Python mne.write_evokeds函数代码示例

 def events_save_events(self,evt=None,condition=None,postfix="evt",
                             picks=None,reject=None,proj=False,
                             save_condition={"events":True,"epochs":True,"evoked":True}):
     
     from jumeg.jumeg_4raw_data_plot import jumeg_4raw_data_plot as jplt
     jplt.verbose = self.verbose
   
     ep,bc = self.events_apply_epochs_and_baseline(self.raw,evt=evt,reject=reject,proj=proj,picks=picks)      
   
     postfix += '_' + condition
     if bc:
        postfix += '_bc'
            
   #--- save events to txt file    
     if save_condition["events"]:
        fname = jumeg_base.get_fif_name(raw=self.raw,postfix=postfix,extention=".eve",update_raw_fname=False)
        mne.event.write_events( fname,evt['events'] )
        print" ---> done jumeg epocher save events as => EVENTS :" +fname
       
   #--- save epoch data
     if save_condition["epochs"]:
        fname = jumeg_base.get_fif_name(raw=self.raw,postfix=postfix,extention="-epo.fif",update_raw_fname=False)
        ep.save( fname )
        print" ---> done jumeg epocher save events as => EPOCHS :" +fname
       
   #--- save averaged data
        if save_condition["evoked"]:
           fname = jumeg_base.get_fif_name(raw=self.raw,postfix=postfix,extention="-ave.fif",update_raw_fname=False)
           mne.write_evokeds( fname,ep.average() )              
           print" ---> done jumeg epocher save events as => EVOKED (averaged) :" +fname 
           fname = jumeg_base.get_fif_name(raw=self.raw,postfix=postfix,extention="-ave",update_raw_fname=False)  
         #--- plot evoked
           fname = jplt.plot_evoked(ep,fname=fname,condition=condition,show_plot=False,save_plot=True,plot_dir='plots')
           print" ---> done jumeg epocher plot evoked (averaged) :" +fname 

def test_evoked_resample():
    """Test for resampling of evoked data
    """
    tempdir = _TempDir()
    # upsample, write it out, read it in
    ave = read_evokeds(fname, 0)
    sfreq_normal = ave.info['sfreq']
    ave.resample(2 * sfreq_normal)
    write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave)
    ave_up = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 0)

    # compare it to the original
    ave_normal = read_evokeds(fname, 0)

    # and compare the original to the downsampled upsampled version
    ave_new = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 0)
    ave_new.resample(sfreq_normal)

    assert_array_almost_equal(ave_normal.data, ave_new.data, 2)
    assert_array_almost_equal(ave_normal.times, ave_new.times)
    assert_equal(ave_normal.nave, ave_new.nave)
    assert_equal(ave_normal._aspect_kind, ave_new._aspect_kind)
    assert_equal(ave_normal.kind, ave_new.kind)
    assert_equal(ave_normal.last, ave_new.last)
    assert_equal(ave_normal.first, ave_new.first)

    # for the above to work, the upsampling just about had to, but
    # we'll add a couple extra checks anyway
    assert_true(len(ave_up.times) == 2 * len(ave_normal.times))
    assert_true(ave_up.data.shape[1] == 2 * ave_normal.data.shape[1])

def test_evoked_standard_error():
    """Test calculation and read/write of standard error
    """
    raw, events, picks = _get_data()
    tempdir = _TempDir()
    epochs = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks,
                    baseline=(None, 0))
    evoked = [epochs.average(), epochs.standard_error()]
    write_evokeds(op.join(tempdir, 'evoked-ave.fif'), evoked)
    evoked2 = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), [0, 1])
    evoked3 = [read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 'Unknown'),
               read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 'Unknown',
                            kind='standard_error')]
    for evoked_new in [evoked2, evoked3]:
        assert_true(evoked_new[0]._aspect_kind ==
                    FIFF.FIFFV_ASPECT_AVERAGE)
        assert_true(evoked_new[0].kind == 'average')
        assert_true(evoked_new[1]._aspect_kind ==
                    FIFF.FIFFV_ASPECT_STD_ERR)
        assert_true(evoked_new[1].kind == 'standard_error')
        for ave, ave2 in zip(evoked, evoked_new):
            assert_array_almost_equal(ave.data, ave2.data)
            assert_array_almost_equal(ave.times, ave2.times)
            assert_equal(ave.nave, ave2.nave)
            assert_equal(ave._aspect_kind, ave2._aspect_kind)
            assert_equal(ave.kind, ave2.kind)
            assert_equal(ave.last, ave2.last)
            assert_equal(ave.first, ave2.first)

