Python moves.zip函数代码示例

def test_add_patch_info():
    """Test adding patch info to source space."""
    # let's setup a small source space
    src = read_source_spaces(fname_small)
    src_new = read_source_spaces(fname_small)
    for s in src_new:
        s['nearest'] = None
        s['nearest_dist'] = None
        s['pinfo'] = None

    # test that no patch info is added for small dist_limit
    try:
        add_source_space_distances(src_new, dist_limit=0.00001)
    except RuntimeError:  # what we throw when scipy version is wrong
        pass
    else:
        assert all(s['nearest'] is None for s in src_new)
        assert all(s['nearest_dist'] is None for s in src_new)
        assert all(s['pinfo'] is None for s in src_new)

    # now let's use one that works
    add_source_space_distances(src_new)

    for s1, s2 in zip(src, src_new):
        assert_array_equal(s1['nearest'], s2['nearest'])
        assert_allclose(s1['nearest_dist'], s2['nearest_dist'], atol=1e-7)
        assert_equal(len(s1['pinfo']), len(s2['pinfo']))
        for p1, p2 in zip(s1['pinfo'], s2['pinfo']):
            assert_array_equal(p1, p2)

def test_crop():
    """Test cropping raw files
    """
    # split a concatenated file to test a difficult case
    raw = Raw([fif_fname, fif_fname], preload=False)
    split_size = 10.  # in seconds
    sfreq = raw.info['sfreq']
    nsamp = (raw.last_samp - raw.first_samp + 1)

    # do an annoying case (off-by-one splitting)
    tmins = np.r_[1., np.round(np.arange(0., nsamp - 1, split_size * sfreq))]
    tmins = np.sort(tmins)
    tmaxs = np.concatenate((tmins[1:] - 1, [nsamp - 1]))
    tmaxs /= sfreq
    tmins /= sfreq
    raws = [None] * len(tmins)
    for ri, (tmin, tmax) in enumerate(zip(tmins, tmaxs)):
        raws[ri] = raw.crop(tmin, tmax, True)
    all_raw_2 = concatenate_raws(raws, preload=False)
    assert_equal(raw.first_samp, all_raw_2.first_samp)
    assert_equal(raw.last_samp, all_raw_2.last_samp)
    assert_array_equal(raw[:, :][0], all_raw_2[:, :][0])

    tmins = np.round(np.arange(0., nsamp - 1, split_size * sfreq))
    tmaxs = np.concatenate((tmins[1:] - 1, [nsamp - 1]))
    tmaxs /= sfreq
    tmins /= sfreq

    # going in revere order so the last fname is the first file (need it later)
    raws = [None] * len(tmins)
    for ri, (tmin, tmax) in enumerate(zip(tmins, tmaxs)):
        raws[ri] = raw.copy()
        raws[ri].crop(tmin, tmax, False)
    # test concatenation of split file
    all_raw_1 = concatenate_raws(raws, preload=False)

    all_raw_2 = raw.crop(0, None, True)
    for ar in [all_raw_1, all_raw_2]:
        assert_equal(raw.first_samp, ar.first_samp)
        assert_equal(raw.last_samp, ar.last_samp)
        assert_array_equal(raw[:, :][0], ar[:, :][0])

    # test shape consistency of cropped raw
    data = np.zeros((1, 1002001))
    info = create_info(1, 1000)
    raw = RawArray(data, info)
    for tmin in range(0, 1001, 100):
        raw1 = raw.crop(tmin=tmin, tmax=tmin + 2, copy=True)
        assert_equal(raw1[:][0].shape, (1, 2001))

def test_subject_info():
    """Test reading subject information
    """
    tempdir = _TempDir()
    raw = Raw(fif_fname).crop(0, 1, False)
    assert_true(raw.info['subject_info'] is None)
    # fake some subject data
    keys = ['id', 'his_id', 'last_name', 'first_name', 'birthday', 'sex',
            'hand']
    vals = [1, 'foobar', 'bar', 'foo', (1901, 2, 3), 0, 1]
    subject_info = dict()
    for key, val in zip(keys, vals):
        subject_info[key] = val
    raw.info['subject_info'] = subject_info
    out_fname = op.join(tempdir, 'test_subj_info_raw.fif')
    raw.save(out_fname, overwrite=True)
    raw_read = Raw(out_fname)
    for key in keys:
        assert_equal(subject_info[key], raw_read.info['subject_info'][key])
    assert_equal(raw.info['meas_date'], raw_read.info['meas_date'])
    raw.anonymize()
    raw.save(out_fname, overwrite=True)
    raw_read = Raw(out_fname)
    for this_raw in (raw, raw_read):
        assert_true(this_raw.info.get('subject_info') is None)
        assert_equal(this_raw.info['meas_date'], [0, 0])
    assert_equal(raw.info['file_id']['secs'], 0)
    assert_equal(raw.info['meas_id']['secs'], 0)
    # When we write out with raw.save, these get overwritten with the
    # new save time
    assert_true(raw_read.info['file_id']['secs'] > 0)
    assert_true(raw_read.info['meas_id']['secs'] > 0)

