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# -*- coding: utf-8 -*-
"""Some miscellaneous utility functions."""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
#
# License: BSD-3-Clause
from contextlib import contextmanager, ExitStack
import fnmatch
import gc
import inspect
from math import log
import os
from queue import Queue, Empty
from string import Formatter
import subprocess
import sys
from threading import Thread
import traceback
import numpy as np
from ..utils import _check_option, _validate_type
from ._logging import logger, verbose, warn
def _pl(x, non_pl='', pl='s'):
"""Determine if plural should be used."""
len_x = x if isinstance(x, (int, np.generic)) else len(x)
return non_pl if len_x == 1 else pl
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
def _sort_keys(x):
"""Sort and return keys of dict."""
keys = list(x.keys()) # note: not thread-safe
idx = np.argsort([str(k) for k in keys])
keys = [keys[ii] for ii in idx]
return keys
class _DefaultEventParser:
"""Parse none standard events."""
def __init__(self):
self.event_ids = dict()
def __call__(self, description, offset=1):
if description not in self.event_ids:
self.event_ids[description] = offset + len(self.event_ids)
return self.event_ids[description]
class _FormatDict(dict):
"""Help pformat() work properly."""
def __missing__(self, key):
return "{" + key + "}"
def pformat(temp, **fmt):
"""Format a template string partially.
Examples
--------
>>> pformat("{a}_{b}", a='x')
'x_{b}'
"""
formatter = Formatter()
mapping = _FormatDict(fmt)
return formatter.vformat(temp, (), mapping)
def _enqueue_output(out, queue):
for line in iter(out.readline, b''):
queue.put(line)
@verbose
def run_subprocess(command, return_code=False, verbose=None, *args, **kwargs):
"""Run command using subprocess.Popen.
Run command and wait for command to complete. If the return code was zero
then return, otherwise raise CalledProcessError.
By default, this will also add stdout= and stderr=subproces.PIPE
to the call to Popen to suppress printing to the terminal.
Parameters
----------
command : list of str | str
Command to run as subprocess (see subprocess.Popen documentation).
return_code : bool
If True, return the return code instead of raising an error if it's
non-zero.
.. versionadded:: 0.20
%(verbose)s
*args, **kwargs : arguments
Additional arguments to pass to subprocess.Popen.
Returns
-------
stdout : str
Stdout returned by the process.
stderr : str
Stderr returned by the process.
code : int
The return code, only returned if ``return_code == True``.
"""
all_out = ''
all_err = ''
# non-blocking adapted from https://stackoverflow.com/questions/375427/non-blocking-read-on-a-subprocess-pipe-in-python#4896288 # noqa: E501
out_q = Queue()
err_q = Queue()
control_stdout = 'stdout' not in kwargs
control_stderr = 'stderr' not in kwargs
with running_subprocess(command, *args, **kwargs) as p:
if control_stdout:
out_t = Thread(target=_enqueue_output, args=(p.stdout, out_q))
out_t.daemon = True
out_t.start()
if control_stderr:
err_t = Thread(target=_enqueue_output, args=(p.stderr, err_q))
err_t.daemon = True
err_t.start()
while True:
do_break = p.poll() is not None
# read all current lines without blocking
while True: # process stdout
try:
out = out_q.get(timeout=0.01)
except Empty:
break
else:
out = out.decode('utf-8')
# Strip newline at end of the string, otherwise we'll end
# up with two subsequent newlines (as the logger adds one)
#
# XXX Once we drop support for Python <3.9, uncomment the
# following line and remove the if/else block below.
#
# log_out = out.removesuffix('\n')
if sys.version_info[:2] >= (3, 9):
log_out = out.removesuffix('\n')
elif out.endswith('\n'):
log_out = out[:-1]
else:
log_out = out
logger.info(log_out)
all_out += out
while True: # process stderr
try:
err = err_q.get(timeout=0.01)
except Empty:
break
else:
err = err.decode('utf-8')