def _calc_evoked(params):
    subject, events_id, epochs = params
    evoked = {}
    for cond_name in events_id.keys():
        evoked[cond_name] = epochs[cond_name].average()
        evo = op.join(LOCAL_ROOT_DIR, 'evo', '{}_ecr_{}-ave.fif'.format(subject, cond_name))
        mne.write_evokeds(evo, evoked[cond_name])
    return evoked

def compute_epochs_cov_evokeds(subject):
    """Epoch, compute noise covariance and average.

    params:
    subject : str
        the subject id to be loaded
    """
    raw = Raw(save_folder + "%s_filtered_ica_mc_raw_tsss.fif" % subject,
              preload=True)
    # Select events to extract epochs from.
    event_id = {'ent_left': 1,
                'ent_right': 2,
                'ctl_left': 4,
                'ctl_right': 8}

    #   Setup for reading the raw data
    events = mne.find_events(raw, min_duration=0.01)

    picks = mne.pick_types(raw.info, meg=True, eeg=True, stim=False, eog=False,
                           include=include, exclude='bads')
    # Read epochs
    epochs = mne.Epochs(raw, events, event_id, tmin, tmax, picks=picks,
                        baseline=(None, 0), reject=reject,
                        preload=True)

    epochs.save(epochs_folder + "%s_filtered_ica_mc_tsss-epo.fif" % subject)

    # Plot epochs.
    # epochs.plot(trellis=False)

    # Look at channels that caused dropped events, showing that the subject's
    # blinks were likely to blame for most epochs being dropped
    epochs.drop_bad_epochs()
    fig = epochs.plot_drop_log(subject=subject, show=False)
    fig.savefig(epochs_folder + "pics/%s_drop_log.png" % subject)

    # Make noise cov
    cov = compute_covariance(epochs, tmin=None, tmax=0, method="auto")
    mne.write_cov(epochs_folder + "%s-cov.fif" % subject, cov)

    # Average epochs and get evoked data corresponding to the left stimulation
    ###########################################################################
    # Save evoked responses for different conditions to disk

    # average epochs and get Evoked datasets
    evokeds = [epochs[cond].average() for cond in ['ent_left', 'ent_right',
                                                   'ctl_left', 'ctl_right']]

    evokeds = [epochs[cond].average() for cond in epochs.event_id.keys()]

    # save evoked data to disk
    mne.write_evokeds(epochs_folder +
                      '%s_filtered_ica_mc_raw_tsss-ave.fif' % subject, evokeds)

    plt.close("all")

def calc_evoked(indices, epochs_fname, overwrite_epochs=False, overwrite_evoked=False):
    epochs = mne.read_epochs(epochs_fname, preload=False)
    print(epochs.events.shape)
    for event_name, event_indices in indices.items():
        evoked_event_fname = meg.get_cond_fname(meg.EVO, event_name)
        epochs_event_fname = meg.get_cond_fname(meg.EPO, event_name)
        if not op.isfile(epochs_event_fname) or overwrite_epochs:
            print('Saving {} epochs to {}, events num: {}'.format(event_name, epochs_event_fname, len(event_indices)))
            event_epochs = epochs[event_indices]
            event_epochs.save(epochs_event_fname)
        if not op.isfile(evoked_event_fname) or overwrite_evoked:
            print('Saving {} evoked to {}'.format(event_name, evoked_event_fname))
            mne.write_evokeds(evoked_event_fname, event_epochs.average())

def test_io_evoked():
    """Test IO for evoked data (fif + gz) with integer and str args
    """
    tempdir = _TempDir()
    ave = read_evokeds(fname, 0)

    write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave)
    ave2 = read_evokeds(op.join(tempdir, 'evoked-ave.fif'))[0]

    # This not being assert_array_equal due to windows rounding
    assert_true(np.allclose(ave.data, ave2.data, atol=1e-16, rtol=1e-3))
    assert_array_almost_equal(ave.times, ave2.times)
    assert_equal(ave.nave, ave2.nave)
    assert_equal(ave._aspect_kind, ave2._aspect_kind)
    assert_equal(ave.kind, ave2.kind)
    assert_equal(ave.last, ave2.last)
    assert_equal(ave.first, ave2.first)
    assert_true(repr(ave))

