1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494
|
# -*- coding: utf-8 -*-
"""Some utility functions."""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
#
# License: BSD-3-Clause
import contextlib
from decorator import FunctionMaker
import importlib
import inspect
from io import StringIO
import re
import sys
import logging
import os.path as op
import warnings
from typing import Any, Callable, TypeVar
from .docs import fill_doc
logger = logging.getLogger('mne') # one selection here used across mne-python
logger.propagate = False # don't propagate (in case of multiple imports)
# class to provide frame information (should be low overhead, just on logger
# calls)
class _FrameFilter(logging.Filter):
def __init__(self):
self.add_frames = 0
def filter(self, record):
record.frame_info = 'Unknown'
if self.add_frames:
# 5 is the offset necessary to get out of here and the logging
# module, reversal is to put the oldest at the top
frame_info = _frame_info(5 + self.add_frames)[5:][::-1]
if len(frame_info):
frame_info[-1] = (frame_info[-1] + ' :').ljust(30)
if len(frame_info) > 1:
frame_info[0] = '┌' + frame_info[0]
frame_info[-1] = '└' + frame_info[-1]
for ii, info in enumerate(frame_info[1:-1], 1):
frame_info[ii] = '├' + info
record.frame_info = '\n'.join(frame_info)
return True
_filter = _FrameFilter()
logger.addFilter(_filter)
# Provide help for static type checkers:
# https://mypy.readthedocs.io/en/stable/generics.html#declaring-decorators
_FuncT = TypeVar('_FuncT', bound=Callable[..., Any])
def verbose(function: _FuncT) -> _FuncT:
"""Verbose decorator to allow functions to override log-level.
Parameters
----------
function : callable
Function to be decorated by setting the verbosity level.
Returns
-------
dec : callable
The decorated function.
See Also
--------
set_log_level
set_config
Notes
-----
This decorator is used to set the verbose level during a function or method
call, such as :func:`mne.compute_covariance`. The `verbose` keyword
argument can be 'DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL', True (an
alias for 'INFO'), or False (an alias for 'WARNING'). To set the global
verbosity level for all functions, use :func:`mne.set_log_level`.
This function also serves as a docstring filler.
Examples
--------
You can use the ``verbose`` argument to set the verbose level on the fly::
>>> import mne
>>> cov = mne.compute_raw_covariance(raw, verbose='WARNING') # doctest: +SKIP
>>> cov = mne.compute_raw_covariance(raw, verbose='INFO') # doctest: +SKIP
Using up to 49 segments
Number of samples used : 5880
[done]
""" # noqa: E501
# See https://decorator.readthedocs.io/en/latest/tests.documentation.html
# #dealing-with-third-party-decorators
try:
fill_doc(function)
except TypeError: # nothing to add
pass
# Anything using verbose should have `verbose=None` in the signature.
# This code path will raise an error if this is not the case.
body = """\
def %(name)s(%(signature)s):\n
try:
do_level_change = verbose is not None
except (NameError, UnboundLocalError):
raise RuntimeError('Function/method %%s does not accept verbose '
'parameter' %% (_function_,)) from None
if do_level_change:
with _use_log_level_(verbose):
return _function_(%(shortsignature)s)
else:
return _function_(%(shortsignature)s)"""
evaldict = dict(
_use_log_level_=use_log_level, _function_=function)
fm = FunctionMaker(function, None, None, None, None, function.__module__)
attrs = dict(__wrapped__=function, __qualname__=function.__qualname__,
__globals__=function.__globals__)
return fm.make(body, evaldict, addsource=True, **attrs)
@fill_doc
class use_log_level:
"""Context manager for logging level.
Parameters
----------
%(verbose)s
%(add_frames)s
See Also
--------
mne.verbose
Notes
-----
See the :ref:`logging documentation <tut-logging>` for details.
Examples
--------
>>> from mne import use_log_level
>>> from mne.utils import logger
>>> with use_log_level(False):
... # Most MNE logger messages are "info" level, False makes them not
... # print:
... logger.info('This message will not be printed')
>>> with use_log_level(True):
... # Using verbose=True in functions, methods, or this context manager
... # will ensure they are printed
... logger.info('This message will be printed!')
This message will be printed!
"""
def __init__(self, verbose=None, *, add_frames=None): # noqa: D102
self._level = verbose
self._add_frames = add_frames
self._old_frames = _filter.add_frames
def __enter__(self): # noqa: D105
self._old_level = set_log_level(
self._level, return_old_level=True, add_frames=self._add_frames)
def __exit__(self, *args): # noqa: D105
add_frames = self._old_frames if self._add_frames is not None else None
set_log_level(self._old_level, add_frames=add_frames)
_LOGGING_TYPES = dict(DEBUG=logging.DEBUG, INFO=logging.INFO,
WARNING=logging.WARNING, ERROR=logging.ERROR,
CRITICAL=logging.CRITICAL)
@fill_doc
def set_log_level(verbose=None, return_old_level=False, add_frames=None):
"""Set the logging level.
