"""Testing functions."""
# Authors: The MNE-Python contributors.
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.
import inspect
import os
import sys
import tempfile
import traceback
from functools import wraps
from shutil import rmtree
from unittest import SkipTest
import numpy as np
from numpy.testing import assert_allclose, assert_array_equal
from scipy import linalg
from ._logging import ClosingStringIO, warn
from .check import check_version
from .misc import run_subprocess
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):
self._path = self.__str__()
def __del__(self): # noqa: D105
rmtree(self._path, ignore_errors=True)
def requires_mne(func):
"""Decorate a function as requiring MNE."""
return requires_mne_mark()(func)
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", "2.5.6"), reason="Requires OpenMEEG >= 2.5.6"
)
def requires_freesurfer(arg):
"""Require Freesurfer."""
import pytest
reason = "Requires Freesurfer"
if isinstance(arg, str):
# Calling as @requires_freesurfer('progname'): return decorator
# after checking for progname existence
reason += f" command: {arg}"
try:
run_subprocess([arg, "--version"])
except Exception:
skip = True
else:
skip = False
return pytest.mark.skipif(skip, reason=reason)
else:
# Calling directly as @requires_freesurfer: return decorated function
# and just check env var existence
return pytest.mark.skipif(not has_freesurfer(), reason="Requires Freesurfer")(
arg
)
def requires_good_network(func):
import pytest
return pytest.mark.skipif(
int(os.environ.get("MNE_SKIP_NETWORK_TESTS", 0)),
reason="MNE_SKIP_NETWORK_TESTS is set",
)(func)
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:
"""Temporarily set sys.argv."""
def __init__(self, args=(), disable_stdout=True, disable_stderr=True):
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
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 import BaseRaw
if isinstance(annotations, BaseRaw): # allow either input
annotations = annotations.annotations
for key in ("EDGE", "BAD"):
idx = np.where(annotations.description == f"{key} boundary")[0]
assert len(idx) == n
annotations.delete(idx)
def assert_object_equal(a, b, *, err_msg="Object mismatch", allclose=False):
"""Assert two objects are equal."""
d = object_diff(a, b, allclose=allclose)
assert d == "", f"{err_msg}\n{d}"
def _raw_annot(meas_date, orig_time):
from .._fiff.meas_info import create_info
from ..annotations import Annotations, _handle_meas_date
from ..io import RawArray
info = create_info(ch_names=10, sfreq=10.0)
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([0.5], [0.2], ["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 = f" ({msg})" if msg != "" else msg
assert bad_count == 0, (
f"SNR (worst {snr:0.2f}) < {min_tol:0.2f} "
f"for {bad_count}/{len(picks)} channels{msg}"
)
# median tol
snr = np.median(snrs)
assert snr >= med_tol, f"{kind} SNR median {snr:0.2f} < {med_tol:0.2f}{msg}"
def assert_meg_snr(
actual, desired, min_tol, med_tol=500.0, chpi_med_tol=500.0, 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 .._fiff.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, 0.0, chpi_med_tol, msg, kind="cHPI")
def assert_snr(actual, desired, tol):
"""Assert actual and desired arrays are within some SNR tolerance."""
with np.errstate(divide="ignore"): # allow infinite
snr = linalg.norm(desired, ord="fro") / linalg.norm(desired - actual, ord="fro")
assert snr >= tol, 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 .._fiff.constants import FIFF
from .._fiff.meas_info import Info
from ..bem import fit_sphere_to_headshape
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=f"Failure on {ii}:\n{d_py['r']}\n{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)
def _get_suptitle(fig):
"""Get fig suptitle (shim for matplotlib < 3.8.0)."""
# TODO: obsolete when minimum MPL version is 3.8
if check_version("matplotlib", "3.8"):
return fig.get_suptitle()
else:
# unreliable hack; should work in most tests as we rarely use `sup_{x,y}label`
return fig.texts[0].get_text()