def test_subject_info():
    """Test reading subject information
    """
    tempdir = _TempDir()
    raw = Raw(fif_fname)
    raw.crop(0, 1, False)
    assert_true(raw.info['subject_info'] is None)
    # fake some subject data
    keys = ['id', 'his_id', 'last_name', 'first_name', 'birthday', 'sex',
            'hand']
    vals = [1, 'foobar', 'bar', 'foo', (1901, 2, 3), 0, 1]
    subject_info = dict()
    for key, val in zip(keys, vals):
        subject_info[key] = val
    raw.info['subject_info'] = subject_info
    out_fname = op.join(tempdir, 'test_subj_info_raw.fif')
    raw.save(out_fname, overwrite=True)
    raw_read = Raw(out_fname)
    for key in keys:
        assert_equal(subject_info[key], raw_read.info['subject_info'][key])
    raw_read.anonymize()
    assert_true(raw_read.info.get('subject_info') is None)
    out_fname_anon = op.join(tempdir, 'test_subj_info_anon_raw.fif')
    raw_read.save(out_fname_anon, overwrite=True)
    raw_read = Raw(out_fname_anon)
    assert_true(raw_read.info.get('subject_info') is None)

def test_evoked_standard_error():
    """Test calculation and read/write of standard error
    """
    epochs = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks,
                    baseline=(None, 0))
    evoked = [epochs.average(), epochs.standard_error()]
    io.write_evokeds(op.join(tempdir, 'evoked.fif'), evoked)
    evoked2 = read_evokeds(op.join(tempdir, 'evoked.fif'), [0, 1])
    evoked3 = [read_evokeds(op.join(tempdir, 'evoked.fif'), 'Unknown'),
               read_evokeds(op.join(tempdir, 'evoked.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 test_drop_epochs_mult():
    """Test that subselecting epochs or making less epochs is equivalent"""
    for preload in [True, False]:
        epochs1 = Epochs(raw, events, {'a': 1, 'b': 2},
                         tmin, tmax, picks=picks, reject=reject,
                         preload=preload)['a']
        epochs2 = Epochs(raw, events, {'a': 1},
                         tmin, tmax, picks=picks, reject=reject,
                         preload=preload)

        if preload:
            # In the preload case you cannot know the bads if already ignored
            assert_equal(len(epochs1.drop_log), len(epochs2.drop_log))
            for d1, d2 in zip(epochs1.drop_log, epochs2.drop_log):
                if d1 == ['IGNORED']:
                    assert_true(d2 == ['IGNORED'])
                if d1 != ['IGNORED'] and d1 != []:
                    assert_true((d2 == d1) or (d2 == ['IGNORED']))
                if d1 == []:
                    assert_true(d2 == [])
            assert_array_equal(epochs1.events, epochs2.events)
            assert_array_equal(epochs1.selection, epochs2.selection)
        else:
            # In the non preload is should be exactly the same
            assert_equal(epochs1.drop_log, epochs2.drop_log)
            assert_array_equal(epochs1.events, epochs2.events)
            assert_array_equal(epochs1.selection, epochs2.selection)