    # test compressed i/o
    ave2 = read_evokeds(fname_gz, 0)
    assert_true(np.allclose(ave.data, ave2.data, atol=1e-16, rtol=1e-8))

    # test str access
    condition = 'Left Auditory'
    assert_raises(ValueError, read_evokeds, fname, condition, kind='stderr')
    assert_raises(ValueError, read_evokeds, fname, condition,
                  kind='standard_error')
    ave3 = read_evokeds(fname, condition)
    assert_array_almost_equal(ave.data, ave3.data, 19)

    # test read_evokeds and write_evokeds
    aves1 = read_evokeds(fname)[1::2]
    aves2 = read_evokeds(fname, [1, 3])
    aves3 = read_evokeds(fname, ['Right Auditory', 'Right visual'])
    write_evokeds(op.join(tempdir, 'evoked-ave.fif'), aves1)
    aves4 = read_evokeds(op.join(tempdir, 'evoked-ave.fif'))
    for aves in [aves2, aves3, aves4]:
        for [av1, av2] in zip(aves1, aves):
            assert_array_almost_equal(av1.data, av2.data)
            assert_array_almost_equal(av1.times, av2.times)
            assert_equal(av1.nave, av2.nave)
            assert_equal(av1.kind, av2.kind)
            assert_equal(av1._aspect_kind, av2._aspect_kind)
            assert_equal(av1.last, av2.last)
            assert_equal(av1.first, av2.first)
            assert_equal(av1.comment, av2.comment)

    # test warnings on bad filenames
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter('always')
        fname2 = op.join(tempdir, 'test-bad-name.fif')
        write_evokeds(fname2, ave)
        read_evokeds(fname2)
    assert_naming(w, 'test_evoked.py', 2)

    # constructor
    assert_raises(TypeError, Evoked, fname)

def test_shift_time_evoked():
    """ Test for shifting of time scale
    """
    tempdir = _TempDir()
    # Shift backward
    ave = read_evokeds(fname, 0)
    ave.shift_time(-0.1, relative=True)
    write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave)

    # Shift forward twice the amount
    ave_bshift = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 0)
    ave_bshift.shift_time(0.2, relative=True)
    write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave_bshift)

    # Shift backward again
    ave_fshift = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 0)
    ave_fshift.shift_time(-0.1, relative=True)
    write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave_fshift)

    ave_normal = read_evokeds(fname, 0)
    ave_relative = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 0)

    assert_true(np.allclose(ave_normal.data, ave_relative.data,
                            atol=1e-16, rtol=1e-3))
    assert_array_almost_equal(ave_normal.times, ave_relative.times, 10)

    assert_equal(ave_normal.last, ave_relative.last)
    assert_equal(ave_normal.first, ave_relative.first)

    # Absolute time shift
    ave = read_evokeds(fname, 0)
    ave.shift_time(-0.3, relative=False)
    write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave)

    ave_absolute = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 0)

    assert_true(np.allclose(ave_normal.data, ave_absolute.data,
                            atol=1e-16, rtol=1e-3))
    assert_equal(ave_absolute.first, int(-0.3 * ave.info['sfreq']))

picks = mne.pick_types(raw.info, meg=False, eeg=True, stim=False, eog=True,
                       include=include, exclude='bads')
# Read epochs
epochs = mne.Epochs(raw, events, event_ids, tmin, tmax, picks=picks,
                    baseline=(None, 0), reject=dict(eeg=80e-6, eog=150e-6))
# Let's equalize the trial counts in each condition
epochs.equalize_event_counts(['AudL', 'AudR', 'VisL', 'VisR'], copy=False)
# Now let's combine some conditions
combine_event_ids(epochs, ['AudL', 'AudR'], {'Auditory': 12}, copy=False)
combine_event_ids(epochs, ['VisL', 'VisR'], {'Visual': 34}, copy=False)

