Python io.read_info函数代码示例

def test_helmet():
    """Test loading helmet surfaces."""
    base_dir = op.join(op.dirname(__file__), '..', 'io')
    fname_raw = op.join(base_dir, 'tests', 'data', 'test_raw.fif')
    fname_kit_raw = op.join(base_dir, 'kit', 'tests', 'data',
                            'test_bin_raw.fif')
    fname_bti_raw = op.join(base_dir, 'bti', 'tests', 'data',
                            'exported4D_linux_raw.fif')
    fname_ctf_raw = op.join(base_dir, 'tests', 'data', 'test_ctf_raw.fif')
    fname_trans = op.join(base_dir, 'tests', 'data',
                          'sample-audvis-raw-trans.txt')
    trans = _get_trans(fname_trans)[0]
    new_info = read_info(fname_raw)
    artemis_info = new_info.copy()
    for pick in pick_types(new_info):
        new_info['chs'][pick]['coil_type'] = 9999
        artemis_info['chs'][pick]['coil_type'] = \
            FIFF.FIFFV_COIL_ARTEMIS123_GRAD
    for info, n, name in [(read_info(fname_raw), 304, '306m'),
                          (read_info(fname_kit_raw), 304, 'KIT'),
                          (read_info(fname_bti_raw), 304, 'Magnes'),
                          (read_info(fname_ctf_raw), 342, 'CTF'),
                          (new_info, 102, 'unknown'),
                          (artemis_info, 102, 'ARTEMIS123')
                          ]:
        with catch_logging() as log:
            helmet = get_meg_helmet_surf(info, trans, verbose=True)
        log = log.getvalue()
        assert name in log
        assert_equal(len(helmet['rr']), n)
        assert_equal(len(helmet['rr']), len(helmet['nn']))

def test_read_write_info():
    """Test IO of info
    """
    tempdir = _TempDir()
    info = read_info(raw_fname)
    temp_file = op.join(tempdir, 'info.fif')
    # check for bug `#1198`
    info['dev_head_t']['trans'] = np.eye(4)
    t1 = info['dev_head_t']['trans']
    write_info(temp_file, info)
    info2 = read_info(temp_file)
    t2 = info2['dev_head_t']['trans']
    assert_true(len(info['chs']) == len(info2['chs']))
    assert_array_equal(t1, t2)
    # proc_history (e.g., GH#1875)
    creator = u'é'
    info = read_info(chpi_fname)
    info['proc_history'][0]['creator'] = creator
    info['hpi_meas'][0]['creator'] = creator
    info['subject_info']['his_id'] = creator
    write_info(temp_file, info)
    info = read_info(temp_file)
    assert_equal(info['proc_history'][0]['creator'], creator)
    assert_equal(info['hpi_meas'][0]['creator'], creator)
    assert_equal(info['subject_info']['his_id'], creator)

def test_read_write_info():
    """Test IO of info."""
    tempdir = _TempDir()
    info = read_info(raw_fname)
    temp_file = op.join(tempdir, 'info.fif')
    # check for bug `#1198`
    info['dev_head_t']['trans'] = np.eye(4)
    t1 = info['dev_head_t']['trans']
    write_info(temp_file, info)
    info2 = read_info(temp_file)
    t2 = info2['dev_head_t']['trans']
    assert_true(len(info['chs']) == len(info2['chs']))
    assert_array_equal(t1, t2)
    # proc_history (e.g., GH#1875)
    creator = u'é'
    info = read_info(chpi_fname)
    info['proc_history'][0]['creator'] = creator
    info['hpi_meas'][0]['creator'] = creator
    info['subject_info']['his_id'] = creator

    if info['gantry_angle'] is None:  # future testing data may include it
        info['gantry_angle'] = 0.  # Elekta supine position
    gantry_angle = info['gantry_angle']

    write_info(temp_file, info)
    info = read_info(temp_file)
    assert_equal(info['proc_history'][0]['creator'], creator)
    assert_equal(info['hpi_meas'][0]['creator'], creator)
    assert_equal(info['subject_info']['his_id'], creator)
    assert_equal(info['gantry_angle'], gantry_angle)

