def test_calculate_chpi_positions():
    """Test calculation of cHPI positions
    """
    trans, rot, t = head_pos_to_trans_rot_t(read_head_pos(pos_fname))
    with warnings.catch_warnings(record=True):
        raw = Raw(chpi_fif_fname, allow_maxshield=True, preload=True)
    t -= raw.first_samp / raw.info['sfreq']
    quats = _calculate_chpi_positions(raw, verbose='debug')
    trans_est, rot_est, t_est = head_pos_to_trans_rot_t(quats)
    _compare_positions((trans, rot, t), (trans_est, rot_est, t_est), 0.003)

    # degenerate conditions
    raw_no_chpi = Raw(test_fif_fname)
    assert_raises(RuntimeError, _calculate_chpi_positions, raw_no_chpi)
    raw_bad = raw.copy()
    for d in raw_bad.info['dig']:
        if d['kind'] == FIFF.FIFFV_POINT_HPI:
            d['coord_frame'] = 999
            break
    assert_raises(RuntimeError, _calculate_chpi_positions, raw_bad)
    raw_bad = raw.copy()
    for d in raw_bad.info['dig']:
        if d['kind'] == FIFF.FIFFV_POINT_HPI:
            d['r'] = np.ones(3)
    raw_bad.crop(0, 1., copy=False)
    with warnings.catch_warnings(record=True):  # bad pos
        with catch_logging() as log_file:
            _calculate_chpi_positions(raw_bad, verbose=True)
    # ignore HPI info header and [done] footer
    for line in log_file.getvalue().strip().split('\n')[4:-1]:
        assert_true('0/5 good' in line)

def test_make_inverse_operator():
    """Test MNE inverse computation (precomputed and non-precomputed)."""
    # Test old version of inverse computation starting from forward operator
    evoked = _get_evoked()
    noise_cov = read_cov(fname_cov)
    inverse_operator = read_inverse_operator(fname_inv)
    fwd_op = convert_forward_solution(read_forward_solution_meg(fname_fwd),
                                      surf_ori=True, copy=False)
    with catch_logging() as log:
        my_inv_op = make_inverse_operator(evoked.info, fwd_op, noise_cov,
                                          loose=0.2, depth=0.8,
                                          limit_depth_chs=False, verbose=True)
    log = log.getvalue()
    assert 'rank 302 (3 small eigenvalues omitted)' in log
    _compare_io(my_inv_op)
    assert_equal(inverse_operator['units'], 'Am')
    _compare_inverses_approx(my_inv_op, inverse_operator, evoked,
                             rtol=1e-2, atol=1e-5, depth_atol=1e-3)
    # Test MNE inverse computation starting from forward operator
    with catch_logging() as log:
        my_inv_op = make_inverse_operator(evoked.info, fwd_op, noise_cov,
                                          loose=0.2, depth=0.8, verbose=True)
    log = log.getvalue()
    assert 'rank 302 (3 small eigenvalues omitted)' in log
    _compare_io(my_inv_op)
    _compare_inverses_approx(my_inv_op, inverse_operator, evoked,
                             rtol=1e-3, atol=1e-5)
    assert ('dev_head_t' in my_inv_op['info'])
    assert ('mri_head_t' in my_inv_op)

def test_chpi_subtraction():
    """Test subtraction of cHPI signals."""
    raw = read_raw_fif(chpi_fif_fname, allow_maxshield='yes', preload=True)
    raw.info['bads'] = ['MEG0111']
    raw.del_proj()
    with catch_logging() as log:
        filter_chpi(raw, include_line=False, verbose=True)
    assert 'No average EEG' not in log.getvalue()
    assert '5 cHPI' in log.getvalue()
    # MaxFilter doesn't do quite as well as our algorithm with the last bit
    raw.crop(0, 16)
    # remove cHPI status chans
    raw_c = read_raw_fif(sss_hpisubt_fname).crop(0, 16).load_data()
    raw_c.pick_types(
        meg=True, eeg=True, eog=True, ecg=True, stim=True, misc=True)
    assert_meg_snr(raw, raw_c, 143, 624)

