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# -*- coding: utf-8 -*-
"""The check functions."""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
#
# License: BSD (3-clause)
from distutils.version import LooseVersion
import operator
import os
import os.path as op
from pathlib import Path
import numpy as np
from ._logging import warn, logger
def _ensure_int(x, name='unknown', must_be='an int'):
"""Ensure a variable is an integer."""
# This is preferred over numbers.Integral, see:
# https://github.com/scipy/scipy/pull/7351#issuecomment-299713159
try:
x = int(operator.index(x))
except TypeError:
raise TypeError('%s must be %s, got %s' % (name, must_be, type(x)))
return x
def check_fname(fname, filetype, endings, endings_err=()):
"""Enforce MNE filename conventions.
Parameters
----------
fname : str
Name of the file.
filetype : str
Type of file. e.g., ICA, Epochs etc.
endings : tuple
Acceptable endings for the filename.
endings_err : tuple
Obligatory possible endings for the filename.
"""
_validate_type(fname, 'path-like', 'fname')
fname = str(fname)
if len(endings_err) > 0 and not fname.endswith(endings_err):
print_endings = ' or '.join([', '.join(endings_err[:-1]),
endings_err[-1]])
raise IOError('The filename (%s) for file type %s must end with %s'
% (fname, filetype, print_endings))
print_endings = ' or '.join([', '.join(endings[:-1]), endings[-1]])
if not fname.endswith(endings):
warn('This filename (%s) does not conform to MNE naming conventions. '
'All %s files should end with %s'
% (fname, filetype, print_endings))
def check_version(library, min_version):
r"""Check minimum library version required.
Parameters
----------
library : str
The library name to import. Must have a ``__version__`` property.
min_version : str
The minimum version string. Anything that matches
``'(\d+ | [a-z]+ | \.)'``. Can also be empty to skip version
check (just check for library presence).
Returns
-------
ok : bool
True if the library exists with at least the specified version.
"""
ok = True
try:
library = __import__(library)
except ImportError:
ok = False
else:
if min_version and \
LooseVersion(library.__version__) < LooseVersion(min_version):
ok = False
return ok
def _check_mayavi_version(min_version='4.3.0'):
"""Check mayavi version."""
if not check_version('mayavi', min_version):
raise RuntimeError("Need mayavi >= %s" % min_version)
# adapted from scikit-learn utils/validation.py
def check_random_state(seed):
"""Turn seed into a numpy.random.mtrand.RandomState instance.
If seed is None, return the RandomState singleton used by np.random.mtrand.
If seed is an int, return a new RandomState instance seeded with seed.
If seed is already a RandomState instance, return it.
Otherwise raise ValueError.
"""
if seed is None or seed is np.random:
return np.random.mtrand._rand
if isinstance(seed, (int, np.integer)):
return np.random.mtrand.RandomState(seed)
if isinstance(seed, np.random.mtrand.RandomState):
return seed
try:
# Generator is only available in numpy >= 1.17
if isinstance(seed, np.random.Generator):
return seed
except AttributeError:
pass
raise ValueError('%r cannot be used to seed a '
'numpy.random.mtrand.RandomState instance' % seed)
def _check_event_id(event_id, events):
"""Check event_id and convert to default format."""
# check out event_id dict
if event_id is None: # convert to int to make typing-checks happy
event_id = list(np.unique(events[:, 2]))
if isinstance(event_id, dict):
for key in event_id.keys():
_validate_type(key, str, 'Event names')
event_id = {key: _ensure_int(val, 'event_id[%s]' % key)
for key, val in event_id.items()}
elif isinstance(event_id, list):
event_id = [_ensure_int(v, 'event_id[%s]' % vi)
for vi, v in enumerate(event_id)]
event_id = dict(zip((str(i) for i in event_id), event_id))
else:
event_id = _ensure_int(event_id, 'event_id')
event_id = {str(event_id): event_id}
return event_id
def _check_fname(fname, overwrite=False, must_exist=False):
"""Check for file existence."""
