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import os.path as op
import itertools as itt
from numpy.testing import assert_array_equal
import numpy as np
import pytest
from mne import (read_evokeds, read_cov, compute_raw_covariance, pick_types,
pick_info)
from mne.cov import prepare_noise_cov
from mne.datasets import testing
from mne.io import read_raw_fif
from mne.io.pick import channel_type, _picks_by_type
from mne.io.proj import _has_eeg_average_ref_proj
from mne.proj import compute_proj_raw
from mne.rank import (estimate_rank, compute_rank, _get_rank_sss,
_compute_rank_int, _estimate_rank_raw)
base_dir = op.join(op.dirname(__file__), '..', 'io', 'tests', 'data')
cov_fname = op.join(base_dir, 'test-cov.fif')
raw_fname = op.join(base_dir, 'test_raw.fif')
ave_fname = op.join(base_dir, 'test-ave.fif')
ctf_fname = op.join(base_dir, 'test_ctf_raw.fif')
hp_fif_fname = op.join(base_dir, 'test_chpi_raw_sss.fif')
testing_path = testing.data_path(download=False)
data_dir = op.join(testing_path, 'MEG', 'sample')
mf_fif_fname = op.join(testing_path, 'SSS', 'test_move_anon_raw_sss.fif')
def test_estimate_rank():
"""Test rank estimation."""
data = np.eye(10)
assert_array_equal(estimate_rank(data, return_singular=True)[1],
np.ones(10))
data[0, 0] = 0
assert estimate_rank(data) == 9
pytest.raises(ValueError, estimate_rank, data, 'foo')
@pytest.mark.slowtest
@pytest.mark.parametrize(
'fname, ref_meg', ((raw_fname, False),
(hp_fif_fname, False),
(ctf_fname, False),
(ctf_fname, True)))
@pytest.mark.parametrize(
'scalings', ('norm', dict(mag=1e11, grad=1e9, eeg=1e5)))
def test_raw_rank_estimation(fname, ref_meg, scalings):
"""Test raw rank estimation."""
if ref_meg and scalings != 'norm':
# Adjust for CTF data (scale factors are quite different)
scalings = dict(mag=1e31, grad=1e11)
raw = read_raw_fif(fname)
raw.crop(0, min(4., raw.times[-1])).load_data()
out = _picks_by_type(raw.info, ref_meg=ref_meg, meg_combined=True)
has_eeg = 'eeg' in raw
if has_eeg:
(_, picks_meg), (_, picks_eeg) = out
else:
(_, picks_meg), = out
picks_eeg = []
n_meg = len(picks_meg)
n_eeg = len(picks_eeg)
if len(raw.info['proc_history']) == 0:
expected_rank = n_meg + n_eeg
else:
expected_rank = _get_rank_sss(raw.info) + n_eeg
got_rank = _estimate_rank_raw(raw, scalings=scalings, with_ref_meg=ref_meg)
assert got_rank == expected_rank
if has_eeg:
with pytest.deprecated_call():
assert raw.estimate_rank(picks=picks_eeg,
scalings=scalings) == n_eeg
if 'sss' in fname:
raw.add_proj(compute_proj_raw(raw))
raw.apply_proj()
n_proj = len(raw.info['projs'])
want_rank = expected_rank - (0 if 'sss' in fname else n_proj)
got_rank = _estimate_rank_raw(raw, scalings=scalings, with_ref_meg=ref_meg)
assert got_rank == want_rank
@pytest.mark.slowtest
@pytest.mark.parametrize('meg', ('separate', 'combined'))
@pytest.mark.parametrize('rank_method, proj', [('info', True),
('info', False),
(None, True),
(None, False)])
def test_cov_rank_estimation(rank_method, proj, meg):
"""Test cov rank estimation."""
