixed'], kind)().magnitude().data,
                         stcs[kind].magnitude().data)
-    assert_allclose(stcs['mixed'].surface().normal(surf_src).data,
-                    stcs['surface'].normal(surf_src).data)
+    with pytest.deprecated_call():
+        assert_allclose(stcs['mixed'].surface().normal(surf_src).data,
+                        stcs['surface'].normal(surf_src).data)
 
 
 run_tests_if_main()

mne/source_estimate.py

@@ -17,7 +17,6 @@
 from .cov import Covariance
 from .evoked import _get_peak
 from .filter import resample
-from .fixes import einsum
 from .io.constants import FIFF
 from .surface import read_surface, _get_ico_surface, mesh_edges
 from .source_space import (_ensure_src, _get_morph_src_reordering,
@@ -1786,6 +1785,8 @@ def magnitude(self):
             data_mag, self.vertices, self.tmin, self.tstep, self.subject,
             self.verbose)
 
+    @deprecated('stc.normal(src) is deprecated and will be removed in 0.22, '
+                'use stc.project("normal", src)[0] instead')
     @fill_doc
     def normal(self, src, use_cps=True):
         """Compute activity orthogonal to the cortex.
@@ -1806,13 +1807,97 @@ def normal(self, src, use_cps=True):
             The source estimate only retaining the activity orthogonal to the
             cortex.
         """
-        _check_src_normal('normal', src)
+        return self.project('normal', src, use_cps)[0]
+
+    def _get_src_normals(self, src, use_cps):
         normals = np.vstack([_get_src_nn(s, use_cps, v) for s, v in
-                             zip(src, self.vertices)])
-        data_norm = einsum('ijk,ij->ik', self.data, normals)
-        return self._scalar_class(
+                            zip(src, self.vertices)])
+        return normals
+
+    @fill_doc
+    def project(self, directions, src=None, use_cps=True):
+        """Project the data for each vertex in a given direction.
+
+        Parameters
+        ----------
+        directions : ndarray, shape (n_vertices, 3) | str
+            Can be:
+
+            - ``'normal'``
+                Project onto the source space normals.
+            - ``'pca'``
+                SVD will be used to project onto the direction of maximal
+                power for each source.
+            - :class:`~numpy.ndarray`, shape (n_vertices, 3)
+                Projection directions for each source.
+        src : instance of SourceSpaces | None
+            The source spaces corresponding to the source estimate.
+            Not used when ``directions`` is an array, optional when
+            ``directions='pca'``.
+        %(use_cps)s
+            Should be the same value that was used when the forward model
+            was computed (typically True).
+
+        Returns
+        -------
+        stc : instance of SourceEstimate
+            The projected source estimate.
+        directions : ndarray, shape (n_vertices, 3)
+            The directions that were computed (or just used).
+
+        Notes
+        -----
+        When using SVD, there is a sign ambiguity for the direction of maximal
+        power. When ``src is None``, the direction is chosen that makes the
+        resulting time waveform sum positive (i.e., have positive amplitudes).
+        When ``src`` is provided, the directions are flipped in the direction
+        of the source normals, i.e., outward from cortex for surface source
+        spaces and in the +Z / superior direction for volume source spaces.
+
+        .. versionadded:: 0.21
+        """
+        _validate_type(directions, (str, np.ndarray), 'directions')
+        _validate_type(src, (None, SourceSpaces), 'src')
+        if isinstance(directions, str):
+            _check_option('directions', directions, ('normal', 'pca'),
+                          extra='when str')
+
+            if directions == 'normal':
+                if src is None:
+                    raise ValueError(
+                        'If directions="normal", src cannot be None')
+                _check_src_normal('normal', src)
+                directions = self._get_src_normals(src, use_cps)
+            else:
+                assert directions == 'pca'
+                x = self.data
+                if not np.isrealobj(self.data):
+                    _check_option('stc.data.dtype', self.data.dtype,
+                                  (np.complex64, np.complex128))
+                    dtype = \
+                        np.float32 if x.dtype == np.complex64 else np.float64
+                    x = x.view(dtype)
+                    assert x.shape[-1] == 2 * self.data.shape[-1]
+                u, _, v = np.linalg.svd(x, full_matrices=False)
+                directions = u[:, :, 0]
+                # The sign is arbitrary, so let's flip it in the direction that
+                # makes the resulting time series the most positive:
+                if src is None:
+                    signs = np.sum(v[:, 0].real, axis=1, keepdims=True)
+                else:
+                    normals = self._get_src_normals(src, use_cps)
+                    signs = np.sum(directions * normals, axis=1, keepdims=True)
+                assert signs.shape == (self.data.shape[0], 1)
+                signs = np.sign(signs)
+                signs[signs == 0] = 1.
+                directions *= signs
+        _check_option(
+            'directions.shape', directions.shape, [(self.data.shape[0], 3)])
+        data_norm = np.matmul(directions[:, np.newaxis], self.data)[:, 0]
+        stc = self._scalar_class(
             data_norm, self.vertices, self.tmin, self.tstep, self.subject,
             self.verbose)
+        return stc, directions
 