_validate_type(fname, 'path-like', 'fname')
if op.isfile(fname):
if not overwrite:
raise IOError('Destination file exists. Please use option '
'"overwrite=True" to force overwriting.')
elif overwrite != 'read':
logger.info('Overwriting existing file.')
elif must_exist:
raise IOError('File "%s" does not exist' % fname)
return str(fname)
def _check_subject(class_subject, input_subject, raise_error=True,
kind='class subject attribute'):
"""Get subject name from class."""
if input_subject is not None:
_validate_type(input_subject, 'str', "subject input")
if class_subject is not None and input_subject != class_subject:
raise ValueError('%s (%r) did not match input subject (%r)'
% (kind, class_subject, input_subject))
return input_subject
elif class_subject is not None:
_validate_type(class_subject, 'str',
"Either subject input or %s" % (kind,))
return class_subject
elif raise_error is True:
raise ValueError('Neither subject input nor %s was a string' % (kind,))
return None
def _check_preload(inst, msg):
"""Ensure data are preloaded."""
from ..epochs import BaseEpochs
from ..evoked import Evoked
from ..time_frequency import _BaseTFR
if isinstance(inst, (_BaseTFR, Evoked)):
pass
else:
name = "epochs" if isinstance(inst, BaseEpochs) else 'raw'
if not inst.preload:
raise RuntimeError(
"By default, MNE does not load data into main memory to "
"conserve resources. " + msg + ' requires %s data to be '
'loaded. Use preload=True (or string) in the constructor or '
'%s.load_data().' % (name, name))
def _check_compensation_grade(info1, info2, name1,
name2='data', ch_names=None):
"""Ensure that objects have same compensation_grade."""
from ..io import Info
from ..io.pick import pick_channels, pick_info
from ..io.compensator import get_current_comp
for t_info in (info1, info2):
if t_info is None:
return
assert isinstance(t_info, Info), t_info # or internal code is wrong
if ch_names is not None:
info1 = info1.copy()
info2 = info2.copy()
# pick channels
for t_info in [info1, info2]:
if t_info['comps']:
t_info['comps'] = []
picks = pick_channels(t_info['ch_names'], ch_names)
pick_info(t_info, picks, copy=False)
# "or 0" here aliases None -> 0, as they are equivalent
grade1 = get_current_comp(info1) or 0
grade2 = get_current_comp(info2) or 0
# perform check
if grade1 != grade2:
raise RuntimeError(
'Compensation grade of %s (%s) and %s (%s) do not match'
% (name1, grade1, name2, grade2))
def _check_pylsl_installed(strict=True):
"""Aux function."""
try:
import pylsl
return pylsl
except ImportError:
if strict is True:
raise RuntimeError('For this functionality to work, the pylsl '
'library is required.')
else:
return False
def _check_pandas_installed(strict=True):
"""Aux function."""
try:
import pandas
return pandas
except ImportError:
if strict is True:
raise RuntimeError('For this functionality to work, the Pandas '
'library is required.')
else:
return False
def _check_pandas_index_arguments(index, defaults):
"""Check pandas index arguments."""
if not any(isinstance(index, k) for k in (list, tuple)):
index = [index]
invalid_choices = [e for e in index if e not in defaults]
if invalid_choices:
options = [', '.join(e) for e in [invalid_choices, defaults]]
raise ValueError('[%s] is not an valid option. Valid index'
'values are \'None\' or %s' % tuple(options))
def _check_ch_locs(chs):
"""Check if channel locations exist.
Parameters
----------
chs : dict
The channels from info['chs']
"""
locs3d = np.array([ch['loc'][:3] for ch in chs])
return not ((locs3d == 0).all() or
(~np.isfinite(locs3d)).all() or
np.allclose(locs3d, 0.))
def _is_numeric(n):
return isinstance(n, (np.integer, np.floating, int, float))
class _IntLike(object):
@classmethod
def __instancecheck__(cls, other):
try:
_ensure_int(other)
except TypeError:
return False
else:
return True
int_like = _IntLike()
_multi = {
'str': (str,),
'numeric': (np.floating, float, int_like),
'path-like': (str, Path),
'int-like': (int_like,)
}
try:
_multi['path-like'] += (os.PathLike,)
except AttributeError: # only on 3.6+
try:
# At least make PyTest work
from py._path.common import PathBase
except Exception: # no py.path
pass
else:
_multi['path-like'] += (PathBase,)
def _validate_type(item, types=None, item_name=None, type_name=None):
"""Validate that `item` is an instance of `types`.