    # Degenerate cases
    raw_nohpi = read_raw_fif(test_fif_fname, preload=True)
    pytest.raises(RuntimeError, filter_chpi, raw_nohpi)

    # When MaxFliter downsamples, like::
    #     $ maxfilter -nosss -ds 2 -f test_move_anon_raw.fif \
    #           -o test_move_anon_ds2_raw.fif
    # it can strip out some values of info, which we emulate here:
    raw = read_raw_fif(chpi_fif_fname, allow_maxshield='yes')
    raw = raw.crop(0, 1).load_data().resample(600., npad='auto')
    raw.info['lowpass'] = 200.
    del raw.info['maxshield']
    del raw.info['hpi_results'][0]['moments']
    del raw.info['hpi_subsystem']['event_channel']
    with catch_logging() as log:
        filter_chpi(raw, verbose=True)
    pytest.raises(ValueError, filter_chpi, raw, t_window=-1)
    assert '2 cHPI' in log.getvalue()

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_chpi_adjust():
    """Test cHPI logging and adjustment"""
    raw = read_raw_fif(chpi_fif_fname, allow_maxshield='yes')
    with catch_logging() as log:
        _get_hpi_info(raw.info, adjust=True, verbose='debug')

    # Ran MaxFilter (with -list, -v, -movecomp, etc.), and got:
    msg = ['HPIFIT: 5 coils digitized in order 5 1 4 3 2',
           'HPIFIT: 3 coils accepted: 1 2 4',
           'Hpi coil moments (3 5):',
           '2.08542e-15 -1.52486e-15 -1.53484e-15',
           '2.14516e-15 2.09608e-15 7.30303e-16',
           '-3.2318e-16 -4.25666e-16 2.69997e-15',
           '5.21717e-16 1.28406e-15 1.95335e-15',
           '1.21199e-15 -1.25801e-19 1.18321e-15',
           'HPIFIT errors:  0.3, 0.3, 5.3, 0.4, 3.2 mm.',
           'HPI consistency of isotrak and hpifit is OK.',
           'HP fitting limits: err = 5.0 mm, gval = 0.980.',
           'Using 5 HPI coils: 83 143 203 263 323 Hz',  # actually came earlier
           ]

    log = log.getvalue().splitlines()
    assert_true(set(log) == set(msg), '\n' + '\n'.join(set(msg) - set(log)))

    # Then took the raw file, did this:
    raw.info['dig'][5]['r'][2] += 1.
    # And checked the result in MaxFilter, which changed the logging as:
    msg = msg[:8] + [
        'HPIFIT errors:  0.3, 0.3, 5.3, 999.7, 3.2 mm.',
        'Note: HPI coil 3 isotrak is adjusted by 5.3 mm!',
        'Note: HPI coil 5 isotrak is adjusted by 3.2 mm!'] + msg[-2:]
    with catch_logging() as log:
        _get_hpi_info(raw.info, adjust=True, verbose='debug')
    log = log.getvalue().splitlines()
    assert_true(set(log) == set(msg), '\n' + '\n'.join(set(msg) - set(log)))

