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# -*- coding: utf-8 -*-
"""The config functions."""
# Authors: Eric Larson <larson.eric.d@gmail.com>
#
# License: BSD-3-Clause
import atexit
from functools import partial
import json
import os
import os.path as op
import platform
import shutil
import subprocess
import sys
import tempfile
import re
from .check import (_validate_type, _check_qt_version, _check_option,
_check_fname)
from .docs import fill_doc
from .misc import _pl
from ._logging import warn, logger
_temp_home_dir = None
def set_cache_dir(cache_dir):
"""Set the directory to be used for temporary file storage.
This directory is used by joblib to store memmapped arrays,
which reduces memory requirements and speeds up parallel
computation.
Parameters
----------
cache_dir : str or None
Directory to use for temporary file storage. None disables
temporary file storage.
"""
if cache_dir is not None and not op.exists(cache_dir):
raise IOError('Directory %s does not exist' % cache_dir)
set_config('MNE_CACHE_DIR', cache_dir, set_env=False)
def set_memmap_min_size(memmap_min_size):
"""Set the minimum size for memmaping of arrays for parallel processing.
Parameters
----------
memmap_min_size : str or None
Threshold on the minimum size of arrays that triggers automated memory
mapping for parallel processing, e.g., '1M' for 1 megabyte.
Use None to disable memmaping of large arrays.
"""
if memmap_min_size is not None:
if not isinstance(memmap_min_size, str):
raise ValueError('\'memmap_min_size\' has to be a string.')
if memmap_min_size[-1] not in ['K', 'M', 'G']:
raise ValueError('The size has to be given in kilo-, mega-, or '
'gigabytes, e.g., 100K, 500M, 1G.')
set_config('MNE_MEMMAP_MIN_SIZE', memmap_min_size, set_env=False)
# List the known configuration values
known_config_types = (
'MNE_3D_OPTION_ANTIALIAS',
'MNE_3D_OPTION_DEPTH_PEELING',
'MNE_3D_OPTION_MULTI_SAMPLES',
'MNE_3D_OPTION_SMOOTH_SHADING',
'MNE_3D_OPTION_THEME',
'MNE_BROWSE_RAW_SIZE',
'MNE_BROWSER_BACKEND',
'MNE_BROWSER_OVERVIEW_MODE',
'MNE_BROWSER_PRECOMPUTE',
'MNE_BROWSER_THEME',
'MNE_BROWSER_USE_OPENGL',
'MNE_CACHE_DIR',
'MNE_COREG_ADVANCED_RENDERING',
'MNE_COREG_COPY_ANNOT',
'MNE_COREG_FULLSCREEN',
'MNE_COREG_GUESS_MRI_SUBJECT',
'MNE_COREG_HEAD_HIGH_RES',
'MNE_COREG_HEAD_OPACITY',
'MNE_COREG_HEAD_INSIDE',
'MNE_COREG_INTERACTION',
'MNE_COREG_MARK_INSIDE',
'MNE_COREG_PREPARE_BEM',
'MNE_COREG_ORIENT_TO_SURFACE',
'MNE_COREG_SCALE_LABELS',
'MNE_COREG_SCALE_BY_DISTANCE',
'MNE_COREG_SCENE_SCALE',
'MNE_COREG_WINDOW_HEIGHT',
'MNE_COREG_WINDOW_WIDTH',
'MNE_COREG_SUBJECTS_DIR',
'MNE_CUDA_DEVICE',
'MNE_CUDA_IGNORE_PRECISION',
'MNE_DATA',
'MNE_DATASETS_BRAINSTORM_PATH',
'MNE_DATASETS_EEGBCI_PATH',
'MNE_DATASETS_EPILEPSY_ECOG_PATH',
'MNE_DATASETS_HF_SEF_PATH',
'MNE_DATASETS_MEGSIM_PATH',
'MNE_DATASETS_MISC_PATH',
'MNE_DATASETS_MTRF_PATH',
'MNE_DATASETS_SAMPLE_PATH',
'MNE_DATASETS_SOMATO_PATH',
'MNE_DATASETS_MULTIMODAL_PATH',
'MNE_DATASETS_FNIRS_MOTOR_PATH',
'MNE_DATASETS_OPM_PATH',
'MNE_DATASETS_SPM_FACE_DATASETS_TESTS',
'MNE_DATASETS_SPM_FACE_PATH',
'MNE_DATASETS_TESTING_PATH',
'MNE_DATASETS_VISUAL_92_CATEGORIES_PATH',
'MNE_DATASETS_KILOWORD_PATH',
'MNE_DATASETS_FIELDTRIP_CMC_PATH',
'MNE_DATASETS_PHANTOM_4DBTI_PATH',
'MNE_DATASETS_LIMO_PATH',
'MNE_DATASETS_REFMEG_NOISE_PATH',
'MNE_DATASETS_SSVEP_PATH',
'MNE_DATASETS_ERP_CORE_PATH',
'MNE_DATASETS_EPILEPSY_ECOG_PATH',
'MNE_FORCE_SERIAL',
'MNE_KIT2FIFF_STIM_CHANNELS',
'MNE_KIT2FIFF_STIM_CHANNEL_CODING',
'MNE_KIT2FIFF_STIM_CHANNEL_SLOPE',
'MNE_KIT2FIFF_STIM_CHANNEL_THRESHOLD',
'MNE_LOGGING_LEVEL',
'MNE_MEMMAP_MIN_SIZE',
'MNE_REPR_HTML',
'MNE_SKIP_FTP_TESTS',
'MNE_SKIP_NETWORK_TESTS',
'MNE_SKIP_TESTING_DATASET_TESTS',
'MNE_STIM_CHANNEL',
'MNE_TQDM',
'MNE_USE_CUDA',
'MNE_USE_NUMBA',
'SUBJECTS_DIR',
)
# These allow for partial matches, e.g. 'MNE_STIM_CHANNEL_1' is okay key
known_config_wildcards = (
'MNE_STIM_CHANNEL',
'MNE_DATASETS_FNIRS',
'MNE_NIRS',
)
def _load_config(config_path, raise_error=False):
"""Safely load a config file."""
