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check.py
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check.py
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# -*- coding: utf-8 -*-
"""The check functions."""
# Authors: Alexandre Gramfort <[email protected]>
#
# License: BSD (3-clause)
from builtins import input # no-op here but facilitates testing
from difflib import get_close_matches
from distutils.version import LooseVersion
import operator
import os
import os.path as op
from pathlib import Path
import sys
import warnings
import numpy as np
from ..fixes import _median_complex
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:
# someone passing True/False is much more likely to be an error than
# intentional usage
if isinstance(x, bool):
raise TypeError()
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='0.0'):
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 _require_version(lib, what, version='0.0'):
"""Require library for a purpose."""
if not check_version(lib, version):
extra = f' (version >= {version})' if version != '0.0' else ''
raise ImportError(f'The {lib} package{extra} is required to {what}')
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, name='File',
need_dir=False):
"""Check for file existence."""
_validate_type(fname, 'path-like', name)
if op.exists(fname):
if not overwrite:
raise FileExistsError('Destination file exists. Please use option '
'"overwrite=True" to force overwriting.')
elif overwrite != 'read':
logger.info('Overwriting existing file.')
if must_exist:
if need_dir:
if not op.isdir(fname):
raise IOError(
f'Need a directory for {name} but found a file '
f'at {fname}')
else:
if not op.isfile(fname):
raise IOError(
f'Need a file for {name} but found a directory '
f'at {fname}')
if not os.access(fname, os.R_OK):
raise PermissionError(
f'{name} does not have read permissions: {fname}')
elif must_exist:
raise FileNotFoundError(f'{name} does not exist: {fname}')
return str(op.abspath(fname))
def _check_subject(first, second, *, raise_error=True,
first_kind='class subject attribute',
second_kind='input subject'):
"""Get subject name from class."""
if second is not None:
_validate_type(second, 'str', "subject input")
if first is not None and first != second:
raise ValueError(
f'{first_kind} ({repr(first)}) did not match '
f'{second_kind} ({second})')
return second
elif first is not None:
_validate_type(
first, 'str', f"Either {second_kind} subject or {first_kind}")
return first
elif raise_error is True:
raise ValueError(f'Neither {second_kind} subject nor {first_kind} '
'was a string')
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_eeglabio_installed(strict=True):
"""Aux function."""
try:
import eeglabio
return eeglabio
except ImportError:
if strict is True:
raise RuntimeError('For this functionality to work, the eeglabio '
'library is required.')
else:
return False
def _check_pandas_index_arguments(index, valid):
"""Check pandas index arguments."""
if index is None:
return
if isinstance(index, str):
index = [index]
if not isinstance(index, list):
raise TypeError('index must be `None` or a string or list of strings,'
' got type {}.'.format(type(index)))
invalid = set(index) - set(valid)
if invalid:
plural = ('is not a valid option',
'are not valid options')[int(len(invalid) > 1)]
raise ValueError('"{}" {}. Valid index options are `None`, "{}".'
.format('", "'.join(invalid), plural,
'", "'.join(valid)))
return index
def _check_time_format(time_format, valid, meas_date=None):
"""Check time_format argument."""
if time_format not in valid and time_format is not None:
valid_str = '", "'.join(valid)
raise ValueError('"{}" is not a valid time format. Valid options are '
'"{}" and None.'.format(time_format, valid_str))
# allow datetime only if meas_date available
if time_format == 'datetime' and meas_date is None:
warn("Cannot convert to Datetime when raw.info['meas_date'] is "
"None. Falling back to Timedelta.")
time_format = 'timedelta'
return time_format
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()
path_like = (str, Path)
class _Callable(object):
@classmethod
def __instancecheck__(cls, other):
return callable(other)
_multi = {
'str': (str,),
'numeric': (np.floating, float, int_like),
'path-like': path_like,
'int-like': (int_like,),
'callable': (_Callable(),),
}
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',
'callable'}.
item_name : str | None
Name of the item to show inside the error message.
type_name : str | None
Possible types to show inside the error message that the checked item
can be.
"""
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)
_item_name = 'Item' if item_name is None else item_name
raise TypeError(f"{_item_name} must be an instance of {type_name}, "
f"got {type(item)} instead")
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."""