Parameters
----------
verbose : bool, str, int, or None
The verbosity of messages to print. If a str, it can be either DEBUG,
INFO, WARNING, ERROR, or CRITICAL. Note that these are for
convenience and are equivalent to passing in logging.DEBUG, etc.
For bool, True is the same as 'INFO', False is the same as 'WARNING'.
If None, the environment variable MNE_LOGGING_LEVEL is read, and if
it doesn't exist, defaults to INFO.
return_old_level : bool
If True, return the old verbosity level.
%(add_frames)s
Returns
-------
old_level : int
The old level. Only returned if ``return_old_level`` is True.
"""
from .config import get_config
from .check import _check_option, _validate_type
_validate_type(verbose, (bool, str, int, None), 'verbose')
if verbose is None:
verbose = get_config('MNE_LOGGING_LEVEL', 'INFO')
elif isinstance(verbose, bool):
if verbose is True:
verbose = 'INFO'
else:
verbose = 'WARNING'
if isinstance(verbose, str):
verbose = verbose.upper()
_check_option('verbose', verbose, _LOGGING_TYPES, '(when a string)')
verbose = _LOGGING_TYPES[verbose]
old_verbose = logger.level
if verbose != old_verbose:
logger.setLevel(verbose)
if add_frames is not None:
_filter.add_frames = int(add_frames)
fmt = '%(frame_info)s ' if add_frames else ''
fmt += '%(message)s'
fmt = logging.Formatter(fmt)
for handler in logger.handlers:
handler.setFormatter(fmt)
return (old_verbose if return_old_level else None)
def set_log_file(fname=None, output_format='%(message)s', overwrite=None):
"""Set the log to print to a file.
Parameters
----------
fname : str, or None
Filename of the log to print to. If None, stdout is used.
To suppress log outputs, use set_log_level('WARNING').
output_format : str
Format of the output messages. See the following for examples:
https://docs.python.org/dev/howto/logging.html
e.g., "%(asctime)s - %(levelname)s - %(message)s".
overwrite : bool | None
Overwrite the log file (if it exists). Otherwise, statements
will be appended to the log (default). None is the same as False,
but additionally raises a warning to notify the user that log
entries will be appended.
"""
_remove_close_handlers(logger)
if fname is not None:
if op.isfile(fname) and overwrite is None:
# Don't use warn() here because we just want to
# emit a warnings.warn here (not logger.warn)
warnings.warn('Log entries will be appended to the file. Use '
'overwrite=False to avoid this message in the '
'future.', RuntimeWarning, stacklevel=2)
overwrite = False
mode = 'w' if overwrite else 'a'
lh = logging.FileHandler(fname, mode=mode)
else:
""" we should just be able to do:
lh = logging.StreamHandler(sys.stdout)
but because doctests uses some magic on stdout, we have to do this:
"""
lh = logging.StreamHandler(WrapStdOut())
lh.setFormatter(logging.Formatter(output_format))
# actually add the stream handler
logger.addHandler(lh)
def _remove_close_handlers(logger):
for h in list(logger.handlers):
# only remove our handlers (get along nicely with nose)
if isinstance(h, (logging.FileHandler, logging.StreamHandler)):
if isinstance(h, logging.FileHandler):
h.close()
logger.removeHandler(h)
class ClosingStringIO(StringIO):
"""StringIO that closes after getvalue()."""
def getvalue(self, close=True):
"""Get the value."""
out = super().getvalue()
if close:
self.close()
return out
class catch_logging(object):
"""Store logging.
This will remove all other logging handlers, and return the handler to
stdout when complete.
"""
def __init__(self, verbose=None):
self.verbose = verbose
def __enter__(self): # noqa: D105
if self.verbose is not None:
self._ctx = use_log_level(self.verbose)
else:
self._ctx = contextlib.nullcontext()
self._data = ClosingStringIO()
self._lh = logging.StreamHandler(self._data)
self._lh.setFormatter(logging.Formatter('%(message)s'))
self._lh._mne_file_like = True # monkey patch for warn() use
_remove_close_handlers(logger)
logger.addHandler(self._lh)
self._ctx.__enter__()
return self._data
def __exit__(self, *args): # noqa: D105
self._ctx.__exit__(*args)
logger.removeHandler(self._lh)
set_log_file(None)
@contextlib.contextmanager
def _record_warnings():
# this is a helper that mostly acts like pytest.warns(None) did before
# pytest 7
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
yield w
class WrapStdOut(object):
"""Dynamically wrap to sys.stdout.
This makes packages that monkey-patch sys.stdout (e.g.doctest,
sphinx-gallery) work properly.