def test_make_inverse_operator_loose(evoked):
    """Test MNE inverse computation (precomputed and non-precomputed)."""
    # Test old version of inverse computation starting from forward operator
    noise_cov = read_cov(fname_cov)
    inverse_operator = read_inverse_operator(fname_inv)
    fwd_op = convert_forward_solution(read_forward_solution_meg(fname_fwd),
                                      surf_ori=True, copy=False)
    with catch_logging() as log:
        with pytest.deprecated_call():  # limit_depth_chs
            my_inv_op = make_inverse_operator(
                evoked.info, fwd_op, noise_cov, loose=0.2, depth=0.8,
                limit_depth_chs=False, verbose=True)
    log = log.getvalue()
    assert 'MEG: rank 302 computed' in log
    assert 'limit = 1/%d' % fwd_op['nsource'] in log
    _compare_io(my_inv_op)
    assert_equal(inverse_operator['units'], 'Am')
    _compare_inverses_approx(my_inv_op, inverse_operator, evoked,
                             rtol=1e-2, atol=1e-5, depth_atol=1e-3)
    # Test MNE inverse computation starting from forward operator
    with catch_logging() as log:
        my_inv_op = make_inverse_operator(evoked.info, fwd_op, noise_cov,
                                          loose='auto', depth=0.8,
                                          fixed=False, verbose=True)
    log = log.getvalue()
    assert 'MEG: rank 302 computed from 305' in log
    _compare_io(my_inv_op)
    _compare_inverses_approx(my_inv_op, inverse_operator, evoked,
                             rtol=1e-3, atol=1e-5)
    assert ('dev_head_t' in my_inv_op['info'])
    assert ('mri_head_t' in my_inv_op)

def test_chpi_subtraction():
    """Test subtraction of cHPI signals"""
    raw = Raw(chpi_fif_fname, allow_maxshield='yes', preload=True)
    with catch_logging() as log:
        filter_chpi(raw, include_line=False, verbose=True)
    assert_true('5 cHPI' in log.getvalue())
    # MaxFilter doesn't do quite as well as our algorithm with the last bit
    raw.crop(0, 16, copy=False)
    raw_c = Raw(sss_hpisubt_fname, preload=True).crop(0, 16, copy=False)
    raw_c.pick_types(meg=True, eeg=True, eog=True, ecg=True, stim=True,
                     misc=True, copy=False)  # remove cHPI status chans
    assert_meg_snr(raw, raw_c, 143, 624)

    # Degenerate cases
    raw_nohpi = Raw(test_fif_fname, preload=True)
    assert_raises(RuntimeError, filter_chpi, raw_nohpi)

    # When MaxFliter downsamples, like::
    #     $ maxfilter -nosss -ds 2 -f test_move_anon_raw.fif \
    #           -o test_move_anon_ds2_raw.fif
    # it can strip out some values of info, which we emulate here:
    raw = Raw(chpi_fif_fname, allow_maxshield='yes')
    raw.crop(0, 1, copy=False).load_data()
    raw.resample(600., npad='auto')
    raw.info['buffer_size_sec'] = np.float64(2.)
    raw.info['lowpass'] = 200.
    del raw.info['maxshield']
    del raw.info['hpi_results'][0]['moments']
    del raw.info['hpi_subsystem']['event_channel']
    with catch_logging() as log:
        filter_chpi(raw, verbose=True)
    assert_true('2 cHPI' in log.getvalue())

def test_fetch_file(url, tmpdir):
    """Test URL retrieval."""
    tempdir = str(tmpdir)
    archive_name = op.join(tempdir, "download_test")
    with catch_logging() as log:
        _fetch_file(url, archive_name, timeout=30., verbose='debug')
    log = log.getvalue()
    assert 'Resuming at' not in log
    with open(archive_name, 'rb') as fid:
        data = fid.read()
    stop = len(data) // 2
    assert 0 < stop < len(data)
    with open(archive_name + '.part', 'wb') as fid:
        fid.write(data[:stop])
    with catch_logging() as log:
        _fetch_file(url, archive_name, timeout=30., verbose='debug')
    log = log.getvalue()
    assert 'Resuming at %s' % stop in log
    with pytest.raises(Exception, match='unknown url type'):
        _fetch_file('NOT_AN_ADDRESS', op.join(tempdir, 'test'), verbose=False)
    resume_name = op.join(tempdir, "download_resume")
    # touch file
    with open(resume_name + '.part', 'w'):
        os.utime(resume_name + '.part', None)
    _fetch_file(url, resume_name, resume=True, timeout=30.,
                verbose=False)
    with pytest.raises(ValueError, match='Bad hash value'):
        _fetch_file(url, archive_name, hash_='a', verbose=False)
    with pytest.raises(RuntimeError, match='Hash mismatch'):
        _fetch_file(url, archive_name, hash_='a' * 32, verbose=False)