def test_volume_source_space():
    """Test setting up volume source spaces."""
    tempdir = _TempDir()
    src = read_source_spaces(fname_vol)
    temp_name = op.join(tempdir, 'temp-src.fif')
    surf = read_bem_surfaces(fname_bem, s_id=FIFF.FIFFV_BEM_SURF_ID_BRAIN)
    surf['rr'] *= 1e3  # convert to mm
    # The one in the testing dataset (uses bem as bounds)
    for bem, surf in zip((fname_bem, None), (None, surf)):
        src_new = setup_volume_source_space(
            'sample', pos=7.0, bem=bem, surface=surf, mri='T1.mgz',
            subjects_dir=subjects_dir)
        write_source_spaces(temp_name, src_new, overwrite=True)
        src[0]['subject_his_id'] = 'sample'  # XXX: to make comparison pass
        _compare_source_spaces(src, src_new, mode='approx')
        del src_new
        src_new = read_source_spaces(temp_name)
        _compare_source_spaces(src, src_new, mode='approx')
    pytest.raises(IOError, setup_volume_source_space, 'sample',
                  pos=7.0, bem=None, surface='foo',  # bad surf
                  mri=fname_mri, subjects_dir=subjects_dir)
    assert repr(src) == repr(src_new)
    assert src.kind == 'volume'
    # Spheres
    sphere = make_sphere_model(r0=(0., 0., 0.), head_radius=0.1,
                               relative_radii=(0.9, 1.0), sigmas=(0.33, 1.0))
    src = setup_volume_source_space(pos=10)
    src_new = setup_volume_source_space(pos=10, sphere=sphere)
    _compare_source_spaces(src, src_new, mode='exact')
    pytest.raises(ValueError, setup_volume_source_space, sphere='foo')
    # Need a radius
    sphere = make_sphere_model(head_radius=None)
    pytest.raises(ValueError, setup_volume_source_space, sphere=sphere)

def test_add_source_space_distances_limited():
    """Test adding distances to source space with a dist_limit."""
    tempdir = _TempDir()
    src = read_source_spaces(fname)
    src_new = read_source_spaces(fname)
    del src_new[0]['dist']
    del src_new[1]['dist']
    n_do = 200  # limit this for speed
    src_new[0]['vertno'] = src_new[0]['vertno'][:n_do].copy()
    src_new[1]['vertno'] = src_new[1]['vertno'][:n_do].copy()
    out_name = op.join(tempdir, 'temp-src.fif')
    try:
        add_source_space_distances(src_new, dist_limit=0.007)
    except RuntimeError:  # what we throw when scipy version is wrong
        raise SkipTest('dist_limit requires scipy > 0.13')
    write_source_spaces(out_name, src_new)
    src_new = read_source_spaces(out_name)

    for so, sn in zip(src, src_new):
        assert_array_equal(so['dist_limit'], np.array([-0.007], np.float32))
        assert_array_equal(sn['dist_limit'], np.array([0.007], np.float32))
        do = so['dist']
        dn = sn['dist']

        # clean out distances > 0.007 in C code
        do.data[do.data > 0.007] = 0
        do.eliminate_zeros()

        # make sure we have some comparable distances
        assert np.sum(do.data < 0.007) > 400

        # do comparison over the region computed
        d = (do - dn)[:sn['vertno'][n_do - 1]][:, :sn['vertno'][n_do - 1]]
        assert_allclose(np.zeros_like(d.data), d.data, rtol=0, atol=1e-6)

def test_morphed_source_space_return():
    """Test returning a morphed source space to the original subject"""
    # let's create some random data on fsaverage
    data = rng.randn(20484, 1)
    tmin, tstep = 0, 1.
    src_fs = read_source_spaces(fname_fs)
    stc_fs = SourceEstimate(data, [s['vertno'] for s in src_fs],
                            tmin, tstep, 'fsaverage')

    # Create our morph source space
    src_morph = morph_source_spaces(src_fs, 'sample',
                                    subjects_dir=subjects_dir)

    # Morph the data over using standard methods
    stc_morph = stc_fs.morph('sample', [s['vertno'] for s in src_morph],
                             smooth=1, subjects_dir=subjects_dir)

    # We can now pretend like this was real data we got e.g. from an inverse.
    # To be complete, let's remove some vertices
    keeps = [np.sort(rng.permutation(np.arange(len(v)))[:len(v) - 10])
             for v in stc_morph.vertices]
    stc_morph = SourceEstimate(
        np.concatenate([stc_morph.lh_data[keeps[0]],
                        stc_morph.rh_data[keeps[1]]]),
        [v[k] for v, k in zip(stc_morph.vertices, keeps)], tmin, tstep,
        'sample')

    # Return it to the original subject
    stc_morph_return = stc_morph.to_original_src(
        src_fs, subjects_dir=subjects_dir)

    # Compare to the original data
    stc_morph_morph = stc_morph.morph('fsaverage', stc_morph_return.vertices,
                                      smooth=1,
                                      subjects_dir=subjects_dir)
    assert_equal(stc_morph_return.subject, stc_morph_morph.subject)
    for ii in range(2):
        assert_array_equal(stc_morph_return.vertices[ii],
                           stc_morph_morph.vertices[ii])
    # These will not match perfectly because morphing pushes data around
    corr = np.corrcoef(stc_morph_return.data[:, 0],
                       stc_morph_morph.data[:, 0])[0, 1]
    assert_true(corr > 0.99, corr)