# average epochs and get Evoked datasets
evokeds = [epochs[cond].average() for cond in ['Auditory', 'Visual']]

# save evoked data to disk
mne.write_evokeds('sample_auditory_and_visual_eeg-ave.fif', evokeds)

###############################################################################
# View evoked response
import matplotlib.pyplot as plt
plt.clf()
ax = plt.subplot(2, 1, 1)
evokeds[0].plot(axes=ax)
plt.title('EEG evoked potential, auditory trials')
plt.ylabel('Potential (uV)')
ax = plt.subplot(2, 1, 2)
evokeds[1].plot(axes=ax)
plt.title('EEG evoked potential, visual trials')
plt.ylabel('Potential (uV)')
plt.show()

old_data = epochs_tmp.get_data()
data = np.empty_like(old_data)
for ii, e in enumerate(old_data):
    data[ii] = np.dot(projector, e)
# got the threshold from Brainstorm (http://neuroimage.usc.edu/brainstorm/Tutorials/TutRawAvg, 2000 fT)
epochs_clean = mne.epochs.EpochsArray(data, info, epochs_tmp.events, reject=dict(mag=2e-12), event_id=epochs_tmp.event_id, tmin=np.min(epochs_tmp.times))

# and check how different the averages get
evokeds_clean = [epochs_clean[name].average() for name in conds[:3]]
title = 'Averaged data after EOG and bad trials removal'
mne.viz.plot_topo(evokeds_clean, color=colors, title=title)

# save evoked responses for all 5 conditions
print 'Saving evoked data...'
evokeds_clean = [epochs_clean[name].average() for name in conds]
mne.write_evokeds(evoked_dir + subj + '_stop_BP1-35_DS120-ave.fif', evokeds_clean)

# output number of averages
for ev in evokeds_clean:
    print ev.comment, ': %d averages'%ev.nave

# For the data tracker
print '=== Add to data tracker ==='
print 'Y\t%s\t%d\t%d\t%d'%(comps2use,evokeds_clean[1].nave,evokeds_clean[4].nave,evokeds_clean[0].nave) 
print '==============='

# now that we know which epochs to drop, copy the log to the actual epochs structure and drop them
bad_epochs = [i for i,j in enumerate(epochs_clean.drop_log) if len(j)>0]
epochs.drop_epochs(bad_epochs)
# save epochs with (optional) EOG projection
print 'Saving epochs with optional SSP operators...'

def test_dipole_fitting():
    """Test dipole fitting"""
    amp = 10e-9
    tempdir = _TempDir()
    rng = np.random.RandomState(0)
    fname_dtemp = op.join(tempdir, 'test.dip')
    fname_sim = op.join(tempdir, 'test-ave.fif')
    fwd = convert_forward_solution(read_forward_solution(fname_fwd),
                                   surf_ori=False, force_fixed=True)
    evoked = read_evokeds(fname_evo)[0]
    cov = read_cov(fname_cov)
    n_per_hemi = 5
    vertices = [np.sort(rng.permutation(s['vertno'])[:n_per_hemi])
                for s in fwd['src']]
    nv = sum(len(v) for v in vertices)
    stc = SourceEstimate(amp * np.eye(nv), vertices, 0, 0.001)
    with warnings.catch_warnings(record=True):  # semi-def cov
        evoked = generate_evoked(fwd, stc, evoked, cov, snr=20,
                                 random_state=rng)
    # For speed, let's use a subset of channels (strange but works)
    picks = np.sort(np.concatenate([
        pick_types(evoked.info, meg=True, eeg=False)[::2],
        pick_types(evoked.info, meg=False, eeg=True)[::2]]))
    evoked.pick_channels([evoked.ch_names[p] for p in picks])
    evoked.add_proj(make_eeg_average_ref_proj(evoked.info))
    write_evokeds(fname_sim, evoked)

    # Run MNE-C version
    run_subprocess([
        'mne_dipole_fit', '--meas', fname_sim, '--meg', '--eeg',
        '--noise', fname_cov, '--dip', fname_dtemp,
        '--mri', fname_fwd, '--reg', '0', '--tmin', '0',
    ])
    dip_c = read_dipole(fname_dtemp)

    # Run mne-python version
    sphere = make_sphere_model(head_radius=0.1)
    dip, residuals = fit_dipole(evoked, fname_cov, sphere, fname_fwd)

    # Sanity check: do our residuals have less power than orig data?
    data_rms = np.sqrt(np.sum(evoked.data ** 2, axis=0))
    resi_rms = np.sqrt(np.sum(residuals ** 2, axis=0))
    assert_true((data_rms > resi_rms).all())

    # Compare to original points
    transform_surface_to(fwd['src'][0], 'head', fwd['mri_head_t'])
    transform_surface_to(fwd['src'][1], 'head', fwd['mri_head_t'])
    src_rr = np.concatenate([s['rr'][v] for s, v in zip(fwd['src'], vertices)],
                            axis=0)
    src_nn = np.concatenate([s['nn'][v] for s, v in zip(fwd['src'], vertices)],
                            axis=0)