with open(config_path, 'r') as fid:
try:
config = json.load(fid)
except ValueError:
# No JSON object could be decoded --> corrupt file?
msg = ('The MNE-Python config file (%s) is not a valid JSON '
'file and might be corrupted' % config_path)
if raise_error:
raise RuntimeError(msg)
warn(msg)
config = dict()
return config
def get_config_path(home_dir=None):
r"""Get path to standard mne-python config file.
Parameters
----------
home_dir : str | None
The folder that contains the .mne config folder.
If None, it is found automatically.
Returns
-------
config_path : str
The path to the mne-python configuration file. On windows, this
will be '%USERPROFILE%\.mne\mne-python.json'. On every other
system, this will be ~/.mne/mne-python.json.
"""
val = op.join(_get_extra_data_path(home_dir=home_dir),
'mne-python.json')
return val
def get_config(key=None, default=None, raise_error=False, home_dir=None,
use_env=True):
"""Read MNE-Python preferences from environment or config file.
Parameters
----------
key : None | str
The preference key to look for. The os environment is searched first,
then the mne-python config file is parsed.
If None, all the config parameters present in environment variables or
the path are returned. If key is an empty string, a list of all valid
keys (but not values) is returned.
default : str | None
Value to return if the key is not found.
raise_error : bool
If True, raise an error if the key is not found (instead of returning
default).
home_dir : str | None
The folder that contains the .mne config folder.
If None, it is found automatically.
use_env : bool
If True, consider env vars, if available.
If False, only use MNE-Python configuration file values.
.. versionadded:: 0.18
Returns
-------
value : dict | str | None
The preference key value.
See Also
--------
set_config
"""
_validate_type(key, (str, type(None)), "key", 'string or None')
if key == '':
return known_config_types
# first, check to see if key is in env
if use_env and key is not None and key in os.environ:
return os.environ[key]
# second, look for it in mne-python config file
config_path = get_config_path(home_dir=home_dir)
if not op.isfile(config_path):
config = {}
else:
config = _load_config(config_path)
if key is None:
# update config with environment variables
if use_env:
env_keys = (set(config).union(known_config_types).
intersection(os.environ))
config.update({key: os.environ[key] for key in env_keys})
return config
elif raise_error is True and key not in config:
loc_env = 'the environment or in the ' if use_env else ''
meth_env = ('either os.environ["%s"] = VALUE for a temporary '
'solution, or ' % key) if use_env else ''
extra_env = (' You can also set the environment variable before '
'running python.' if use_env else '')
meth_file = ('mne.utils.set_config("%s", VALUE, set_env=True) '
'for a permanent one' % key)
raise KeyError('Key "%s" not found in %s'
'the mne-python config file (%s). '
'Try %s%s.%s'
% (key, loc_env, config_path, meth_env, meth_file,
extra_env))
else:
return config.get(key, default)
def set_config(key, value, home_dir=None, set_env=True):
"""Set a MNE-Python preference key in the config file and environment.
Parameters
----------
key : str
The preference key to set.
value : str | None
The value to assign to the preference key. If None, the key is
deleted.
home_dir : str | None
The folder that contains the .mne config folder.
If None, it is found automatically.
set_env : bool
If True (default), update :data:`os.environ` in addition to
updating the MNE-Python config file.
