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# -*- coding: utf-8 -*-
# Author: Eric Larson <larson.eric.d@gmail.com>
#
# License: BSD (3-clause)
import os
import os.path as op
import shutil
import sys
import warnings
import pytest
# For some unknown reason, on Travis-xenial there are segfaults caused on
# the line pytest -> pdb.Pdb.__init__ -> "import readline". Forcing an
# import here seems to prevent them (!?). This suggests a potential problem
# with some other library stepping on memory where it shouldn't. It only
# seems to happen on the Linux runs that install Mayavi. Anectodally,
# @larsoner has had problems a couple of years ago where a mayavi import
# seemed to corrupt SciPy linalg function results (!), likely due to the
# associated VTK import, so this could be another manifestation of that.
try:
import readline # noqa
except Exception:
pass
import numpy as np
import mne
from mne.datasets import testing
from mne.fixes import _fn35
test_path = testing.data_path(download=False)
s_path = op.join(test_path, 'MEG', 'sample')
fname_evoked = op.join(s_path, 'sample_audvis_trunc-ave.fif')
fname_cov = op.join(s_path, 'sample_audvis_trunc-cov.fif')
fname_fwd = op.join(s_path, 'sample_audvis_trunc-meg-eeg-oct-4-fwd.fif')
subjects_dir = op.join(test_path, 'subjects')
def pytest_configure(config):
"""Configure pytest options."""
# Markers
for marker in ('slowtest', 'ultraslowtest'):
config.addinivalue_line('markers', marker)
# Fixtures
for fixture in ('matplotlib_config', 'fix_pytest_tmpdir_35'):
config.addinivalue_line('usefixtures', fixture)
# Warnings
# - Once SciPy updates not to have non-integer and non-tuple errors (1.2.0)
# we should remove them from here.
# - This list should also be considered alongside reset_warnings in
# doc/conf.py.
warning_lines = """
error::
ignore::ImportWarning
ignore:the matrix subclass:PendingDeprecationWarning
ignore:numpy.dtype size changed:RuntimeWarning
ignore:.*HasTraits.trait_.*:DeprecationWarning
ignore:.*takes no parameters:DeprecationWarning
ignore:joblib not installed:RuntimeWarning
ignore:Using a non-tuple sequence for multidimensional indexing:FutureWarning
ignore:using a non-integer number instead of an integer will result in an error:DeprecationWarning
ignore:Importing from numpy.testing.decorators is deprecated:DeprecationWarning
ignore:np.loads is deprecated, use pickle.loads instead:DeprecationWarning
ignore:The oldnumeric module will be dropped:DeprecationWarning
ignore:Collection picker None could not be converted to float:UserWarning
ignore:covariance is not positive-semidefinite:RuntimeWarning
ignore:Can only plot ICA components:RuntimeWarning
ignore:Matplotlib is building the font cache using fc-list:UserWarning
ignore:Using or importing the ABCs from 'collections':DeprecationWarning
ignore:`formatargspec` is deprecated:DeprecationWarning
# This is only necessary until sklearn updates their wheels for NumPy 1.16
ignore:numpy.ufunc size changed:RuntimeWarning
ignore:.*mne-realtime.*:DeprecationWarning
ignore:.*imp.*:DeprecationWarning
always:.*get_data.* is deprecated in favor of.*:DeprecationWarning
""" # noqa: E501
for warning_line in warning_lines.split('\n'):
warning_line = warning_line.strip()
if warning_line and not warning_line.startswith('#'):
config.addinivalue_line('filterwarnings', warning_line)
@pytest.fixture(scope='session')
def matplotlib_config():
"""Configure matplotlib for viz tests."""