    # MNE-C skips the last "time" point :(
    dip.crop(dip_c.times[0], dip_c.times[-1])
    src_rr, src_nn = src_rr[:-1], src_nn[:-1]

    # check that we did at least as well
    corrs, dists, gc_dists, amp_errs, gofs = [], [], [], [], []
    for d in (dip_c, dip):
        new = d.pos
        diffs = new - src_rr
        corrs += [np.corrcoef(src_rr.ravel(), new.ravel())[0, 1]]
        dists += [np.sqrt(np.mean(np.sum(diffs * diffs, axis=1)))]
        gc_dists += [180 / np.pi * np.mean(np.arccos(np.sum(src_nn * d.ori,
                                                     axis=1)))]
        amp_errs += [np.sqrt(np.mean((amp - d.amplitude) ** 2))]
        gofs += [np.mean(d.gof)]
    assert_true(dists[0] >= dists[1], 'dists: %s' % dists)
    assert_true(corrs[0] <= corrs[1], 'corrs: %s' % corrs)
    assert_true(gc_dists[0] >= gc_dists[1], 'gc-dists (ori): %s' % gc_dists)
    assert_true(amp_errs[0] >= amp_errs[1], 'amplitude errors: %s' % amp_errs)

def test_io_evoked():
    """Test IO for evoked data (fif + gz) with integer and str args
    """
    ave = read_evokeds(fname, 0)

    write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave)
    ave2 = read_evokeds(op.join(tempdir, 'evoked-ave.fif'))[0]

    # This not being assert_array_equal due to windows rounding
    assert_true(np.allclose(ave.data, ave2.data, atol=1e-16, rtol=1e-3))
    assert_array_almost_equal(ave.times, ave2.times)
    assert_equal(ave.nave, ave2.nave)
    assert_equal(ave._aspect_kind, ave2._aspect_kind)
    assert_equal(ave.kind, ave2.kind)
    assert_equal(ave.last, ave2.last)
    assert_equal(ave.first, ave2.first)

    # test compressed i/o
    ave2 = read_evokeds(fname_gz, 0)
    assert_true(np.allclose(ave.data, ave2.data, atol=1e-16, rtol=1e-8))

    # test str access
    condition = 'Left Auditory'
    assert_raises(ValueError, read_evokeds, fname, condition, kind='stderr')
    assert_raises(ValueError, read_evokeds, fname, condition,
                  kind='standard_error')
    ave3 = read_evokeds(fname, condition)
    assert_array_almost_equal(ave.data, ave3.data, 19)

    # test deprecation warning for read_evoked and write_evoked
    # XXX should be deleted for 0.9 release
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter('always')
        ave = read_evoked(fname, setno=0)
        assert_true(w[0].category == DeprecationWarning)
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter('always')
        write_evoked(op.join(tempdir, 'evoked-ave.fif'), ave)
        assert_true(w[0].category == DeprecationWarning)

    # test read_evokeds and write_evokeds
    types = ['Left Auditory', 'Right Auditory', 'Left visual', 'Right visual']
    aves1 = read_evokeds(fname)
    aves2 = read_evokeds(fname, [0, 1, 2, 3])
    aves3 = read_evokeds(fname, types)
    write_evokeds(op.join(tempdir, 'evoked-ave.fif'), aves1)
    aves4 = read_evokeds(op.join(tempdir, 'evoked-ave.fif'))
    for aves in [aves2, aves3, aves4]:
        for [av1, av2] in zip(aves1, aves):
            assert_array_almost_equal(av1.data, av2.data)
            assert_array_almost_equal(av1.times, av2.times)
            assert_equal(av1.nave, av2.nave)
            assert_equal(av1.kind, av2.kind)
            assert_equal(av1._aspect_kind, av2._aspect_kind)
            assert_equal(av1.last, av2.last)
            assert_equal(av1.first, av2.first)
            assert_equal(av1.comment, av2.comment)

    # test warnings on bad filenames
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter('always')
        fname2 = op.join(tempdir, 'test-bad-name.fif')
        write_evokeds(fname2, ave)
        read_evokeds(fname2)
    assert_true(len(w) == 2)

def test_io_evoked():
    """Test IO for evoked data (fif + gz) with integer and str args."""
    tempdir = _TempDir()
    ave = read_evokeds(fname, 0)

    write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave)
    ave2 = read_evokeds(op.join(tempdir, 'evoked-ave.fif'))[0]