def test_chpi_subtraction():
    """Test subtraction of cHPI signals"""
    raw = Raw(chpi_fif_fname, allow_maxshield="yes", preload=True)
    with catch_logging() as log:
        filter_chpi(raw, include_line=False, verbose=True)
    assert_true("5 cHPI" in log.getvalue())
    # MaxFilter doesn't do quite as well as our algorithm with the last bit
    raw.crop(0, 16, copy=False)
    # remove cHPI status chans
    raw_c = Raw(sss_hpisubt_fname).crop(0, 16, copy=False).load_data()
    raw_c.pick_types(meg=True, eeg=True, eog=True, ecg=True, stim=True, misc=True)
    assert_meg_snr(raw, raw_c, 143, 624)

    # Degenerate cases
    raw_nohpi = Raw(test_fif_fname, preload=True)
    assert_raises(RuntimeError, filter_chpi, raw_nohpi)

    # When MaxFliter downsamples, like::
    #     $ maxfilter -nosss -ds 2 -f test_move_anon_raw.fif \
    #           -o test_move_anon_ds2_raw.fif
    # it can strip out some values of info, which we emulate here:
    raw = Raw(chpi_fif_fname, allow_maxshield="yes")
    with warnings.catch_warnings(record=True):  # uint cast suggestion
        raw = raw.crop(0, 1).load_data().resample(600.0, npad="auto")
    raw.info["buffer_size_sec"] = np.float64(2.0)
    raw.info["lowpass"] = 200.0
    del raw.info["maxshield"]
    del raw.info["hpi_results"][0]["moments"]
    del raw.info["hpi_subsystem"]["event_channel"]
    with catch_logging() as log:
        filter_chpi(raw, verbose=True)
    assert_true("2 cHPI" in log.getvalue())

def test_head_translation():
    """Test Maxwell filter head translation."""
    raw = read_crop(raw_fname, (0., 1.))
    # 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, read_crop(sss_std_fname, (0., 1.)), 200.)
    # Now with default
    with pytest.warns(RuntimeWarning, match='over 25 mm'):
        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 ('over 25 mm' in log.getvalue())
    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'):
        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 ('= 25.6 mm' in log.getvalue())
    assert_meg_snr(raw_sss, read_crop(sss_trans_sample_fname), 350.)
    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(0.0, 1.0, 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(0.0, 1.0, False), 200.0)
    # Now with default
    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), 125.0)
    # Now to sample's head pos
    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), 350.0)
    # Degenerate cases
    assert_raises(RuntimeError, maxwell_filter, raw, destination=mf_head_origin, coord_frame="meg")
    assert_raises(ValueError, maxwell_filter, raw, destination=[0.0] * 4)

