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# -*- coding: utf-8 -*-
"""Testing functions."""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
#
# License: BSD-3-Clause
from functools import partial, wraps
import os
import inspect
from io import StringIO
from shutil import rmtree
import sys
import tempfile
import traceback
from unittest import SkipTest
import numpy as np
from numpy.testing import assert_array_equal, assert_allclose
from ._logging import warn, ClosingStringIO
from .check import check_version
from .numerics import object_diff
def _explain_exception(start=-1, stop=None, prefix='> '):
"""Explain an exception."""
# start=-1 means "only the most recent caller"
etype, value, tb = sys.exc_info()
string = traceback.format_list(traceback.extract_tb(tb)[start:stop])
string = (''.join(string).split('\n') +
traceback.format_exception_only(etype, value))
string = ':\n' + prefix + ('\n' + prefix).join(string)
return string
class _TempDir(str):
"""Create and auto-destroy temp dir.
This is designed to be used with testing modules. Instances should be
defined inside test functions. Instances defined at module level can not
guarantee proper destruction of the temporary directory.
When used at module level, the current use of the __del__() method for
cleanup can fail because the rmtree function may be cleaned up before this
object (an alternative could be using the atexit module instead).
"""
def __new__(self): # noqa: D105
new = str.__new__(self, tempfile.mkdtemp(prefix='tmp_mne_tempdir_'))
return new
def __init__(self): # noqa: D102
self._path = self.__str__()
def __del__(self): # noqa: D105
rmtree(self._path, ignore_errors=True)
def requires_nibabel():
"""Wrap to requires_module with a function call (fewer lines to change)."""
return partial(requires_module, name='nibabel')
def requires_dipy():
"""Check for dipy."""
import pytest
# for some strange reason on CIs we can get:
#
# can get weird ImportError: dlopen: cannot load any more object
# with static TLS
#
# so let's import everything in the decorator.
try:
from dipy.align import imaffine, imwarp, metrics, transforms # noqa, analysis:ignore
from dipy.align.reslice import reslice # noqa, analysis:ignore
from dipy.align.imaffine import AffineMap # noqa, analysis:ignore
from dipy.align.imwarp import DiffeomorphicMap # noqa, analysis:ignore
except Exception as exc:
have = False
why = str(exc)
else:
why = ''
have = True
return pytest.mark.skipif(
not have, reason=f'Requires dipy >= 0.10.1, got: {why}')
def requires_version(library, min_version='0.0'):
"""Check for a library version."""
import pytest
reason = f'Requires {library}'
if min_version != '0.0':
reason += f' version >= {min_version}'
return pytest.mark.skipif(not check_version(library, min_version),
reason=reason)
def requires_module(function, name, call=None):
"""Skip a test if package is not available (decorator)."""
import pytest
call = ('import %s' % name) if call is None else call
reason = 'Test %s skipped, requires %s.' % (function.__name__, name)
try:
exec(call) in globals(), locals()
except Exception as exc:
if len(str(exc)) > 0 and str(exc) != 'No module named %s' % name:
reason += ' Got exception (%s)' % (exc,)
skip = True
else:
skip = False
return pytest.mark.skipif(skip, reason=reason)(function)
_mne_call = """
if not has_mne_c():
raise ImportError
"""
_fs_call = """
if not has_freesurfer():
raise ImportError
"""
_n2ft_call = """
if 'NEUROMAG2FT_ROOT' not in os.environ:
raise ImportError
"""
requires_pandas = partial(requires_module, name='pandas')
requires_pylsl = partial(requires_module, name='pylsl')
requires_sklearn = partial(requires_module, name='sklearn')
requires_mne = partial(requires_module, name='MNE-C', call=_mne_call)
def requires_mne_mark():
"""Mark pytest tests that require MNE-C."""
import pytest
return pytest.mark.skipif(not has_mne_c(), reason='Requires MNE-C')
def requires_openmeeg_mark():
"""Mark pytest tests that require OpenMEEG."""
import pytest
return pytest.mark.skipif(
not check_version('openmeeg', '2.5.5'), reason='Requires OpenMEEG')
def requires_freesurfer(arg):
"""Require Freesurfer."""
if isinstance(arg, str):
# Calling as @requires_freesurfer('progname'): return decorator
# after checking for progname existence
call = """
from . import run_subprocess
run_subprocess([%r, '--version'])
""" % (arg,)
return partial(
requires_module, name='Freesurfer (%s)' % (arg,), call=call)
else:
# Calling directly as @requires_freesurfer: return decorated function
# and just check env var existence
return requires_module(arg, name='Freesurfer', call=_fs_call)
requires_neuromag2ft = partial(requires_module, name='neuromag2ft',
call=_n2ft_call)
requires_good_network = partial(
requires_module, name='good network connection',
call='if int(os.environ.get("MNE_SKIP_NETWORK_TESTS", 0)):\n'
' raise ImportError')
requires_nitime = partial(requires_module, name='nitime')
# just keep this in case downstream packages need it (no coverage hit here)
requires_h5py = partial(requires_module, name='h5py')
def requires_numpydoc(func):
"""Decorate tests that need numpydoc."""