Parameters
----------
item : object
The thing to be checked.
types : type | str | tuple of types | tuple of str
The types to be checked against.
If str, must be one of {'int', 'str', 'numeric', 'info', 'path-like'}.
"""
if types == "int":
_ensure_int(item, name=item_name)
return # terminate prematurely
elif types == "info":
from mne.io import Info as types
if not isinstance(types, (list, tuple)):
types = [types]
check_types = sum(((type(None),) if type_ is None else (type_,)
if not isinstance(type_, str) else _multi[type_]
for type_ in types), ())
if not isinstance(item, check_types):
if type_name is None:
type_name = ['None' if cls_ is None else cls_.__name__
if not isinstance(cls_, str) else cls_
for cls_ in types]
if len(type_name) == 1:
type_name = type_name[0]
elif len(type_name) == 2:
type_name = ' or '.join(type_name)
else:
type_name[-1] = 'or ' + type_name[-1]
type_name = ', '.join(type_name)
raise TypeError('%s must be an instance of %s, got %s instead'
% (item_name, type_name, type(item),))
def _check_path_like(item):
"""Validate that `item` is `path-like`.
Parameters
----------
item : object
The thing to be checked.
Returns
-------
bool
``True`` if `item` is a `path-like` object; ``False`` otherwise.
"""
try:
_validate_type(item, types='path-like')
return True
except TypeError:
return False
def _check_if_nan(data, msg=" to be plotted"):
"""Raise if any of the values are NaN."""
if not np.isfinite(data).all():
raise ValueError("Some of the values {} are NaN.".format(msg))
def _check_info_inv(info, forward, data_cov=None, noise_cov=None):
"""Return good channels common to forward model and covariance matrices."""
from .. import pick_types
# get a list of all channel names:
fwd_ch_names = forward['info']['ch_names']
# handle channels from forward model and info:
ch_names = _compare_ch_names(info['ch_names'], fwd_ch_names, info['bads'])
# make sure that no reference channels are left:
ref_chs = pick_types(info, meg=False, ref_meg=True)
ref_chs = [info['ch_names'][ch] for ch in ref_chs]
ch_names = [ch for ch in ch_names if ch not in ref_chs]
# inform about excluding channels:
if (data_cov is not None and set(info['bads']) != set(data_cov['bads']) and
(len(set(ch_names).intersection(data_cov['bads'])) > 0)):
logger.info('info["bads"] and data_cov["bads"] do not match, '
'excluding bad channels from both.')
if (noise_cov is not None and
set(info['bads']) != set(noise_cov['bads']) and
(len(set(ch_names).intersection(noise_cov['bads'])) > 0)):
logger.info('info["bads"] and noise_cov["bads"] do not match, '
'excluding bad channels from both.')
# handle channels from data cov if data cov is not None
# Note: data cov is supposed to be None in tf_lcmv
if data_cov is not None:
ch_names = _compare_ch_names(ch_names, data_cov.ch_names,
data_cov['bads'])
# handle channels from noise cov if noise cov available:
if noise_cov is not None:
ch_names = _compare_ch_names(ch_names, noise_cov.ch_names,
noise_cov['bads'])
picks = [info['ch_names'].index(k) for k in ch_names if k in
info['ch_names']]
return picks
def _compare_ch_names(names1, names2, bads):
"""Return channel names of common and good channels."""
ch_names = [ch for ch in names1 if ch not in bads and ch in names2]
return ch_names
def _check_channels_spatial_filter(ch_names, filters):
"""Return data channel indices to be used with spatial filter.
Unlike ``pick_channels``, this respects the order of ch_names.