def test_thresholds():
    """Test automatic threshold calculations."""
    # within subjects
    rng = np.random.RandomState(0)
    X = rng.randn(10, 1, 1) + 0.08
    want_thresh = -stats.t.ppf(0.025, len(X) - 1)
    assert 0.03 < stats.ttest_1samp(X[:, 0, 0], 0)[1] < 0.05
    my_fun = partial(ttest_1samp_no_p)
    with catch_logging() as log:
        with pytest.warns(RuntimeWarning, match='threshold is only valid'):
            out = permutation_cluster_1samp_test(X, stat_fun=my_fun,
                                                 verbose=True)
    log = log.getvalue()
    assert str(want_thresh)[:6] in log
    assert len(out[1]) == 1  # 1 cluster
    assert 0.03 < out[2] < 0.05
    # between subjects
    Y = rng.randn(10, 1, 1)
    Z = rng.randn(10, 1, 1) - 0.7
    X = [X, Y, Z]
    want_thresh = stats.f.ppf(1. - 0.05, 2, sum(len(a) for a in X) - len(X))
    p = stats.f_oneway(*X)[1]
    assert 0.03 < p < 0.05
    my_fun = partial(f_oneway)  # just to make the check fail
    with catch_logging() as log:
        with pytest.warns(RuntimeWarning, match='threshold is only valid'):
            out = permutation_cluster_test(X, tail=1, stat_fun=my_fun,
                                           verbose=True)
    log = log.getvalue()
    assert str(want_thresh)[:6] in log
    assert len(out[1]) == 1  # 1 cluster
    assert 0.03 < out[2] < 0.05
    with pytest.warns(RuntimeWarning, match='Ignoring argument "tail"'):
        permutation_cluster_test(X, tail=0)

def test_calculate_chpi_positions():
    """Test calculation of cHPI positions."""
    # Check to make sure our fits match MF decently
    mf_quats = read_head_pos(pos_fname)
    raw = read_raw_fif(chpi_fif_fname, allow_maxshield='yes', preload=True)
    # This is a little hack (aliasing while decimating) to make it much faster
    # for testing purposes only. We can relax this later if we find it breaks
    # something.
    raw_dec = _decimate_chpi(raw, 15)
    with catch_logging() as log:
        py_quats = _calculate_chpi_positions(raw_dec, t_step_max=1.,
                                             verbose='debug')
    assert_true(log.getvalue().startswith('HPIFIT'))
    _assert_quats(py_quats, mf_quats, dist_tol=0.004, angle_tol=2.5)

    # degenerate conditions
    raw_no_chpi = read_raw_fif(test_fif_fname)
    assert_raises(RuntimeError, _calculate_chpi_positions, raw_no_chpi)
    raw_bad = raw.copy()
    del raw_bad.info['hpi_meas'][0]['hpi_coils'][0]['coil_freq']
    assert_raises(RuntimeError, _calculate_chpi_positions, raw_bad)
    raw_bad = raw.copy()
    for d in raw_bad.info['dig']:
        if d['kind'] == FIFF.FIFFV_POINT_HPI:
            d['coord_frame'] = FIFF.FIFFV_COORD_UNKNOWN
            break
    assert_raises(RuntimeError, _calculate_chpi_positions, raw_bad)
    for d in raw_bad.info['dig']:
        if d['kind'] == FIFF.FIFFV_POINT_HPI:
            d['coord_frame'] = FIFF.FIFFV_COORD_HEAD
            d['r'] = np.ones(3)
    raw_bad.crop(0, 1.)
    picks = np.concatenate([np.arange(306, len(raw_bad.ch_names)),
                            pick_types(raw_bad.info, meg=True)[::16]])
    raw_bad.pick_channels([raw_bad.ch_names[pick] for pick in picks])
    with warnings.catch_warnings(record=True):  # bad pos
        with catch_logging() as log_file:
            _calculate_chpi_positions(raw_bad, t_step_min=1., verbose=True)
    # ignore HPI info header and [done] footer
    assert_true('0/5 good' in log_file.getvalue().strip().split('\n')[-2])

    # half the rate cuts off cHPI coils
    raw.info['lowpass'] /= 2.
    assert_raises_regex(RuntimeError, 'above the',
                        _calculate_chpi_positions, raw)