    # This not being assert_array_equal due to windows rounding
    assert (np.allclose(ave.data, ave2.data, atol=1e-16, rtol=1e-3))
    assert_array_almost_equal(ave.times, ave2.times)
    assert_equal(ave.nave, ave2.nave)
    assert_equal(ave._aspect_kind, ave2._aspect_kind)
    assert_equal(ave.kind, ave2.kind)
    assert_equal(ave.last, ave2.last)
    assert_equal(ave.first, ave2.first)
    assert (repr(ave))

    # test compressed i/o
    ave2 = read_evokeds(fname_gz, 0)
    assert (np.allclose(ave.data, ave2.data, atol=1e-16, rtol=1e-8))

    # test str access
    condition = 'Left Auditory'
    pytest.raises(ValueError, read_evokeds, fname, condition, kind='stderr')
    pytest.raises(ValueError, read_evokeds, fname, condition,
                  kind='standard_error')
    ave3 = read_evokeds(fname, condition)
    assert_array_almost_equal(ave.data, ave3.data, 19)

    # test read_evokeds and write_evokeds
    aves1 = read_evokeds(fname)[1::2]
    aves2 = read_evokeds(fname, [1, 3])
    aves3 = read_evokeds(fname, ['Right Auditory', 'Right visual'])
    write_evokeds(op.join(tempdir, 'evoked-ave.fif'), aves1)
    aves4 = read_evokeds(op.join(tempdir, 'evoked-ave.fif'))
    for aves in [aves2, aves3, aves4]:
        for [av1, av2] in zip(aves1, aves):
            assert_array_almost_equal(av1.data, av2.data)
            assert_array_almost_equal(av1.times, av2.times)
            assert_equal(av1.nave, av2.nave)
            assert_equal(av1.kind, av2.kind)
            assert_equal(av1._aspect_kind, av2._aspect_kind)
            assert_equal(av1.last, av2.last)
            assert_equal(av1.first, av2.first)
            assert_equal(av1.comment, av2.comment)

    # test warnings on bad filenames
    fname2 = op.join(tempdir, 'test-bad-name.fif')
    with pytest.warns(RuntimeWarning, match='-ave.fif'):
        write_evokeds(fname2, ave)
    with pytest.warns(RuntimeWarning, match='-ave.fif'):
        read_evokeds(fname2)

    # constructor
    pytest.raises(TypeError, Evoked, fname)

    # MaxShield
    fname_ms = op.join(tempdir, 'test-ave.fif')
    assert (ave.info['maxshield'] is False)
    ave.info['maxshield'] = True
    ave.save(fname_ms)
    pytest.raises(ValueError, read_evokeds, fname_ms)
    with pytest.warns(RuntimeWarning, match='Elekta'):
        aves = read_evokeds(fname_ms, allow_maxshield=True)
    assert all(ave.info['maxshield'] is True for ave in aves)
    aves = read_evokeds(fname_ms, allow_maxshield='yes')
    assert (all(ave.info['maxshield'] is True for ave in aves))

    if num in {88, 89, 92, 100}:
        continue
    for run in runs:
        raw = load_subject(num, run)
        fix_channels(raw)
        add_montage(raw)
        raw.pick_channels(ch_names)

        # Band-pass filter to capture the relevant signal (alpha, beta,
        # and mu ranges). Butterworth filter is implied by method='iir'
        # with iir_params=None or left out.

        raw.filter(7.0, 30.0, method='iir', n_jobs=n_cores)
        ica = ICA(n_components=0.95, random_state=random_state)
        ica.fit(raw, decim=3)
        ica.apply(raw)
        events = find_events(raw, consecutive=False)
        epochs = Epochs(raw,
                        events,
                        event_id,
                        tmin,
                        tmax,
                        baseline=baseline,
                        preload=True,
                        proj=False)
        evoked_avg = [epochs[cond].average() for cond in ['left_fist',
                                                          'right_fist']]
        filename = splitext(raw.info['filename'])[0]
        epochs.save(filename + '-epo.fif')
        write_evokeds(filename + '-ave.fif', evoked_avg)