    # Degenerate cases
    stc_morph.subject = None  # no .subject provided
    assert_raises(ValueError, stc_morph.to_original_src,
                  src_fs, subject_orig='fsaverage', subjects_dir=subjects_dir)
    stc_morph.subject = 'sample'
    del src_fs[0]['subject_his_id']  # no name in src_fsaverage
    assert_raises(ValueError, stc_morph.to_original_src,
                  src_fs, subjects_dir=subjects_dir)
    src_fs[0]['subject_his_id'] = 'fsaverage'  # name mismatch
    assert_raises(ValueError, stc_morph.to_original_src,
                  src_fs, subject_orig='foo', subjects_dir=subjects_dir)
    src_fs[0]['subject_his_id'] = 'sample'
    src = read_source_spaces(fname)  # wrong source space
    assert_raises(RuntimeError, stc_morph.to_original_src,
                  src, subjects_dir=subjects_dir)

def test_crop():
    """Test cropping raw files
    """
    # split a concatenated file to test a difficult case
    raw = Raw([fif_fname, fif_fname], preload=False)
    split_size = 10.0  # in seconds
    sfreq = raw.info["sfreq"]
    nsamp = raw.last_samp - raw.first_samp + 1

    # do an annoying case (off-by-one splitting)
    tmins = np.r_[1.0, np.round(np.arange(0.0, nsamp - 1, split_size * sfreq))]
    tmins = np.sort(tmins)
    tmaxs = np.concatenate((tmins[1:] - 1, [nsamp - 1]))
    tmaxs /= sfreq
    tmins /= sfreq
    raws = [None] * len(tmins)
    for ri, (tmin, tmax) in enumerate(zip(tmins, tmaxs)):
        raws[ri] = raw.crop(tmin, tmax, True)
    all_raw_2 = concatenate_raws(raws, preload=False)
    assert_equal(raw.first_samp, all_raw_2.first_samp)
    assert_equal(raw.last_samp, all_raw_2.last_samp)
    assert_array_equal(raw[:, :][0], all_raw_2[:, :][0])

    tmins = np.round(np.arange(0.0, nsamp - 1, split_size * sfreq))
    tmaxs = np.concatenate((tmins[1:] - 1, [nsamp - 1]))
    tmaxs /= sfreq
    tmins /= sfreq

    # going in revere order so the last fname is the first file (need it later)
    raws = [None] * len(tmins)
    for ri, (tmin, tmax) in enumerate(zip(tmins, tmaxs)):
        raws[ri] = raw.copy()
        raws[ri].crop(tmin, tmax, False)
    # test concatenation of split file
    all_raw_1 = concatenate_raws(raws, preload=False)

    all_raw_2 = raw.crop(0, None, True)
    for ar in [all_raw_1, all_raw_2]:
        assert_equal(raw.first_samp, ar.first_samp)
        assert_equal(raw.last_samp, ar.last_samp)
        assert_array_equal(raw[:, :][0], ar[:, :][0])

def test_triangle_neighbors():
    """Test efficient vertex neighboring triangles for surfaces"""
    this = read_source_spaces(fname)[0]
    this["neighbor_tri"] = [list() for _ in range(this["np"])]
    for p in range(this["ntri"]):
        verts = this["tris"][p]
        this["neighbor_tri"][verts[0]].append(p)
        this["neighbor_tri"][verts[1]].append(p)
        this["neighbor_tri"][verts[2]].append(p)
    this["neighbor_tri"] = [np.array(nb, int) for nb in this["neighbor_tri"]]

    neighbor_tri = _triangle_neighbors(this["tris"], this["np"])
    assert_true(np.array_equal(nt1, nt2) for nt1, nt2 in zip(neighbor_tri, this["neighbor_tri"]))

def test_vertex_to_mni():
    """Test conversion of vertices to MNI coordinates
    """
    # obtained using "tksurfer (sample/fsaverage) (l/r)h white"
    vertices = [100960, 7620, 150549, 96761]
    coords_s = np.array([[-60.86, -11.18, -3.19], [-36.46, -93.18, -2.36],
                         [-38.00, 50.08, -10.61], [47.14, 8.01, 46.93]])
    coords_f = np.array([[-41.28, -40.04, 18.20], [-6.05, 49.74, -18.15],
                         [-61.71, -14.55, 20.52], [21.70, -60.84, 25.02]])
    hemis = [0, 0, 0, 1]
    for coords, subject in zip([coords_s, coords_f], ['sample', 'fsaverage']):
        coords_2 = vertex_to_mni(vertices, hemis, subject, subjects_dir)
        # less than 1mm error
        assert_allclose(coords, coords_2, atol=1.0)

def test_legendre_val():
    """Test Legendre polynomial (derivative) equivalence
    """
    rng = np.random.RandomState(0)
    # check table equiv
    xs = np.linspace(-1., 1., 1000)
    n_terms = 100