"""
def __getattr__(self, name): # noqa: D105
# Even more ridiculous than this class, this must be sys.stdout (not
# just stdout) in order for this to work (tested on OSX and Linux)
if hasattr(sys.stdout, name):
return getattr(sys.stdout, name)
else:
raise AttributeError("'file' object has not attribute '%s'" % name)
_verbose_dec_re = re.compile('^<decorator-gen-[0-9]+>$')
def warn(message, category=RuntimeWarning, module='mne',
ignore_namespaces=('mne',)):
"""Emit a warning with trace outside the mne namespace.
This function takes arguments like warnings.warn, and sends messages
using both ``warnings.warn`` and ``logger.warn``. Warnings can be
generated deep within nested function calls. In order to provide a
more helpful warning, this function traverses the stack until it
reaches a frame outside the ``mne`` namespace that caused the error.
Parameters
----------
message : str
Warning message.
category : instance of Warning
The warning class. Defaults to ``RuntimeWarning``.
module : str
The name of the module emitting the warning.
ignore_namespaces : list of str
Namespaces to ignore when traversing the stack.
.. versionadded:: 0.24
"""
root_dirs = [importlib.import_module(ns) for ns in ignore_namespaces]
root_dirs = [op.dirname(ns.__file__) for ns in root_dirs]
frame = None
if logger.level <= logging.WARNING:
frame = inspect.currentframe()
while frame:
fname = frame.f_code.co_filename
lineno = frame.f_lineno
# in verbose dec
if not _verbose_dec_re.search(fname):
# treat tests as scripts
# and don't capture unittest/case.py (assert_raises)
if not (any(fname.startswith(rd) for rd in root_dirs) or
('unittest' in fname and 'case' in fname)) or \
op.basename(op.dirname(fname)) == 'tests':
break
frame = frame.f_back
del frame
# We need to use this instead of warn(message, category, stacklevel)
# because we move out of the MNE stack, so warnings won't properly
# recognize the module name (and our warnings.simplefilter will fail)
warnings.warn_explicit(
message, category, fname, lineno, module,
globals().get('__warningregistry__', {}))
# To avoid a duplicate warning print, we only emit the logger.warning if
# one of the handlers is a FileHandler. See gh-5592
# But it's also nice to be able to do:
# with mne.utils.use_log_level('warning', add_frames=3):
# so also check our add_frames attribute.
if any(isinstance(h, logging.FileHandler) or getattr(h, '_mne_file_like',
False)
for h in logger.handlers) or _filter.add_frames:
logger.warning(message)
def _get_call_line():
"""Get the call line from within a function."""
frame = inspect.currentframe().f_back.f_back
if _verbose_dec_re.search(frame.f_code.co_filename):
frame = frame.f_back
context = inspect.getframeinfo(frame).code_context
context = 'unknown' if context is None else context[0].strip()
return context
def filter_out_warnings(warn_record, category=None, match=None):
r"""Remove particular records from ``warn_record``.
This helper takes a list of :class:`warnings.WarningMessage` objects,
and remove those matching category and/or text.
Parameters
----------
category: WarningMessage type | None
class of the message to filter out
match : str | None
text or regex that matches the error message to filter out
"""
regexp = re.compile('.*' if match is None else match)
is_category = [w.category == category if category is not None else True
for w in warn_record._list]
is_match = [regexp.match(w.message.args[0]) is not None
for w in warn_record._list]
ind = [ind for ind, (c, m) in enumerate(zip(is_category, is_match))
if c and m]
for i in reversed(ind):
warn_record._list.pop(i)
@contextlib.contextmanager
def wrapped_stdout(indent='', cull_newlines=False):
"""Wrap stdout writes to logger.info, with an optional indent prefix.
Parameters
----------
indent : str
The indentation to add.
cull_newlines : bool
If True, cull any new/blank lines at the end.
"""
orig_stdout = sys.stdout
my_out = ClosingStringIO()
sys.stdout = my_out
try:
yield
finally:
sys.stdout = orig_stdout
pending_newlines = 0
for line in my_out.getvalue().split('\n'):
if not line.strip() and cull_newlines:
pending_newlines += 1
continue
for _ in range(pending_newlines):
logger.info('\n')
logger.info(indent + line)
def _frame_info(n):
frame = inspect.currentframe()
try:
frame = frame.f_back
infos = list()
for _ in range(n):
try:
name = frame.f_globals['__name__']
except KeyError: # in our verbose dec
pass
else:
infos.append(f'{name.lstrip("mne.")}:{frame.f_lineno}')
frame = frame.f_back
if frame is None:
break
return infos
except Exception:
return ['unknown']
finally:
del frame
def _verbose_safe_false(*, level='warning'):
lev = _LOGGING_TYPES[level.upper()]
return lev if logger.level <= lev else None
|