return requires_version('numpydoc', '1.0')(func) # validate needs 1.0
def run_command_if_main():
"""Run a given command if it's __main__."""
local_vars = inspect.currentframe().f_back.f_locals
if local_vars.get('__name__', '') == '__main__':
local_vars['run']()
class ArgvSetter(object):
"""Temporarily set sys.argv."""
def __init__(self, args=(), disable_stdout=True,
disable_stderr=True): # noqa: D102
self.argv = list(('python',) + args)
self.stdout = ClosingStringIO() if disable_stdout else sys.stdout
self.stderr = ClosingStringIO() if disable_stderr else sys.stderr
def __enter__(self): # noqa: D105
self.orig_argv = sys.argv
sys.argv = self.argv
self.orig_stdout = sys.stdout
sys.stdout = self.stdout
self.orig_stderr = sys.stderr
sys.stderr = self.stderr
return self
def __exit__(self, *args): # noqa: D105
sys.argv = self.orig_argv
sys.stdout = self.orig_stdout
sys.stderr = self.orig_stderr
class SilenceStdout(object):
"""Silence stdout."""
def __init__(self, close=True):
self.close = close
def __enter__(self): # noqa: D105
self.stdout = sys.stdout
sys.stdout = StringIO()
return sys.stdout
def __exit__(self, *args): # noqa: D105
if self.close:
sys.stdout.close()
sys.stdout = self.stdout
def has_nibabel():
"""Determine if nibabel is installed.
Returns
-------
has : bool
True if the user has nibabel.
"""
try:
import nibabel # noqa
except ImportError:
return False
else:
return True
def has_mne_c():
"""Check for MNE-C."""
return 'MNE_ROOT' in os.environ
def has_freesurfer():
"""Check for Freesurfer."""
return 'FREESURFER_HOME' in os.environ
def buggy_mkl_svd(function):
"""Decorate tests that make calls to SVD and intermittently fail."""
@wraps(function)
def dec(*args, **kwargs):
try:
return function(*args, **kwargs)
except np.linalg.LinAlgError as exp:
if 'SVD did not converge' in str(exp):
msg = 'Intel MKL SVD convergence error detected, skipping test'
warn(msg)
raise SkipTest(msg)
raise
return dec
def assert_and_remove_boundary_annot(annotations, n=1):
"""Assert that there are boundary annotations and remove them."""
from ..io.base import BaseRaw
if isinstance(annotations, BaseRaw): # allow either input
annotations = annotations.annotations
for key in ('EDGE', 'BAD'):
idx = np.where(annotations.description == '%s boundary' % key)[0]
assert len(idx) == n
annotations.delete(idx)
def assert_object_equal(a, b):
"""Assert two objects are equal."""
d = object_diff(a, b)
assert d == '', d
def _raw_annot(meas_date, orig_time):
from .. import Annotations, create_info
from ..annotations import _handle_meas_date
from ..io import RawArray
info = create_info(ch_names=10, sfreq=10.)
raw = RawArray(data=np.empty((10, 10)), info=info, first_samp=10)
if meas_date is not None:
meas_date = _handle_meas_date(meas_date)
with raw.info._unlock(check_after=True):
raw.info['meas_date'] = meas_date
annot = Annotations([.5], [.2], ['dummy'], orig_time)
raw.set_annotations(annotations=annot)
return raw
def _get_data(x, ch_idx):
"""Get the (n_ch, n_times) data array."""
from ..evoked import Evoked
from ..io import BaseRaw
if isinstance(x, BaseRaw):
return x[ch_idx][0]
elif isinstance(x, Evoked):
return x.data[ch_idx]
def _check_snr(actual, desired, picks, min_tol, med_tol, msg, kind='MEG'):
"""Check the SNR of a set of channels."""
actual_data = _get_data(actual, picks)
desired_data = _get_data(desired, picks)
bench_rms = np.sqrt(np.mean(desired_data * desired_data, axis=1))
error = actual_data - desired_data
error_rms = np.sqrt(np.mean(error * error, axis=1))
np.clip(error_rms, 1e-60, np.inf, out=error_rms) # avoid division by zero
snrs = bench_rms / error_rms
# min tol
snr = snrs.min()
bad_count = (snrs < min_tol).sum()
msg = ' (%s)' % msg if msg != '' else msg
assert bad_count == 0, ('SNR (worst %0.2f) < %0.2f for %s/%s '
'channels%s' % (snr, min_tol, bad_count,
len(picks), msg))
# median tol
snr = np.median(snrs)
assert snr >= med_tol, ('%s SNR median %0.2f < %0.2f%s'
% (kind, snr, med_tol, msg))
def assert_meg_snr(actual, desired, min_tol, med_tol=500., chpi_med_tol=500.,
msg=None):
"""Assert channel SNR of a certain level.