 
 class _BaseVolSourceEstimate(_BaseSourceEstimate):

mne/tests/test_source_estimate.py

@@ -11,6 +11,7 @@
                            assert_allclose, assert_equal)
 import pytest
 from scipy import sparse
+from scipy.optimize import fmin_cobyla
 
 from mne import (stats, SourceEstimate, VectorSourceEstimate,
                  VolSourceEstimate, Label, read_source_spaces,
@@ -1119,23 +1120,32 @@ def test_mixed_stc(tmpdir):
     (VolVectorSourceEstimate, 'discrete'),
     (MixedVectorSourceEstimate, 'mixed'),
 ])
-def test_vec_stc_basic(tmpdir, klass, kind):
+@pytest.mark.parametrize('dtype', [
+    np.float32, np.float64, np.complex64, np.complex128])
+def test_vec_stc_basic(tmpdir, klass, kind, dtype):
     """Test (vol)vector source estimate."""
     nn = np.array([
         [1, 0, 0],
         [0, 1, 0],
-        [0, 0, 1],
+        [np.sqrt(1. / 2.), 0, np.sqrt(1. / 2.)],
         [np.sqrt(1 / 3.)] * 3
-    ])
+    ], np.float32)
 
     data = np.array([
         [1, 0, 0],
         [0, 2, 0],
-        [3, 0, 0],
+        [-3, 0, 0],
         [1, 1, 1],
-    ])[:, :, np.newaxis]
-    magnitudes = np.linalg.norm(data, axis=1)[:, 0]
-    normals = np.array([1, 2, 0, np.sqrt(3)])
+    ], dtype)[:, :, np.newaxis]
+    amplitudes = np.array([1, 2, 3, np.sqrt(3)], dtype)
+    magnitudes = amplitudes.copy()
+    normals = np.array([1, 2, -3. / np.sqrt(2), np.sqrt(3)], dtype)
+    if dtype in (np.complex64, np.complex128):
+        data *= 1j
+        amplitudes *= 1j
+        normals *= 1j
+    directions = np.array(
+        [[1, 0, 0], [0, 1, 0], [-1, 0, 0], [1. / np.sqrt(3)] * 3])
     vol_kind = kind if kind in ('discrete', 'vol') else 'vol'
     vol_src = SourceSpaces([dict(nn=nn, type=vol_kind)])
     assert vol_src.kind == dict(vol='volume').get(vol_kind, vol_kind)
@@ -1155,20 +1165,35 @@ def test_vec_stc_basic(tmpdir, klass, kind):
         verts = surf_verts + vol_verts
         assert src.kind == 'mixed'
         data = np.tile(data, (2, 1, 1))
+        amplitudes = np.tile(amplitudes, 2)
         magnitudes = np.tile(magnitudes, 2)
         normals = np.tile(normals, 2)
+        directions = np.tile(directions, (2, 1))
     stc = klass(data, verts, 0, 1, 'foo')
+    amplitudes = amplitudes[:, np.newaxis]
+    magnitudes = magnitudes[:, np.newaxis]
 
     # Magnitude of the vectors
-    assert_array_equal(stc.magnitude().data[:, 0], magnitudes)
+    assert_array_equal(stc.magnitude().data, magnitudes)
 