# Test that our rank estimation works properly on a simple case
evoked = read_evokeds(ave_fname, condition=0, baseline=(None, 0),
proj=False)
cov = read_cov(cov_fname)
ch_names = [ch for ch in evoked.info['ch_names'] if '053' not in ch and
ch.startswith('EEG')]
cov = prepare_noise_cov(cov, evoked.info, ch_names, None)
assert cov['eig'][0] <= 1e-25 # avg projector should set this to zero
assert (cov['eig'][1:] > 1e-16).all() # all else should be > 0
# Now do some more comprehensive tests
raw_sample = read_raw_fif(raw_fname)
assert not _has_eeg_average_ref_proj(raw_sample.info['projs'])
raw_sss = read_raw_fif(hp_fif_fname)
assert not _has_eeg_average_ref_proj(raw_sss.info['projs'])
raw_sss.add_proj(compute_proj_raw(raw_sss, meg=meg))
cov_sample = compute_raw_covariance(raw_sample)
cov_sample_proj = compute_raw_covariance(raw_sample.copy().apply_proj())
cov_sss = compute_raw_covariance(raw_sss)
cov_sss_proj = compute_raw_covariance(raw_sss.copy().apply_proj())
picks_all_sample = pick_types(raw_sample.info, meg=True, eeg=True)
picks_all_sss = pick_types(raw_sss.info, meg=True, eeg=True)
info_sample = pick_info(raw_sample.info, picks_all_sample)
picks_stack_sample = [('eeg', pick_types(info_sample, meg=False,
eeg=True))]
picks_stack_sample += [('meg', pick_types(info_sample, meg=True))]
picks_stack_sample += [('all',
pick_types(info_sample, meg=True, eeg=True))]
info_sss = pick_info(raw_sss.info, picks_all_sss)
picks_stack_somato = [('eeg', pick_types(info_sss, meg=False, eeg=True))]
picks_stack_somato += [('meg', pick_types(info_sss, meg=True))]
picks_stack_somato += [('all',
pick_types(info_sss, meg=True, eeg=True))]
iter_tests = list(itt.product(
[(cov_sample, picks_stack_sample, info_sample),
(cov_sample_proj, picks_stack_sample, info_sample),
(cov_sss, picks_stack_somato, info_sss),
(cov_sss_proj, picks_stack_somato, info_sss)], # sss
[dict(mag=1e15, grad=1e13, eeg=1e6)],
))
for (cov, picks_list, iter_info), scalings in iter_tests:
rank = compute_rank(cov, rank_method, scalings, iter_info,
proj=proj)
rank['all'] = sum(rank.values())
for ch_type, picks in picks_list:
this_info = pick_info(iter_info, picks)
# compute subset of projs, active and inactive
n_projs_applied = sum(proj['active'] and
len(set(proj['data']['col_names']) &
set(this_info['ch_names'])) > 0
for proj in cov['projs'])
n_projs_info = sum(len(set(proj['data']['col_names']) &
set(this_info['ch_names'])) > 0
for proj in this_info['projs'])
# count channel types
ch_types = [channel_type(this_info, idx)
for idx in range(len(picks))]
n_eeg, n_mag, n_grad = [ch_types.count(k) for k in
['eeg', 'mag', 'grad']]
n_meg = n_mag + n_grad
has_sss = (n_meg > 0 and len(this_info['proc_history']) > 0)
if has_sss:
n_meg = _get_rank_sss(this_info)
expected_rank = n_meg + n_eeg
if rank_method is None:
if meg == 'combined' or not has_sss:
if proj:
expected_rank -= n_projs_info
else:
expected_rank -= n_projs_applied
else:
# XXX for now it just uses the total count
assert rank_method == 'info'
if proj:
expected_rank -= n_projs_info
assert rank[ch_type] == expected_rank
@testing.requires_testing_data
@pytest.mark.parametrize('fname, rank_orig', ((hp_fif_fname, 120),
(mf_fif_fname, 67)))
@pytest.mark.parametrize('n_proj, meg', ((0, 'combined'),
(10, 'combined'),
(10, 'separate')))
def test_maxfilter_get_rank(n_proj, fname, rank_orig, meg):
"""Test maxfilter rank lookup."""
raw = read_raw_fif(fname).crop(0, 5).load_data().pick_types()
assert raw.info['projs'] == []
mf = raw.info['proc_history'][0]['max_info']
assert mf['sss_info']['nfree'] == rank_orig
assert _get_rank_sss(raw) == rank_orig
mult = 1 + (meg == 'separate')
rank = rank_orig - mult * n_proj
if n_proj > 0:
# Let's do some projection
raw.add_proj(compute_proj_raw(raw, n_mag=n_proj, n_grad=n_proj,
meg=meg, verbose=True))
raw.apply_proj()
data_orig = raw[:][0]
# degenerate cases
with pytest.raises(ValueError, match='tol must be'):
_estimate_rank_raw(raw, tol='foo')
with pytest.raises(TypeError, match='must be a string or a number'):
_estimate_rank_raw(raw, tol=None)
allowed_rank = [rank_orig if meg == 'separate' else rank]
if fname == mf_fif_fname:
# Here we permit a -1 because for mf_fif_fname we miss by 1, which is
# probably acceptable. If we use the entire duration instead of 5 sec
# this problem goes away, but the test is much slower.
allowed_rank.append(allowed_rank[0] - 1)
# multiple ways of hopefully getting the same thing
# default tol=1e-4, scalings='norm'
rank_new = _estimate_rank_raw(raw)
assert rank_new in allowed_rank
tol = 'float32' # temporary option until we can fix things
rank_new = _estimate_rank_raw(raw, tol=tol)
assert rank_new in allowed_rank
rank_new = _estimate_rank_raw(raw, scalings=dict(), tol=tol)
assert rank_new in allowed_rank
scalings = dict(grad=1e13, mag=1e15)
rank_new = _compute_rank_int(raw, None, scalings=scalings, tol=tol,
verbose='debug')
assert rank_new in allowed_rank
# XXX default scalings mis-estimate sometimes :(
if fname == hp_fif_fname:
allowed_rank.append(allowed_rank[0] - 2)
rank_new = _compute_rank_int(raw, None, tol=tol, verbose='debug')
assert rank_new in allowed_rank
del allowed_rank
rank_new = _compute_rank_int(raw, 'info')
assert rank_new == rank
assert_array_equal(raw[:][0], data_orig)
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