"""
sel = []
# first check for channel discrepancies between filter and data:
for ch_name in filters['ch_names']:
if ch_name not in ch_names:
raise ValueError('The spatial filter was computed with channel %s '
'which is not present in the data. You should '
'compute a new spatial filter restricted to the '
'good data channels.' % ch_name)
# then compare list of channels and get selection based on data:
sel = [ii for ii, ch_name in enumerate(ch_names)
if ch_name in filters['ch_names']]
return sel
def _check_rank(rank):
"""Check rank parameter and deal with deprecation."""
err_msg = ('rank must be None, dict, "full", or int, '
'got %s (type %s)' % (rank, type(rank)))
if isinstance(rank, str):
# XXX we can use rank='' to deprecate to get to None eventually:
# if rank == '':
# warn('The rank parameter default in 0.18 of "full" will change '
# 'to None in 0.19, set it explicitly to avoid this warning',
# DeprecationWarning)
# rank = 'full'
if rank not in ['full', 'info']:
raise ValueError('rank, if str, must be "full" or "info", '
'got %s' % (rank,))
elif isinstance(rank, bool):
raise TypeError(err_msg)
elif rank is not None and not isinstance(rank, dict):
try:
rank = int(operator.index(rank))
except TypeError:
raise TypeError(err_msg)
else:
warn('rank as int is deprecated and will be removed in 0.19. '
'use rank=dict(meg=...) instead.', DeprecationWarning)
rank = dict(meg=rank)
return rank
def _check_one_ch_type(method, info, forward, data_cov=None, noise_cov=None):
"""Check number of sensor types and presence of noise covariance matrix."""
from ..cov import make_ad_hoc_cov, Covariance
from ..io.pick import pick_info
from ..channels.channels import _contains_ch_type
picks = _check_info_inv(info, forward, data_cov=data_cov,
noise_cov=noise_cov)
info_pick = pick_info(info, picks)
ch_types =\
[_contains_ch_type(info_pick, tt) for tt in ('mag', 'grad', 'eeg')]
if sum(ch_types) > 1:
if method == 'lcmv' and noise_cov is None:
raise ValueError('Source reconstruction with several sensor types'
' requires a noise covariance matrix to be '
'able to apply whitening.')
if method == 'dics':
raise RuntimeError(
'The use of several sensor types with the DICS beamformer is '
'not supported yet.')
if noise_cov is None:
noise_cov = make_ad_hoc_cov(info_pick, std=1.)
else:
noise_cov = noise_cov.copy()
if 'estimator' in noise_cov:
del noise_cov['estimator']
_validate_type(noise_cov, Covariance, 'noise_cov')
return noise_cov, picks
def _check_depth(depth, kind='depth_mne'):
"""Check depth options."""
from ..defaults import _handle_default
if not isinstance(depth, dict):
depth = dict(exp=None if depth is None else float(depth))
return _handle_default(kind, depth)
def _check_option(parameter, value, allowed_values):
"""Check the value of a parameter against a list of valid options.
Raises a ValueError with a readable error message if the value was invalid.
Parameters
----------
parameter : str
The name of the parameter to check. This is used in the error message.
value : any type
The value of the parameter to check.
allowed_values : list
The list of allowed values for the parameter.
Raises
------
ValueError
When the value of the parameter was not one of the valid options.
"""
if value in allowed_values:
return True
# Prepare a nice error message for the user
msg = ("Invalid value for the '{parameter}' parameter. "
'{options}, but got {value!r} instead.')
if len(allowed_values) == 1:
options = 'The only allowed value is %r' % allowed_values[0]
else:
options = 'Allowed values are '
options += ', '.join(['%r' % v for v in allowed_values[:-1]])
options += ' and %r' % allowed_values[-1]
raise ValueError(msg.format(parameter=parameter, options=options,
value=value))
def _check_all_same_channel_names(instances):
"""Check if a collection of instances all have the same channels."""
ch_names = instances[0].info["ch_names"]
for inst in instances:
if ch_names != inst.info["ch_names"]:
return False
return True
def _check_combine(mode, valid=('mean', 'median', 'std')):
if mode == "mean":
def fun(data):
return np.mean(data, axis=0)
elif mode == "std":
def fun(data):
return np.std(data, axis=0)
elif mode == "median":
def fun(data):
return np.median(data, axis=0)
elif callable(mode):
fun = mode
else:
raise ValueError("Combine option must be " + ", ".join(valid) +
" or callable, got %s (type %s)." %
(mode, type(mode)))
return fun
def _check_src_normal(pick_ori, src):
from ..source_space import SourceSpaces
_validate_type(src, SourceSpaces, 'src')
if pick_ori == 'normal' and src.kind not in ('surface', 'discrete'):
raise RuntimeError('Normal source orientation is supported only for '
'surface or discrete SourceSpaces, got type '
'%s' % (src.kind,))
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