    # test on 5k artemis data
    raw = read_raw_artemis123(art_fname, preload=True)
    mf_quats = read_head_pos(art_mc_fname)
    with catch_logging() as log:
        py_quats = _calculate_chpi_positions(raw, t_step_min=2.,
                                             verbose='debug')
    _assert_quats(py_quats, mf_quats, dist_tol=0.004, angle_tol=2.5)

def test_calculate_chpi_positions():
    """Test calculation of cHPI positions
    """
    trans, rot, t = head_pos_to_trans_rot_t(read_head_pos(pos_fname))
    raw = Raw(chpi_fif_fname, allow_maxshield="yes", preload=True)
    t -= raw.first_samp / raw.info["sfreq"]
    quats = _calculate_chpi_positions(raw, verbose="debug")
    trans_est, rot_est, t_est = head_pos_to_trans_rot_t(quats)
    _compare_positions((trans, rot, t), (trans_est, rot_est, t_est), 0.003)

    # degenerate conditions
    raw_no_chpi = Raw(test_fif_fname)
    assert_raises(RuntimeError, _calculate_chpi_positions, raw_no_chpi)
    raw_bad = raw.copy()
    for d in raw_bad.info["dig"]:
        if d["kind"] == FIFF.FIFFV_POINT_HPI:
            d["coord_frame"] = 999
            break
    assert_raises(RuntimeError, _calculate_chpi_positions, raw_bad)
    raw_bad = raw.copy()
    for d in raw_bad.info["dig"]:
        if d["kind"] == FIFF.FIFFV_POINT_HPI:
            d["r"] = np.ones(3)
    raw_bad.crop(0, 1.0, copy=False)
    with warnings.catch_warnings(record=True):  # bad pos
        with catch_logging() as log_file:
            _calculate_chpi_positions(raw_bad, verbose=True)
    # ignore HPI info header and [done] footer
    for line in log_file.getvalue().strip().split("\n")[4:-1]:
        assert_true("0/5 good" in line)

    # half the rate cuts off cHPI coils
    with warnings.catch_warnings(record=True):  # uint cast suggestion
        raw.resample(300.0, npad="auto")
    assert_raises_regex(RuntimeError, "above the", _calculate_chpi_positions, raw)

def test_notch_filters():
    """Test notch filters
    """
    # let's use an ugly, prime sfreq for fun
    sfreq = 487.0
    sig_len_secs = 20
    t = np.arange(0, int(sig_len_secs * sfreq)) / sfreq
    freqs = np.arange(60, 241, 60)

    # make a "signal"
    rng = np.random.RandomState(0)
    a = rng.randn(int(sig_len_secs * sfreq))
    orig_power = np.sqrt(np.mean(a ** 2))
    # make line noise
    a += np.sum([np.sin(2 * np.pi * f * t) for f in freqs], axis=0)

    # only allow None line_freqs with 'spectrum_fit' mode
    assert_raises(ValueError, notch_filter, a, sfreq, None, "fft")
    assert_raises(ValueError, notch_filter, a, sfreq, None, "iir")
    methods = ["spectrum_fit", "spectrum_fit", "fft", "fft", "iir"]
    filter_lengths = [None, None, None, 8192, None]
    line_freqs = [None, freqs, freqs, freqs, freqs]
    tols = [2, 1, 1, 1]
    for meth, lf, fl, tol in zip(methods, line_freqs, filter_lengths, tols):
        with catch_logging() as log_file:
            b = notch_filter(a, sfreq, lf, filter_length=fl, method=meth, verbose="INFO")

        if lf is None:
            out = log_file.getvalue().split("\n")[:-1]
            if len(out) != 2:
                raise ValueError("Detected frequencies not logged properly")
            out = np.fromstring(out[1], sep=", ")
            assert_array_almost_equal(out, freqs)
        new_power = np.sqrt(sum_squared(b) / b.size)
        assert_almost_equal(new_power, orig_power, tol)