_validate_type(rank, (None, dict, str), 'rank')
if isinstance(rank, str):
if rank not in ['full', 'info']:
raise ValueError('rank, if str, must be "full" or "info", '
'got %s' % (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 ..time_frequency.csd import CrossSpectralDensity
from ..io.pick import pick_info
from ..channels.channels import _contains_ch_type
if isinstance(data_cov, CrossSpectralDensity):
_validate_type(noise_cov, [None, CrossSpectralDensity], 'noise_cov')
# FIXME
picks = list(range(len(data_cov.ch_names)))
info_pick = info
else:
_validate_type(noise_cov, [None, Covariance], 'noise_cov')
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 noise_cov is None:
raise ValueError('Source reconstruction with several sensor types'
' requires a noise covariance matrix to be '
'able to apply whitening.')
if noise_cov is None:
noise_cov = make_ad_hoc_cov(info_pick, std=1.)
allow_mismatch = True
else:
noise_cov = noise_cov.copy()
if isinstance(noise_cov, Covariance) and 'estimator' in noise_cov:
del noise_cov['estimator']
allow_mismatch = False
_validate_type(noise_cov, (Covariance, CrossSpectralDensity), 'noise_cov')
return noise_cov, picks, allow_mismatch
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, extra=''):
"""Check the value of a parameter against a list of valid options.
Return the value if it is valid, otherwise raise a ValueError with a
readable error message.
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.
extra : str
Extra string to append to the invalid value sentence, e.g.
"when using ico mode".
Raises
------
ValueError
When the value of the parameter is not one of the valid options.
Returns
-------
value : any type
The value if it is valid.
"""
if value in allowed_values:
return value
# Prepare a nice error message for the user
extra = ' ' + extra if extra else extra
msg = ("Invalid value for the '{parameter}' parameter{extra}. "
'{options}, but got {value!r} instead.')
allowed_values = list(allowed_values) # e.g., if a dict was given
if len(allowed_values) == 1:
options = f'The only allowed value is {repr(allowed_values[0])}'
else:
options = 'Allowed values are '
options += ', '.join([f'{repr(v)}' for v in allowed_values[:-1]])
options += f', and {repr(allowed_values[-1])}'
raise ValueError(msg.format(parameter=parameter, options=options,
value=value, extra=extra))
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" or mode == np.median:
def fun(data):
return _median_complex(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,))
def _check_stc_units(stc, threshold=1e-7): # 100 nAm threshold for warning
max_cur = np.max(np.abs(stc.data))
if max_cur > threshold:
warn('The maximum current magnitude is %0.1f nAm, which is very large.'
' Are you trying to apply the forward model to noise-normalized '
'(dSPM, sLORETA, or eLORETA) values? The result will only be '
'correct if currents (in units of Am) are used.'
% (1e9 * max_cur))
def _check_pyqt5_version():
bad = True
try:
from PyQt5.Qt import PYQT_VERSION_STR as version
except Exception:
version = 'unknown'
else:
if LooseVersion(version) >= LooseVersion('5.10'):
bad = False
bad &= sys.platform == 'darwin'
if bad:
warn('macOS users should use PyQt5 >= 5.10 for GUIs, got %s. '
'Please upgrade e.g. with:\n\n'
' pip install "PyQt5>=5.10,<5.14"\n'
% (version,))
return version
def _check_sphere(sphere, info=None, sphere_units='m'):
from ..defaults import HEAD_SIZE_DEFAULT
from ..bem import fit_sphere_to_headshape, ConductorModel, get_fitting_dig
if sphere is None:
sphere = HEAD_SIZE_DEFAULT
if info is not None:
# Decide if we have enough dig points to do the auto fit
try:
get_fitting_dig(info, 'extra', verbose='error')
except (RuntimeError, ValueError):
pass
else:
sphere = 'auto'
if isinstance(sphere, str):
if sphere != 'auto':
raise ValueError('sphere, if str, must be "auto", got %r'
% (sphere))
R, r0, _ = fit_sphere_to_headshape(info, verbose=False, units='m')
sphere = tuple(r0) + (R,)
sphere_units = 'm'
elif isinstance(sphere, ConductorModel):
if not sphere['is_sphere'] or len(sphere['layers']) == 0:
raise ValueError('sphere, if a ConductorModel, must be spherical '
'with multiple layers, not a BEM or single-layer '
'sphere (got %s)' % (sphere,))
sphere = tuple(sphere['r0']) + (sphere['layers'][0]['rad'],)
sphere_units = 'm'
sphere = np.array(sphere, dtype=float)
if sphere.shape == ():
sphere = np.concatenate([[0.] * 3, [sphere]])
if sphere.shape != (4,):
raise ValueError('sphere must be float or 1D array of shape (4,), got '
'array-like of shape %s' % (sphere.shape,))
_check_option('sphere_units', sphere_units, ('m', 'mm'))
if sphere_units == 'mm':
sphere /= 1000.