# Strip newline at end of the string, otherwise we'll end
# up with two subsequent newlines (as the logger adds one)
#
# XXX Once we drop support for Python <3.9, uncomment the
# following line and remove the if/else block below.
#
# err_out = err.removesuffix('\n')
if sys.version_info[:2] >= (3, 9):
err_out = err.removesuffix('\n')
elif err.endswith('\n'):
err_out = err[:-1]
else:
err_out = err
# Leave this as logger.warning rather than warn(...) to
# mirror the logger.info above for stdout. This function
# is basically just a version of subprocess.call, and
# shouldn't emit Python warnings due to stderr outputs
# (the calling function can check for stderr output and
# emit a warning if it wants).
logger.warning(err_out)
all_err += err
if do_break:
break
output = (all_out, all_err)
if return_code:
output = output + (p.returncode,)
elif p.returncode:
stdout = all_out if control_stdout else None
stderr = all_err if control_stderr else None
raise subprocess.CalledProcessError(
p.returncode, command, output=stdout, stderr=stderr)
return output
@contextmanager
def running_subprocess(command, after="wait", verbose=None, *args, **kwargs):
"""Context manager to do something with a command running via Popen.
Parameters
----------
command : list of str | str
Command to run as subprocess (see :class:`python:subprocess.Popen`).
after : str
Can be:
- "wait" to use :meth:`~python:subprocess.Popen.wait`
- "communicate" to use :meth:`~python.subprocess.Popen.communicate`
- "terminate" to use :meth:`~python:subprocess.Popen.terminate`
- "kill" to use :meth:`~python:subprocess.Popen.kill`
%(verbose)s
*args, **kwargs : arguments
Additional arguments to pass to subprocess.Popen.
Returns
-------
p : instance of Popen
The process.
"""
_validate_type(after, str, 'after')
_check_option('after', after, ['wait', 'terminate', 'kill', 'communicate'])
contexts = list()
for stdxxx in ('stderr', 'stdout'):
if stdxxx not in kwargs:
kwargs[stdxxx] = subprocess.PIPE
contexts.append(stdxxx)
# Check the PATH environment variable. If run_subprocess() is to be called
# frequently this should be refactored so as to only check the path once.
env = kwargs.get('env', os.environ)
if any(p.startswith('~') for p in env['PATH'].split(os.pathsep)):
warn('Your PATH environment variable contains at least one path '
'starting with a tilde ("~") character. Such paths are not '
'interpreted correctly from within Python. It is recommended '
'that you use "$HOME" instead of "~".')
if isinstance(command, str):
command_str = command
else:
command = [str(s) for s in command]
command_str = ' '.join(s for s in command)
logger.info("Running subprocess: %s" % command_str)
try:
p = subprocess.Popen(command, *args, **kwargs)
except Exception:
if isinstance(command, str):
command_name = command.split()[0]
else:
command_name = command[0]
logger.error('Command not found: %s' % command_name)
raise
try:
with ExitStack() as stack:
for context in contexts:
stack.enter_context(getattr(p, context))
yield p
finally:
getattr(p, after)()
p.wait()
def _clean_names(names, remove_whitespace=False, before_dash=True):
"""Remove white-space on topo matching.
This function handles different naming
conventions for old VS new VectorView systems (`remove_whitespace`).
Also it allows to remove system specific parts in CTF channel names
(`before_dash`).
Usage
-----
# for new VectorView (only inside layout)
ch_names = _clean_names(epochs.ch_names, remove_whitespace=True)
# for CTF
ch_names = _clean_names(epochs.ch_names, before_dash=True)
"""
cleaned = []
for name in names:
if ' ' in name and remove_whitespace:
name = name.replace(' ', '')
if '-' in name and before_dash:
name = name.split('-')[0]
if name.endswith('_v'):
name = name[:-2]
cleaned.append(name)
return cleaned
def _get_argvalues():
"""Return all arguments (except self) and values of read_raw_xxx."""