def test_cache_dir():
    """Test use of cache dir
    """
    tempdir = _TempDir()
    orig_dir = os.getenv('MNE_CACHE_DIR', None)
    orig_size = os.getenv('MNE_MEMMAP_MIN_SIZE', None)
    rng = np.random.RandomState(0)
    X = rng.randn(9, 2, 10)
    try:
        os.environ['MNE_MEMMAP_MIN_SIZE'] = '1K'
        os.environ['MNE_CACHE_DIR'] = tempdir
        # Fix error for #1507: in-place when memmapping
        with catch_logging() as log_file:
            permutation_cluster_1samp_test(
                X, buffer_size=None, n_jobs=2, n_permutations=1,
                seed=0, stat_fun=ttest_1samp_no_p, verbose=False)
            # ensure that non-independence yields warning
            stat_fun = partial(ttest_1samp_no_p, sigma=1e-3)
            assert_true('independently' not in log_file.getvalue())
            with warnings.catch_warnings(record=True):  # independently
                permutation_cluster_1samp_test(
                    X, buffer_size=10, n_jobs=2, n_permutations=1,
                    seed=0, stat_fun=stat_fun, verbose=False)
            assert_true('independently' in log_file.getvalue())
    finally:
        if orig_dir is not None:
            os.environ['MNE_CACHE_DIR'] = orig_dir
        else:
            del os.environ['MNE_CACHE_DIR']
        if orig_size is not None:
            os.environ['MNE_MEMMAP_MIN_SIZE'] = orig_size
        else:
            del os.environ['MNE_MEMMAP_MIN_SIZE']

def test_calculate_chpi_positions():
    """Test calculation of cHPI positions
    """
    trans, rot, t = get_chpi_positions(pos_fname)
    with warnings.catch_warnings(record=True):
        raw = Raw(raw_fif_fname, allow_maxshield=True, preload=True)
    t -= raw.first_samp / raw.info['sfreq']
    trans_est, rot_est, t_est = _calculate_chpi_positions(raw, verbose='debug')
    _compare_positions((trans, rot, t), (trans_est, rot_est, t_est))

    # degenerate conditions
    raw_no_chpi = Raw(test_fif_fname)
    assert_raises(RuntimeError, _calculate_chpi_positions, raw_no_chpi)
    raw_bad = raw.copy()
    for d in raw_bad.info['dig']:
        if d['kind'] == FIFF.FIFFV_POINT_HPI:
            d['coord_frame'] = 999
            break
    assert_raises(RuntimeError, _calculate_chpi_positions, raw_bad)
    raw_bad = raw.copy()
    for d in raw_bad.info['dig']:
        if d['kind'] == FIFF.FIFFV_POINT_HPI:
            d['r'] = np.ones(3)
    raw_bad.crop(0, 1., copy=False)
    with catch_logging() as log_file:
        _calculate_chpi_positions(raw_bad)
    for line in log_file.getvalue().split('\n')[:-1]:
        assert_true('0/5 acceptable' in line)

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_cuda():
    """Test CUDA-based filtering"""
    # NOTE: don't make test_cuda() the last test, or pycuda might spew
    # some warnings about clean-up failing
    # Also, using `n_jobs='cuda'` on a non-CUDA system should be fine,
    # as it should fall back to using n_jobs=1.
    sfreq = 500
    sig_len_secs = 20
    a = rng.randn(sig_len_secs * sfreq)

    with catch_logging() as log_file:
        for fl in ['auto', '10s', 2048]:
            bp = band_pass_filter(a, sfreq, 4, 8, fl, 1.0, 1.0, n_jobs=1,
                                  phase='zero')
            bs = band_stop_filter(a, sfreq, 4 - 1.0, 8 + 1.0, fl, 1.0, 1.0,
                                  n_jobs=1, phase='zero')
            lp = low_pass_filter(a, sfreq, 8, fl, 1.0, n_jobs=1, phase='zero')
            hp = high_pass_filter(lp, sfreq, 4, fl, 1.0, n_jobs=1,
                                  phase='zero')