Mostly useful for operations like Maxwell filtering that modify
MEG channels while leaving EEG and others intact.
"""
from ..io.pick import pick_types
picks = pick_types(desired.info, meg=True, exclude=[])
picks_desired = pick_types(desired.info, meg=True, exclude=[])
assert_array_equal(picks, picks_desired, err_msg='MEG pick mismatch')
chpis = pick_types(actual.info, meg=False, chpi=True, exclude=[])
chpis_desired = pick_types(desired.info, meg=False, chpi=True, exclude=[])
if chpi_med_tol is not None:
assert_array_equal(chpis, chpis_desired, err_msg='cHPI pick mismatch')
others = np.setdiff1d(np.arange(len(actual.ch_names)),
np.concatenate([picks, chpis]))
others_desired = np.setdiff1d(np.arange(len(desired.ch_names)),
np.concatenate([picks_desired,
chpis_desired]))
assert_array_equal(others, others_desired, err_msg='Other pick mismatch')
if len(others) > 0: # if non-MEG channels present
assert_allclose(_get_data(actual, others),
_get_data(desired, others), atol=1e-11, rtol=1e-5,
err_msg='non-MEG channel mismatch')
_check_snr(actual, desired, picks, min_tol, med_tol, msg, kind='MEG')
if chpi_med_tol is not None and len(chpis) > 0:
_check_snr(actual, desired, chpis, 0., chpi_med_tol, msg, kind='cHPI')
def assert_snr(actual, desired, tol):
"""Assert actual and desired arrays are within some SNR tolerance."""
from scipy import linalg
with np.errstate(divide='ignore'): # allow infinite
snr = (linalg.norm(desired, ord='fro') /
linalg.norm(desired - actual, ord='fro'))
assert snr >= tol, '%f < %f' % (snr, tol)
def assert_stcs_equal(stc1, stc2):
"""Check that two STC are equal."""
assert_allclose(stc1.times, stc2.times)
assert_allclose(stc1.data, stc2.data)
assert_array_equal(stc1.vertices[0], stc2.vertices[0])
assert_array_equal(stc1.vertices[1], stc2.vertices[1])
assert_allclose(stc1.tmin, stc2.tmin)
assert_allclose(stc1.tstep, stc2.tstep)
def _dig_sort_key(dig):
"""Sort dig keys."""
return (dig['kind'], dig['ident'])
def assert_dig_allclose(info_py, info_bin, limit=None):
"""Assert dig allclose."""
from ..bem import fit_sphere_to_headshape
from ..io.constants import FIFF
from ..io.meas_info import Info
from ..channels.montage import DigMontage
# test dig positions
dig_py, dig_bin = info_py, info_bin
if isinstance(dig_py, Info):
assert isinstance(dig_bin, Info)
dig_py, dig_bin = dig_py['dig'], dig_bin['dig']
else:
assert isinstance(dig_bin, DigMontage)
assert isinstance(dig_py, DigMontage)
dig_py, dig_bin = dig_py.dig, dig_bin.dig
info_py = info_bin = None
assert isinstance(dig_py, list)
assert isinstance(dig_bin, list)
dig_py = sorted(dig_py, key=_dig_sort_key)
dig_bin = sorted(dig_bin, key=_dig_sort_key)
assert len(dig_py) == len(dig_bin)
for ii, (d_py, d_bin) in enumerate(zip(dig_py[:limit], dig_bin[:limit])):
for key in ('ident', 'kind', 'coord_frame'):
assert d_py[key] == d_bin[key], key
assert_allclose(d_py['r'], d_bin['r'], rtol=1e-5, atol=1e-5,
err_msg='Failure on %s:\n%s\n%s'
% (ii, d_py['r'], d_bin['r']))
if any(d['kind'] == FIFF.FIFFV_POINT_EXTRA for d in dig_py) and \
info_py is not None:
r_bin, o_head_bin, o_dev_bin = fit_sphere_to_headshape(
info_bin, units='m', verbose='error')
r_py, o_head_py, o_dev_py = fit_sphere_to_headshape(
info_py, units='m', verbose='error')
assert_allclose(r_py, r_bin, atol=1e-6)
assert_allclose(o_dev_py, o_dev_bin, rtol=1e-5, atol=1e-6)
assert_allclose(o_head_py, o_head_bin, rtol=1e-5, atol=1e-6)
def _click_ch_name(fig, ch_index=0, button=1):
"""Click on a channel name in a raw/epochs/ICA browse-style plot."""
from ..viz.utils import _fake_click
fig.canvas.draw()
text = fig.mne.ax_main.get_yticklabels()[ch_index]
bbox = text.get_window_extent()
x = bbox.intervalx.mean()
y = bbox.intervaly.mean()
_fake_click(fig, fig.mne.ax_main, (x, y), xform='pix',
button=button)
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