def test_csr_csc():
    """Test CSR and CSC."""
    info = read_info(sss_ctc_fname)
    info = pick_info(info, pick_types(info, meg=True, exclude=[]))
    sss_ctc = info['proc_history'][0]['max_info']['sss_ctc']
    ct = sss_ctc['decoupler'].copy()
    # CSC
    assert isinstance(ct, sparse.csc_matrix)
    tempdir = _TempDir()
    fname = op.join(tempdir, 'test.fif')
    write_info(fname, info)
    info_read = read_info(fname)
    ct_read = info_read['proc_history'][0]['max_info']['sss_ctc']['decoupler']
    assert isinstance(ct_read, sparse.csc_matrix)
    assert_array_equal(ct_read.toarray(), ct.toarray())
    # Now CSR
    csr = ct.tocsr()
    assert isinstance(csr, sparse.csr_matrix)
    assert_array_equal(csr.toarray(), ct.toarray())
    info['proc_history'][0]['max_info']['sss_ctc']['decoupler'] = csr
    fname = op.join(tempdir, 'test1.fif')
    write_info(fname, info)
    info_read = read_info(fname)
    ct_read = info_read['proc_history'][0]['max_info']['sss_ctc']['decoupler']
    assert isinstance(ct_read, sparse.csc_matrix)  # this gets cast to CSC
    assert_array_equal(ct_read.toarray(), ct.toarray())

def test_read_write_info():
    """Test IO of info."""
    tempdir = _TempDir()
    info = read_info(raw_fname)
    temp_file = op.join(tempdir, 'info.fif')
    # check for bug `#1198`
    info['dev_head_t']['trans'] = np.eye(4)
    t1 = info['dev_head_t']['trans']
    write_info(temp_file, info)
    info2 = read_info(temp_file)
    t2 = info2['dev_head_t']['trans']
    assert (len(info['chs']) == len(info2['chs']))
    assert_array_equal(t1, t2)
    # proc_history (e.g., GH#1875)
    creator = u'é'
    info = read_info(chpi_fname)
    info['proc_history'][0]['creator'] = creator
    info['hpi_meas'][0]['creator'] = creator
    info['subject_info']['his_id'] = creator
    info['subject_info']['weight'] = 11.1
    info['subject_info']['height'] = 2.3

    if info['gantry_angle'] is None:  # future testing data may include it
        info['gantry_angle'] = 0.  # Elekta supine position
    gantry_angle = info['gantry_angle']

    meas_id = info['meas_id']
    write_info(temp_file, info)
    info = read_info(temp_file)
    assert info['proc_history'][0]['creator'] == creator
    assert info['hpi_meas'][0]['creator'] == creator
    assert info['subject_info']['his_id'] == creator
    assert info['gantry_angle'] == gantry_angle
    assert info['subject_info']['height'] == 2.3
    assert info['subject_info']['weight'] == 11.1
    for key in ['secs', 'usecs', 'version']:
        assert info['meas_id'][key] == meas_id[key]
    assert_array_equal(info['meas_id']['machid'], meas_id['machid'])

    # Test that writing twice produces the same file
    m1 = hashlib.md5()
    with open(temp_file, 'rb') as fid:
        m1.update(fid.read())
    m1 = m1.hexdigest()
    temp_file_2 = op.join(tempdir, 'info2.fif')
    assert temp_file_2 != temp_file
    write_info(temp_file_2, info)
    m2 = hashlib.md5()
    with open(temp_file_2, 'rb') as fid:
        m2.update(fid.read())
    m2 = m2.hexdigest()
    assert m1 == m2

def test_read_write_info():
    """Test IO of info
    """
    info = io.read_info(raw_fname)
    temp_file = op.join(tempdir, 'info.fif')
    # check for bug `#1198`
    info['dev_head_t']['trans'] = np.eye(4)
    t1 =  info['dev_head_t']['trans']
    io.write_info(temp_file, info)
    info2 = io.read_info(temp_file)
    t2 = info2['dev_head_t']['trans']
    assert_true(len(info['chs']) == len(info2['chs']))
    assert_array_equal(t1, t2)