     # Vector components projected onto the vertex normals
     if kind in ('vol', 'mixed'):
         with pytest.raises(RuntimeError, match='surface or discrete'):
-            stc.normal(src)
+            stc.project('normal', src)[0]
     else:
-        normal = stc.normal(src)
-        assert_array_equal(normal.data[:, 0], normals)
+        normal = stc.project('normal', src)[0]
+        assert_allclose(normal.data[:, 0], normals)
+
+    # Maximal-variance component, either to keep amps pos or to align to src-nn
+    projected, got_directions = stc.project('pca')
+    assert_allclose(got_directions, directions)
+    assert_allclose(projected.data, amplitudes)
+    projected, got_directions = stc.project('pca', src)
+    flips = np.array([[1], [1], [-1.], [1]])
+    if klass is MixedVectorSourceEstimate:
+        flips = np.tile(flips, (2, 1))
+    assert_allclose(got_directions, directions * flips)
+    assert_allclose(projected.data, amplitudes * flips)
 
     out_name = tmpdir.join('temp.h5')
     stc.save(out_name)
@@ -1188,6 +1213,37 @@ def test_vec_stc_basic(tmpdir, klass, kind):
         klass(data, verts, 0, 1)
 
 
+@pytest.mark.parametrize('real', (True, False))
+def test_source_estime_project(real):
+    """Test projecting a source estimate onto direction of max power."""
+    n_src, n_times = 4, 100
+    rng = np.random.RandomState(0)
+    data = rng.randn(n_src, 3, n_times)
+    if not real:
+        data = data + 1j * rng.randn(n_src, 3, n_times)
+        assert data.dtype == np.complex128
+    else:
+        assert data.dtype == np.float64
+
+    # Make sure that the normal we get maximizes the power
+    # (i.e., minimizes the negative power)
+    want_nn = np.empty((n_src, 3))
+    for ii in range(n_src):
+        x0 = np.ones(3)
+
+        def objective(x):
+            x = x / np.linalg.norm(x)
+            return -np.linalg.norm(np.dot(x, data[ii]))
+        want_nn[ii] = fmin_cobyla(objective, x0, (), rhobeg=0.1, rhoend=1e-6)
+    want_nn /= np.linalg.norm(want_nn, axis=1, keepdims=True)
+
+    stc = VolVectorSourceEstimate(data, [np.arange(n_src)], 0, 1)
+    stc_max, directions = stc.project('pca')
+    flips = np.sign(np.sum(directions * want_nn, axis=1, keepdims=True))
+    directions *= flips
+    assert_allclose(directions, want_nn, atol=1e-6)
+
+
 @pytest.fixture(scope='module', params=[testing._pytest_param()])
 def invs():
     """Inverses of various amounts of loose."""
@@ -1251,15 +1307,16 @@ def test_vec_stc_inv_fixed(invs, pick_ori):
     evoked, _, _, _, fixed, fixedish = invs
     stc_fixed = apply_inverse(evoked, fixed)
     stc_fixed_vector = apply_inverse(evoked, fixed, pick_ori='vector')
-    assert_allclose(stc_fixed.data, stc_fixed_vector.normal(fixed['src']).data)
+    assert_allclose(stc_fixed.data,
+                    stc_fixed_vector.project('normal', fixed['src'])[0].data)
     stc_fixedish = apply_inverse(evoked, fixedish, pick_ori=pick_ori)
     if pick_ori == 'vector':
         assert_allclose(stc_fixed_vector.data, stc_fixedish.data, atol=1e-2)
         # two ways here: with magnitude...
         assert_allclose(
             abs(stc_fixed).data, stc_fixedish.magnitude().data, atol=1e-2)
         # ... and when picking the normal (signed)
-        stc_fixedish = stc_fixedish.normal(fixedish['src'])
+        stc_fixedish = stc_fixedish.project('normal', fixedish['src'])[0]
     elif pick_ori is None:
         stc_fixed = abs(stc_fixed)
     else:

mne/utils/check.py

@@ -557,11 +557,11 @@ def _check_option(parameter, value, allowed_values, extra=''):
            '{options}, but got {value!r} instead.')
     allowed_values = list(allowed_values)  # e.g., if a dict was given
     if len(allowed_values) == 1:
-        options = 'The only allowed value is %r' % allowed_values[0]
+        options = f'The only allowed value is {repr(allowed_values[0])}'
     else:
         options = 'Allowed values are '
-        options += ', '.join(['%r' % v for v in allowed_values[:-1]])
-        options += ' and %r' % allowed_values[-1]
+        options += ', '.join([f'{repr(v)}' for v in allowed_values[:-1]])
+        options += f' and {repr(allowed_values[-1])}'
     raise ValueError(msg.format(parameter=parameter, options=options,
                                 value=value, extra=extra))