sphere = np.array(sphere, float)
return sphere
def _check_freesurfer_home():
from .config import get_config
fs_home = get_config('FREESURFER_HOME')
if fs_home is None:
raise RuntimeError(
'The FREESURFER_HOME environment variable is not set.')
return fs_home
def _suggest(val, options, cutoff=0.66):
options = get_close_matches(val, options, cutoff=cutoff)
if len(options) == 0:
return ''
elif len(options) == 1:
return ' Did you mean %r?' % (options[0],)
else:
return ' Did you mean one of %r?' % (options,)
def _check_on_missing(on_missing, name='on_missing'):
_validate_type(on_missing, str, name)
_check_option(name, on_missing, ['raise', 'warn', 'ignore'])
def _on_missing(on_missing, msg, name='on_missing', error_klass=None):
_check_on_missing(on_missing, name)
error_klass = ValueError if error_klass is None else error_klass
on_missing = 'raise' if on_missing == 'error' else on_missing
on_missing = 'warn' if on_missing == 'warning' else on_missing
if on_missing == 'raise':
raise error_klass(msg)
elif on_missing == 'warn':
warn(msg)
else: # Ignore
assert on_missing == 'ignore'
def _safe_input(msg, *, alt=None, use=None):
try:
return input(msg)
except EOFError: # MATLAB or other non-stdin
if use is not None:
return use
raise RuntimeError(
f'Could not use input() to get a response to:\n{msg}\n'
f'You can {alt} to avoid this error.')
def _ensure_events(events):
events_type = type(events)
with warnings.catch_warnings(record=True):
warnings.simplefilter('ignore') # deprecation for object array
events = np.asarray(events)
if not np.issubdtype(events.dtype, np.integer):
raise TypeError('events should be a NumPy array of integers, '
f'got {events_type}')
if events.ndim != 2 or events.shape[1] != 3:
raise ValueError(
f'events must be of shape (N, 3), got {events.shape}')
return events
def _infer_check_export_fmt(fmt, fname, supported_formats):
"""Infer export format from filename extension if auto.
Raises error if fmt is auto and no file extension found,
then checks format against supported formats, raises error if format is not
supported.
Parameters
----------
fmt : str
Format of the export, will only infer the format from filename if fmt
is auto.
fname : str
Name of the target export file, only used when fmt is auto.
supported_formats : dict of str : tuple/list
Dictionary containing supported formats (as keys) and each format's
corresponding file extensions in a tuple/list (e.g. 'eeglab': ('set',))
"""
_validate_type(fmt, str, 'fmt')
fmt = fmt.lower()
if fmt == "auto":
fmt = op.splitext(fname)[1]
if fmt:
fmt = fmt[1:].lower()
# find fmt in supported formats dict's tuples
fmt = next((k for k, v in supported_formats.items() if fmt in v),
fmt) # default to original fmt for raising error later
else:
raise ValueError(f"Couldn't infer format from filename {fname}"
" (no extension found)")
if fmt not in supported_formats:
supported = []
for format, extensions in supported_formats.items():
ext_str = ', '.join(f'*.{ext}' for ext in extensions)
supported.append(f'{format} ({ext_str})')
supported_str = ', '.join(supported)
raise ValueError(f"Format '{fmt}' is not supported. "
f"Supported formats are {supported_str}.")
return fmt