def test_priors():
    """Test prior computations."""
    # Depth prior
    fwd = read_forward_solution(fname_meeg)
    assert not is_fixed_orient(fwd)
    n_sources = fwd['nsource']
    info = read_info(fname_evoked)
    depth_prior = compute_depth_prior(fwd, info, exp=0.8)
    assert depth_prior.shape == (3 * n_sources,)
    depth_prior = compute_depth_prior(fwd, info, exp=0.)
    assert_array_equal(depth_prior, 1.)
    with pytest.raises(ValueError, match='must be "whiten"'):
        compute_depth_prior(fwd, info, limit_depth_chs='foo')
    with pytest.raises(ValueError, match='noise_cov must be a Covariance'):
        compute_depth_prior(fwd, info, limit_depth_chs='whiten')
    fwd_fixed = convert_forward_solution(fwd, force_fixed=True)
    with pytest.deprecated_call():
        depth_prior = compute_depth_prior(
            fwd_fixed['sol']['data'], info, is_fixed_ori=True)
    assert depth_prior.shape == (n_sources,)
    # Orientation prior
    orient_prior = compute_orient_prior(fwd, 1.)
    assert_array_equal(orient_prior, 1.)
    orient_prior = compute_orient_prior(fwd_fixed, 0.)
    assert_array_equal(orient_prior, 1.)
    with pytest.raises(ValueError, match='oriented in surface coordinates'):
        compute_orient_prior(fwd, 0.5)
    fwd_surf_ori = convert_forward_solution(fwd, surf_ori=True)
    orient_prior = compute_orient_prior(fwd_surf_ori, 0.5)
    assert all(np.in1d(orient_prior, (0.5, 1.)))
    with pytest.raises(ValueError, match='between 0 and 1'):
        compute_orient_prior(fwd_surf_ori, -0.5)
    with pytest.raises(ValueError, match='with fixed orientation'):
        compute_orient_prior(fwd_fixed, 0.5)

def test_rename_channels():
    """Test rename channels"""
    info = read_info(raw_fname)
    # Error Tests
    # Test channel name exists in ch_names
    mapping = {'EEG 160': 'EEG060'}
    assert_raises(ValueError, rename_channels, info, mapping)
    # Test improper mapping configuration
    mapping = {'MEG 2641': 1.0}
    assert_raises(ValueError, rename_channels, info, mapping)
    # Test non-unique mapping configuration
    mapping = {'MEG 2641': 'MEG 2642'}
    assert_raises(ValueError, rename_channels, info, mapping)
    # Test bad input
    assert_raises(ValueError, rename_channels, info, 1.)

    # Test successful changes
    # Test ch_name and ch_names are changed
    info2 = deepcopy(info)  # for consistency at the start of each test
    info2['bads'] = ['EEG 060', 'EOG 061']
    mapping = {'EEG 060': 'EEG060', 'EOG 061': 'EOG061'}
    rename_channels(info2, mapping)
    assert_true(info2['chs'][374]['ch_name'] == 'EEG060')
    assert_true(info2['ch_names'][374] == 'EEG060')
    assert_true(info2['chs'][375]['ch_name'] == 'EOG061')
    assert_true(info2['ch_names'][375] == 'EOG061')
    assert_array_equal(['EEG060', 'EOG061'], info2['bads'])
    info2 = deepcopy(info)
    rename_channels(info2, lambda x: x.replace(' ', ''))
    assert_true(info2['chs'][373]['ch_name'] == 'EEG059')
    info2 = deepcopy(info)
    info2['bads'] = ['EEG 060', 'EEG 060']
    rename_channels(info2, mapping)
    assert_array_equal(['EEG060', 'EEG060'], info2['bads'])

def test_rename_channels():
    """Test rename channels
    """
    info = read_info(raw_fname)
    # Error Tests
    # Test channel name exists in ch_names
    mapping = {'EEG 160': 'EEG060'}
    assert_raises(ValueError, rename_channels, info, mapping)
    # Test change to EEG channel
    mapping = {'EOG 061': ('EEG 061', 'eeg')}
    with warnings.catch_warnings(record=True):
        assert_raises(ValueError, rename_channels, info, mapping)
    # Test change to illegal channel type
    mapping = {'EOG 061': ('MEG 061', 'meg')}
    with warnings.catch_warnings(record=True):
        assert_raises(ValueError, rename_channels, info, mapping)
    # Test channel type which you are changing from e.g. MEG
    mapping = {'MEG 2641': ('MEG2641', 'eeg')}
    with warnings.catch_warnings(record=True):
        assert_raises(ValueError, rename_channels, info, mapping)
    # Test improper mapping configuration
    mapping = {'MEG 2641': 1.0}
    assert_raises(ValueError, rename_channels, info, mapping)
    # Test successful changes
    # Test ch_name and ch_names are changed
    info2 = deepcopy(info)  # for consistency at the start of each test
    info2['bads'] = ['EEG 060', 'EOG 061']
    mapping = {'EEG 060': 'EEG060', 'EOG 061': 'EOG061'}
    rename_channels(info2, mapping)
    assert_true(info2['chs'][374]['ch_name'] == 'EEG060')
    assert_true(info2['ch_names'][374] == 'EEG060')
    assert_true('EEG060' in info2['bads'])
    assert_true(info2['chs'][375]['ch_name'] == 'EOG061')
    assert_true(info2['ch_names'][375] == 'EOG061')
    assert_true('EOG061' in info2['bads'])