# call stack
# read_raw_xxx -> <decorator-gen-000> -> BaseRaw.__init__ -> _get_argvalues
# This is equivalent to `frame = inspect.stack(0)[4][0]` but faster
frame = inspect.currentframe()
try:
for _ in range(3):
frame = frame.f_back
fname = frame.f_code.co_filename
if not fnmatch.fnmatch(fname, '*/mne/io/*'):
return None
args, _, _, values = inspect.getargvalues(frame)
finally:
del frame
params = dict()
for arg in args:
params[arg] = values[arg]
params.pop('self', None)
return params
def sizeof_fmt(num):
"""Turn number of bytes into human-readable str.
Parameters
----------
num : int
The number of bytes.
Returns
-------
size : str
The size in human-readable format.
"""
units = ['bytes', 'kB', 'MB', 'GB', 'TB', 'PB']
decimals = [0, 0, 1, 2, 2, 2]
if num > 1:
exponent = min(int(log(num, 1024)), len(units) - 1)
quotient = float(num) / 1024 ** exponent
unit = units[exponent]
num_decimals = decimals[exponent]
format_string = '{0:.%sf} {1}' % (num_decimals)
return format_string.format(quotient, unit)
if num == 0:
return '0 bytes'
if num == 1:
return '1 byte'
def _file_like(obj):
# An alternative would be::
#
# isinstance(obj, (TextIOBase, BufferedIOBase, RawIOBase, IOBase))
#
# but this might be more robust to file-like objects not properly
# inheriting from these classes:
return all(callable(getattr(obj, name, None)) for name in ('read', 'seek'))
def _fullname(obj):
klass = obj.__class__
module = klass.__module__
if module == 'builtins':
return klass.__qualname__
return module + '.' + klass.__qualname__
def _assert_no_instances(cls, when=''):
__tracebackhide__ = True
n = 0
ref = list()
gc.collect()
objs = gc.get_objects()
for obj in objs:
try:
check = isinstance(obj, cls)
except Exception: # such as a weakref
check = False
if check:
if cls.__name__ == 'Brain':
ref.append(
f'Brain._cleaned = {getattr(obj, "_cleaned", None)}')
rr = gc.get_referrers(obj)
count = 0
for r in rr:
if r is not objs and \
r is not globals() and \
r is not locals() and \
not inspect.isframe(r):
if isinstance(r, (list, dict, tuple)):
rep = f'len={len(r)}'
r_ = gc.get_referrers(r)
types = (_fullname(x) for x in r_)
types = "/".join(sorted(set(
x for x in types if x is not None)))
rep += f', {len(r_)} referrers: {types}'
del r_
else:
rep = repr(r)[:100].replace('\n', ' ')
# If it's a __closure__, get more information
if rep.startswith('<cell at '):
try:
rep += f' ({repr(r.cell_contents)[:100]})'
except Exception:
pass
name = _fullname(r)
ref.append(f'{name}: {rep}')
count += 1
del r
del rr
n += count > 0
del obj
del objs
gc.collect()
assert n == 0, f'\n{n} {cls.__name__} @ {when}:\n' + '\n'.join(ref)
def _resource_path(submodule, filename):
"""Return a full system path to a package resource (AKA a file).
Parameters
----------
submodule : str
An import-style module or submodule name
(e.g., "mne.datasets.testing").
filename : str
The file whose full path you want.
Returns
-------
path : str
The full system path to the requested file.
"""
try:
from importlib.resources import files
return files(submodule).joinpath(filename)
except ImportError:
from pkg_resources import resource_filename
return resource_filename(submodule, filename)
def repr_html(f):
"""Decorate _repr_html_ methods.
If a _repr_html_ method is decorated with this decorator, the repr in a
notebook will show HTML or plain text depending on the config value
MNE_REPR_HTML (by default "true", which will render HTML).
Parameters
----------
f : function
The function to decorate.
Returns
-------
wrapper : function
The decorated function.
"""
from ..utils import get_config
def wrapper(*args, **kwargs):
if get_config("MNE_REPR_HTML", "true").lower() == "false":
import html
r = "<pre>" + html.escape(repr(args[0])) + "</pre>"
return r.replace("\n", "<br/>")
else:
return f(*args, **kwargs)
return wrapper
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