def test_dipole_fitting():
    """Test dipole fitting."""
    amp = 100e-9
    tempdir = _TempDir()
    rng = np.random.RandomState(0)
    fname_dtemp = op.join(tempdir, 'test.dip')
    fname_sim = op.join(tempdir, 'test-ave.fif')
    fwd = convert_forward_solution(read_forward_solution(fname_fwd),
                                   surf_ori=False, force_fixed=True,
                                   use_cps=True)
    evoked = read_evokeds(fname_evo)[0]
    cov = read_cov(fname_cov)
    n_per_hemi = 5
    vertices = [np.sort(rng.permutation(s['vertno'])[:n_per_hemi])
                for s in fwd['src']]
    nv = sum(len(v) for v in vertices)
    stc = SourceEstimate(amp * np.eye(nv), vertices, 0, 0.001)
    evoked = simulate_evoked(fwd, stc, evoked.info, cov, nave=evoked.nave,
                             random_state=rng)
    # For speed, let's use a subset of channels (strange but works)
    picks = np.sort(np.concatenate([
        pick_types(evoked.info, meg=True, eeg=False)[::2],
        pick_types(evoked.info, meg=False, eeg=True)[::2]]))
    evoked.pick_channels([evoked.ch_names[p] for p in picks])
    evoked.add_proj(make_eeg_average_ref_proj(evoked.info))
    write_evokeds(fname_sim, evoked)

    # Run MNE-C version
    run_subprocess([
        'mne_dipole_fit', '--meas', fname_sim, '--meg', '--eeg',
        '--noise', fname_cov, '--dip', fname_dtemp,
        '--mri', fname_fwd, '--reg', '0', '--tmin', '0',
    ])
    dip_c = read_dipole(fname_dtemp)

    # Run mne-python version
    sphere = make_sphere_model(head_radius=0.1)
    with pytest.warns(RuntimeWarning, match='projection'):
        dip, residual = fit_dipole(evoked, cov, sphere, fname_fwd)
    assert isinstance(residual, Evoked)

    # Sanity check: do our residuals have less power than orig data?
    data_rms = np.sqrt(np.sum(evoked.data ** 2, axis=0))
    resi_rms = np.sqrt(np.sum(residual.data ** 2, axis=0))
    assert (data_rms > resi_rms * 0.95).all(), \
        '%s (factor: %s)' % ((data_rms / resi_rms).min(), 0.95)

    # Compare to original points
    transform_surface_to(fwd['src'][0], 'head', fwd['mri_head_t'])
    transform_surface_to(fwd['src'][1], 'head', fwd['mri_head_t'])
    assert_equal(fwd['src'][0]['coord_frame'], FIFF.FIFFV_COORD_HEAD)
    src_rr = np.concatenate([s['rr'][v] for s, v in zip(fwd['src'], vertices)],
                            axis=0)
    src_nn = np.concatenate([s['nn'][v] for s, v in zip(fwd['src'], vertices)],
                            axis=0)

    # MNE-C skips the last "time" point :(
    out = dip.crop(dip_c.times[0], dip_c.times[-1])
    assert (dip is out)
    src_rr, src_nn = src_rr[:-1], src_nn[:-1]

    # check that we did about as well
    corrs, dists, gc_dists, amp_errs, gofs = [], [], [], [], []
    for d in (dip_c, dip):
        new = d.pos
        diffs = new - src_rr
        corrs += [np.corrcoef(src_rr.ravel(), new.ravel())[0, 1]]
        dists += [np.sqrt(np.mean(np.sum(diffs * diffs, axis=1)))]
        gc_dists += [180 / np.pi * np.mean(np.arccos(np.sum(src_nn * d.ori,
                                                     axis=1)))]
        amp_errs += [np.sqrt(np.mean((amp - d.amplitude) ** 2))]
        gofs += [np.mean(d.gof)]
    # XXX possibly some OpenBLAS numerical differences make
    # things slightly worse for us
    factor = 0.7
    assert dists[0] / factor >= dists[1], 'dists: %s' % dists
    assert corrs[0] * factor <= corrs[1], 'corrs: %s' % corrs
    assert gc_dists[0] / factor >= gc_dists[1] * 0.8, \
        'gc-dists (ori): %s' % gc_dists
    assert amp_errs[0] / factor >= amp_errs[1],\
        'amplitude errors: %s' % amp_errs
    # This one is weird because our cov/sim/picking is weird
    assert gofs[0] * factor <= gofs[1] * 2, 'gof: %s' % gofs