def test_make_sphere_model():
    """Test making a sphere model."""
    info = read_info(fname_raw)
    pytest.raises(ValueError, make_sphere_model, 'foo', 'auto', info)
    pytest.raises(ValueError, make_sphere_model, 'auto', 'auto', None)
    pytest.raises(ValueError, make_sphere_model, 'auto', 'auto', info,
                  relative_radii=(), sigmas=())
    pytest.raises(ValueError, make_sphere_model, 'auto', 'auto', info,
                  relative_radii=(1,))  # wrong number of radii
    # here we just make sure it works -- the functionality is actually
    # tested more extensively e.g. in the forward and dipole code
    with catch_logging() as log:
        bem = make_sphere_model('auto', 'auto', info, verbose=True)
    log = log.getvalue()
    assert ' RV = ' in log
    for line in log.split('\n'):
        if ' RV = ' in line:
            val = float(line.split()[-2])
            assert val < 0.01  # actually decent fitting
            break
    assert '3 layers' in repr(bem)
    assert 'Sphere ' in repr(bem)
    assert ' mm' in repr(bem)
    bem = make_sphere_model('auto', None, info)
    assert 'no layers' in repr(bem)
    assert 'Sphere ' in repr(bem)
    pytest.raises(ValueError, make_sphere_model, sigmas=(0.33,),
                  relative_radii=(1.0,))

def test_head_translation():
    """Test Maxwell filter head translation."""
    raw = read_crop(raw_fname, (0., 1.))
    # First try with an unchanged destination
    with use_coil_def(elekta_def_fname):
        raw_sss = maxwell_filter(raw, destination=raw_fname,
                                 origin=mf_head_origin, regularize=None,
                                 bad_condition='ignore')
    assert_meg_snr(raw_sss, read_crop(sss_std_fname, (0., 1.)), 200.)
    # Now with default
    with use_coil_def(elekta_def_fname):
        with pytest.warns(RuntimeWarning, match='over 25 mm'):
            raw_sss = maxwell_filter(raw, destination=mf_head_origin,
                                     origin=mf_head_origin, regularize=None,
                                     bad_condition='ignore', verbose=True)
    assert_meg_snr(raw_sss, read_crop(sss_trans_default_fname), 125.)
    destination = np.eye(4)
    destination[2, 3] = 0.04
    assert_allclose(raw_sss.info['dev_head_t']['trans'], destination)
    # Now to sample's head pos
    with pytest.warns(RuntimeWarning, match='= 25.6 mm'):
        raw_sss = maxwell_filter(raw, destination=sample_fname,
                                 origin=mf_head_origin, regularize=None,
                                 bad_condition='ignore', verbose=True)
    assert_meg_snr(raw_sss, read_crop(sss_trans_sample_fname), 13., 100.)
    assert_allclose(raw_sss.info['dev_head_t']['trans'],
                    read_info(sample_fname)['dev_head_t']['trans'])
    # Degenerate cases
    pytest.raises(RuntimeError, maxwell_filter, raw,
                  destination=mf_head_origin, coord_frame='meg')
    pytest.raises(ValueError, maxwell_filter, raw, destination=[0.] * 4)

def test_head_translation():
    """Test Maxwell filter head translation"""
    with warnings.catch_warnings(record=True):  # maxshield
        raw = Raw(raw_fname, allow_maxshield=True).crop(0., 1., False)
    # First try with an unchanged destination
    raw_sss = maxwell_filter(raw, destination=raw_fname,
                             origin=mf_head_origin, regularize=None,
                             bad_condition='ignore')
    assert_meg_snr(raw_sss, Raw(sss_std_fname).crop(0., 1., False), 200.)
    # Now with default
    with warnings.catch_warnings(record=True):
        with catch_logging() as log:
            raw_sss = maxwell_filter(raw, destination=mf_head_origin,
                                     origin=mf_head_origin, regularize=None,
                                     bad_condition='ignore', verbose='warning')
    assert_true('over 25 mm' in log.getvalue())
    assert_meg_snr(raw_sss, Raw(sss_trans_default_fname), 125.)
    destination = np.eye(4)
    destination[2, 3] = 0.04
    assert_allclose(raw_sss.info['dev_head_t']['trans'], destination)
    # Now to sample's head pos
    with warnings.catch_warnings(record=True):
        with catch_logging() as log:
            raw_sss = maxwell_filter(raw, destination=sample_fname,
                                     origin=mf_head_origin, regularize=None,
                                     bad_condition='ignore', verbose='warning')
    assert_true('= 25.6 mm' in log.getvalue())
    assert_meg_snr(raw_sss, Raw(sss_trans_sample_fname), 350.)
    assert_allclose(raw_sss.info['dev_head_t']['trans'],
                    read_info(sample_fname)['dev_head_t']['trans'])
    # Degenerate cases
    assert_raises(RuntimeError, maxwell_filter, raw,
                  destination=mf_head_origin, coord_frame='meg')
    assert_raises(ValueError, maxwell_filter, raw, destination=[0.] * 4)