            bp_c = band_pass_filter(a, sfreq, 4, 8, fl, 1.0, 1.0,
                                    n_jobs='cuda', verbose='INFO',
                                    phase='zero')
            bs_c = band_stop_filter(a, sfreq, 4 - 1.0, 8 + 1.0, fl, 1.0, 1.0,
                                    n_jobs='cuda', verbose='INFO',
                                    phase='zero')
            lp_c = low_pass_filter(a, sfreq, 8, fl, 1.0,
                                   n_jobs='cuda', verbose='INFO',
                                   phase='zero')
            hp_c = high_pass_filter(lp, sfreq, 4, fl, 1.0,
                                    n_jobs='cuda', verbose='INFO',
                                    phase='zero')

            assert_array_almost_equal(bp, bp_c, 12)
            assert_array_almost_equal(bs, bs_c, 12)
            assert_array_almost_equal(lp, lp_c, 12)
            assert_array_almost_equal(hp, hp_c, 12)

    # check to make sure we actually used CUDA
    out = log_file.getvalue().split('\n')[:-1]
    # triage based on whether or not we actually expected to use CUDA
    from mne.cuda import _cuda_capable  # allow above funs to set it
    tot = 12 if _cuda_capable else 0
    assert_true(sum(['Using CUDA for FFT FIR filtering' in o
                     for o in out]) == tot)

    # check resampling
    for window in ('boxcar', 'triang'):
        for N in (997, 1000):  # one prime, one even
            a = rng.randn(2, N)
            for fro, to in ((1, 2), (2, 1), (1, 3), (3, 1)):
                a1 = resample(a, fro, to, n_jobs=1, npad='auto',
                              window=window)
                a2 = resample(a, fro, to, n_jobs='cuda', npad='auto',
                              window=window)
                assert_allclose(a1, a2, rtol=1e-7, atol=1e-14)
    assert_array_almost_equal(a1, a2, 14)
    assert_array_equal(resample([0, 0], 2, 1, n_jobs='cuda'), [0., 0., 0., 0.])
    assert_array_equal(resample(np.zeros(2, np.float32), 2, 1, n_jobs='cuda'),
                       [0., 0., 0., 0.])

def test_calculate_chpi_positions():
    """Test calculation of cHPI positions."""
    trans, rot, t = head_pos_to_trans_rot_t(read_head_pos(pos_fname))
    raw = read_raw_fif(chpi_fif_fname, allow_maxshield='yes', preload=True,
                       add_eeg_ref=False)
    t -= raw.first_samp / raw.info['sfreq']
    quats = _calculate_chpi_positions(raw, verbose='debug')
    trans_est, rot_est, t_est = head_pos_to_trans_rot_t(quats)
    _compare_positions((trans, rot, t), (trans_est, rot_est, t_est), 0.003)

    # degenerate conditions
    raw_no_chpi = read_raw_fif(test_fif_fname, add_eeg_ref=False)
    assert_raises(RuntimeError, _calculate_chpi_positions, raw_no_chpi)
    raw_bad = raw.copy()
    for d in raw_bad.info['dig']:
        if d['kind'] == FIFF.FIFFV_POINT_HPI:
            d['coord_frame'] = 999
            break
    assert_raises(RuntimeError, _calculate_chpi_positions, raw_bad)
    raw_bad = raw.copy()
    for d in raw_bad.info['dig']:
        if d['kind'] == FIFF.FIFFV_POINT_HPI:
            d['r'] = np.ones(3)
    raw_bad.crop(0, 1., copy=False)
    with warnings.catch_warnings(record=True):  # bad pos
        with catch_logging() as log_file:
            _calculate_chpi_positions(raw_bad, verbose=True)
    # ignore HPI info header and [done] footer
    assert_true('0/5 good' in log_file.getvalue().strip().split('\n')[-2])

    # half the rate cuts off cHPI coils
    with warnings.catch_warnings(record=True):  # uint cast suggestion
        raw.resample(300., npad='auto')
    assert_raises_regex(RuntimeError, 'above the',
                        _calculate_chpi_positions, raw)