import matplotlib
# "force" should not really be necessary but should not hurt
kwargs = dict()
with warnings.catch_warnings(record=True): # ignore warning
warnings.filterwarnings('ignore')
matplotlib.use('agg', force=True, **kwargs) # don't pop up windows
import matplotlib.pyplot as plt
assert plt.get_backend() == 'agg'
# overwrite some params that can horribly slow down tests that
# users might have changed locally (but should not otherwise affect
# functionality)
plt.ioff()
plt.rcParams['figure.dpi'] = 100
try:
from traits.etsconfig.api import ETSConfig
except Exception:
pass
else:
ETSConfig.toolkit = 'qt4'
try:
with warnings.catch_warnings(record=True): # traits
from mayavi import mlab
except Exception:
pass
else:
mlab.options.backend = 'test'
def _replace(mod, key):
orig = getattr(mod, key)
def func(x, *args, **kwargs):
return orig(_fn35(x), *args, **kwargs)
setattr(mod, key, func)
@pytest.fixture(scope='session')
def fix_pytest_tmpdir_35():
"""Deal with tmpdir being a LocalPath, which bombs on 3.5."""
if sys.version_info >= (3, 6):
return
for key in ('stat', 'mkdir', 'makedirs'):
_replace(os, key)
for key in ('split', 'splitext', 'realpath', 'join'):
_replace(op, key)
@pytest.fixture(scope='function', params=[testing._pytest_param()])
def evoked():
"""Get evoked data."""
evoked = mne.read_evokeds(fname_evoked, condition='Left Auditory',
baseline=(None, 0))
evoked.crop(0, 0.2)
return evoked
@pytest.fixture(scope='function', params=[testing._pytest_param()])
def noise_cov():
"""Get a noise cov from the testing dataset."""
return mne.read_cov(fname_cov)
@pytest.fixture(scope='function')
def bias_params_free(evoked, noise_cov):
"""Provide inputs for free bias functions."""
fwd = mne.read_forward_solution(fname_fwd)
return _bias_params(evoked, noise_cov, fwd)
@pytest.fixture(scope='function')
def bias_params_fixed(evoked, noise_cov):
"""Provide inputs for fixed bias functions."""
fwd = mne.read_forward_solution(fname_fwd)
fwd = mne.convert_forward_solution(fwd, force_fixed=True, surf_ori=True)
return _bias_params(evoked, noise_cov, fwd)
def _bias_params(evoked, noise_cov, fwd):
evoked.pick_types(meg=True, eeg=True, exclude=())
# restrict to limited set of verts (small src here) and one hemi for speed
vertices = [fwd['src'][0]['vertno'].copy(), []]
stc = mne.SourceEstimate(np.zeros((sum(len(v) for v in vertices), 1)),
vertices, 0., 1.)
fwd = mne.forward.restrict_forward_to_stc(fwd, stc)
assert fwd['sol']['row_names'] == noise_cov['names']
assert noise_cov['names'] == evoked.ch_names
evoked = mne.EvokedArray(fwd['sol']['data'].copy(), evoked.info)
data_cov = noise_cov.copy()
data_cov['data'] = np.dot(fwd['sol']['data'], fwd['sol']['data'].T)
assert data_cov['data'].shape[0] == len(noise_cov['names'])
want = np.arange(fwd['sol']['data'].shape[1])
if not mne.forward.is_fixed_orient(fwd):
want //= 3
return evoked, fwd, noise_cov, data_cov, want
@pytest.fixture(scope="module", params=[
"mayavi",
"pyvista",
])
def backend_name(request):
"""Get the backend name."""
yield request.param
@pytest.yield_fixture
def renderer(backend_name):
"""Yield the 3D backends."""
from mne.viz.backends.renderer import _use_test_3d_backend
from mne.viz.backends.tests._utils import has_mayavi, has_pyvista
if backend_name == 'mayavi':
if not has_mayavi():
pytest.skip("Test skipped, requires mayavi.")
elif backend_name == 'pyvista':
if not has_pyvista():
pytest.skip("Test skipped, requires pyvista.")
with _use_test_3d_backend(backend_name):
from mne.viz.backends import renderer
yield renderer
renderer._close_all()
@pytest.fixture(scope='function', params=[testing._pytest_param()])
def subjects_dir_tmp(tmpdir):
"""Copy MNE-testing-data subjects_dir to a temp dir for manipulation."""
for key in ('sample', 'fsaverage'):
shutil.copytree(op.join(subjects_dir, key), str(tmpdir.join(key)))
return str(tmpdir)
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