def test_make_sphere_model():
    """Test making a sphere model"""
    info = read_info(fname_raw)
    assert_raises(ValueError, make_sphere_model, 'foo', 'auto', info)
    assert_raises(ValueError, make_sphere_model, 'auto', 'auto', None)
    # here we just make sure it works -- the functionality is actually
    # tested more extensively e.g. in the forward and dipole code
    make_sphere_model('auto', 'auto', info)

def test_multipolar_bases():
    """Test multipolar moment basis calculation using sensor information."""
    from scipy.io import loadmat
    # Test our basis calculations
    info = read_info(raw_fname)
    with use_coil_def(elekta_def_fname):
        coils = _prep_meg_channels(info, accurate=True, do_es=True)[0]
    # Check against a known benchmark
    sss_data = loadmat(bases_fname)
    exp = dict(int_order=int_order, ext_order=ext_order)
    for origin in ((0, 0, 0.04), (0, 0.02, 0.02)):
        o_str = ''.join('%d' % (1000 * n) for n in origin)
        exp.update(origin=origin)
        S_tot = _sss_basis_basic(exp, coils, method='alternative')
        # Test our real<->complex conversion functions
        S_tot_complex = _bases_real_to_complex(S_tot, int_order, ext_order)
        S_tot_round = _bases_complex_to_real(S_tot_complex,
                                             int_order, ext_order)
        assert_allclose(S_tot, S_tot_round, atol=1e-7)

        S_tot_mat = np.concatenate([sss_data['Sin' + o_str],
                                    sss_data['Sout' + o_str]], axis=1)
        S_tot_mat_real = _bases_complex_to_real(S_tot_mat,
                                                int_order, ext_order)
        S_tot_mat_round = _bases_real_to_complex(S_tot_mat_real,
                                                 int_order, ext_order)
        assert_allclose(S_tot_mat, S_tot_mat_round, atol=1e-7)
        assert_allclose(S_tot_complex, S_tot_mat, rtol=1e-4, atol=1e-8)
        assert_allclose(S_tot, S_tot_mat_real, rtol=1e-4, atol=1e-8)

        # Now normalize our columns
        S_tot /= np.sqrt(np.sum(S_tot * S_tot, axis=0))[np.newaxis]
        S_tot_complex /= np.sqrt(np.sum(
            (S_tot_complex * S_tot_complex.conj()).real, axis=0))[np.newaxis]
        # Check against a known benchmark
        S_tot_mat = np.concatenate([sss_data['SNin' + o_str],
                                    sss_data['SNout' + o_str]], axis=1)
        # Check this roundtrip
        S_tot_mat_real = _bases_complex_to_real(S_tot_mat,
                                                int_order, ext_order)
        S_tot_mat_round = _bases_real_to_complex(S_tot_mat_real,
                                                 int_order, ext_order)
        assert_allclose(S_tot_mat, S_tot_mat_round, atol=1e-7)
        assert_allclose(S_tot_complex, S_tot_mat, rtol=1e-4, atol=1e-8)

        # Now test our optimized version
        S_tot = _sss_basis_basic(exp, coils)
        with use_coil_def(elekta_def_fname):
            S_tot_fast = _trans_sss_basis(
                exp, all_coils=_prep_mf_coils(info), trans=info['dev_head_t'])
        # there are some sign differences for columns (order/degrees)
        # in here, likely due to Condon-Shortley. Here we use a
        # Magnetometer channel to figure out the flips because the
        # gradiometer channels have effectively zero values for first three
        # external components (i.e., S_tot[grad_picks, 80:83])
        flips = (np.sign(S_tot_fast[2]) != np.sign(S_tot[2]))
        flips = 1 - 2 * flips
        assert_allclose(S_tot, S_tot_fast * flips, atol=1e-16)

def test_pick_chpi():
    """Test picking cHPI."""
    # Make sure we don't mis-classify cHPI channels
    info = read_info(op.join(io_dir, 'tests', 'data', 'test_chpi_raw_sss.fif'))
    _assert_channel_types(info)
    channel_types = {channel_type(info, idx) for idx in range(info['nchan'])}
    assert 'chpi' in channel_types
    assert 'seeg' not in channel_types
    assert 'ecog' not in channel_types