    # True, numpy
    vals_np = legendre.legvander(xs, n_terms - 1)

    # Table approximation
    for fun, nc in zip([_get_legen_lut_fast, _get_legen_lut_accurate],
                       [100, 50]):
        lut, n_fact = _get_legen_table('eeg', n_coeff=nc, force_calc=True)
        vals_i = fun(xs, lut)
        # Need a "1:" here because we omit the first coefficient in our table!
        assert_allclose(vals_np[:, 1:vals_i.shape[1] + 1], vals_i,
                        rtol=1e-2, atol=5e-3)

        # Now let's look at our sums
        ctheta = rng.rand(20, 30) * 2.0 - 1.0
        beta = rng.rand(20, 30) * 0.8
        lut_fun = partial(fun, lut=lut)
        c1 = _comp_sum_eeg(beta.flatten(), ctheta.flatten(), lut_fun, n_fact)
        c1.shape = beta.shape

        # compare to numpy
        n = np.arange(1, n_terms, dtype=float)[:, np.newaxis, np.newaxis]
        coeffs = np.zeros((n_terms,) + beta.shape)
        coeffs[1:] = (np.cumprod([beta] * (n_terms - 1), axis=0) *
                      (2.0 * n + 1.0) * (2.0 * n + 1.0) / n)
        # can't use tensor=False here b/c it isn't in old numpy
        c2 = np.empty((20, 30))
        for ci1 in range(20):
            for ci2 in range(30):
                c2[ci1, ci2] = legendre.legval(ctheta[ci1, ci2],
                                               coeffs[:, ci1, ci2])
        assert_allclose(c1, c2, 1e-2, 1e-3)  # close enough...

    # compare fast and slow for MEG
    ctheta = rng.rand(20 * 30) * 2.0 - 1.0
    beta = rng.rand(20 * 30) * 0.8
    lut, n_fact = _get_legen_table('meg', n_coeff=10, force_calc=True)
    fun = partial(_get_legen_lut_fast, lut=lut)
    coeffs = _comp_sums_meg(beta, ctheta, fun, n_fact, False)
    lut, n_fact = _get_legen_table('meg', n_coeff=20, force_calc=True)
    fun = partial(_get_legen_lut_accurate, lut=lut)
    coeffs = _comp_sums_meg(beta, ctheta, fun, n_fact, False)

def test_output_formats():
    """Test saving and loading raw data using multiple formats
    """
    tempdir = _TempDir()
    formats = ['short', 'int', 'single', 'double']
    tols = [1e-4, 1e-7, 1e-7, 1e-15]

    # let's fake a raw file with different formats
    raw = Raw(test_fif_fname).crop(0, 1, copy=False)

    temp_file = op.join(tempdir, 'raw.fif')
    for ii, (fmt, tol) in enumerate(zip(formats, tols)):
        # Let's test the overwriting error throwing while we're at it
        if ii > 0:
            assert_raises(IOError, raw.save, temp_file, fmt=fmt)
        raw.save(temp_file, fmt=fmt, overwrite=True)
        raw2 = Raw(temp_file)
        raw2_data = raw2[:, :][0]
        assert_allclose(raw2_data, raw[:, :][0], rtol=tol, atol=1e-25)
        assert_equal(raw2.orig_format, fmt)

def test_output_formats():
    """Test saving and loading raw data using multiple formats
    """
    formats = ["short", "int", "single", "double"]
    tols = [1e-4, 1e-7, 1e-7, 1e-15]

    # let's fake a raw file with different formats
    raw = Raw(fif_fname, preload=True)
    raw.crop(0, 1, copy=False)

    temp_file = op.join(tempdir, "raw.fif")
    for ii, (format, tol) in enumerate(zip(formats, tols)):
        # Let's test the overwriting error throwing while we're at it
        if ii > 0:
            assert_raises(IOError, raw.save, temp_file, format=format)
        raw.save(temp_file, format=format, overwrite=True)
        raw2 = Raw(temp_file)
        raw2_data = raw2[:, :][0]
        assert_allclose(raw2_data, raw._data, rtol=tol, atol=1e-25)
        assert_true(raw2.orig_format == format)