See Also
--------
get_config
"""
_validate_type(key, 'str', "key")
# While JSON allow non-string types, we allow users to override config
# settings using env, which are strings, so we enforce that here
_validate_type(value, (str, 'path-like', type(None)), 'value')
if value is not None:
value = str(value)
if key not in known_config_types and not \
any(key.startswith(k) for k in known_config_wildcards):
warn('Setting non-standard config type: "%s"' % key)
# Read all previous values
config_path = get_config_path(home_dir=home_dir)
if op.isfile(config_path):
config = _load_config(config_path, raise_error=True)
else:
config = dict()
logger.info('Attempting to create new mne-python configuration '
'file:\n%s' % config_path)
if value is None:
config.pop(key, None)
if set_env and key in os.environ:
del os.environ[key]
else:
config[key] = value
if set_env:
os.environ[key] = value
# Write all values. This may fail if the default directory is not
# writeable.
directory = op.dirname(config_path)
if not op.isdir(directory):
os.mkdir(directory)
with open(config_path, 'w') as fid:
json.dump(config, fid, sort_keys=True, indent=0)
def _get_extra_data_path(home_dir=None):
"""Get path to extra data (config, tables, etc.)."""
global _temp_home_dir
if home_dir is None:
home_dir = os.environ.get('_MNE_FAKE_HOME_DIR')
if home_dir is None:
# this has been checked on OSX64, Linux64, and Win32
if 'nt' == os.name.lower():
if op.isdir(op.join(os.getenv('APPDATA'), '.mne')):
home_dir = os.getenv('APPDATA')
else:
home_dir = os.getenv('USERPROFILE')
else:
# This is a more robust way of getting the user's home folder on
# Linux platforms (not sure about OSX, Unix or BSD) than checking
# the HOME environment variable. If the user is running some sort
# of script that isn't launched via the command line (e.g. a script
# launched via Upstart) then the HOME environment variable will
# not be set.
if os.getenv('MNE_DONTWRITE_HOME', '') == 'true':
if _temp_home_dir is None:
_temp_home_dir = tempfile.mkdtemp()
atexit.register(partial(shutil.rmtree, _temp_home_dir,
ignore_errors=True))
home_dir = _temp_home_dir
else:
home_dir = os.path.expanduser('~')
if home_dir is None:
raise ValueError('mne-python config file path could '
'not be determined, please report this '
'error to mne-python developers')
return op.join(home_dir, '.mne')
def get_subjects_dir(subjects_dir=None, raise_error=False):
"""Safely use subjects_dir input to return SUBJECTS_DIR.
Parameters
----------
subjects_dir : str | None
If a value is provided, return subjects_dir. Otherwise, look for
SUBJECTS_DIR config and return the result.
raise_error : bool
If True, raise a KeyError if no value for SUBJECTS_DIR can be found
(instead of returning None).
Returns
-------
value : str | None
The SUBJECTS_DIR value.
"""
_validate_type(item=subjects_dir, types=('path-like', None),
item_name='subjects_dir', type_name='str or path-like')
if subjects_dir is None:
subjects_dir = get_config('SUBJECTS_DIR', raise_error=raise_error)
if subjects_dir is not None:
subjects_dir = _check_fname(
fname=subjects_dir, overwrite='read', must_exist=True,
need_dir=True, name='subjects_dir'
)
return subjects_dir
@fill_doc
def _get_stim_channel(stim_channel, info, raise_error=True):
"""Determine the appropriate stim_channel.
First, 'MNE_STIM_CHANNEL', 'MNE_STIM_CHANNEL_1', 'MNE_STIM_CHANNEL_2', etc.
are read. If these are not found, it will fall back to 'STI 014' if
present, then fall back to the first channel of type 'stim', if present.
Parameters
----------
stim_channel : str | list of str | None
The stim channel selected by the user.
%(info_not_none)s
Returns
-------
stim_channel : str | list of str
The name of the stim channel(s) to use
"""
if stim_channel is not None:
if not isinstance(stim_channel, list):
_validate_type(stim_channel, 'str', "Stim channel")
stim_channel = [stim_channel]
for channel in stim_channel:
_validate_type(channel, 'str', "Each provided stim channel")
return stim_channel
stim_channel = list()
ch_count = 0
ch = get_config('MNE_STIM_CHANNEL')
while ch is not None and ch in info['ch_names']:
stim_channel.append(ch)
ch_count += 1
ch = get_config('MNE_STIM_CHANNEL_%d' % ch_count)
if ch_count > 0:
return stim_channel
if 'STI101' in info['ch_names']: # combination channel for newer systems
return ['STI101']
if 'STI 014' in info['ch_names']: # for older systems
return ['STI 014']
from ..io.pick import pick_types
stim_channel = pick_types(info, meg=False, ref_meg=False, stim=True)
if len(stim_channel) > 0:
stim_channel = [info['ch_names'][ch_] for ch_ in stim_channel]
elif raise_error:
raise ValueError("No stim channels found. Consider specifying them "
"manually using the 'stim_channel' parameter.")
return stim_channel
def _get_root_dir():
"""Get as close to the repo root as possible."""
root_dir = op.abspath(op.join(op.dirname(__file__), '..'))
up_dir = op.join(root_dir, '..')
if op.isfile(op.join(up_dir, 'setup.py')) and all(
op.isdir(op.join(up_dir, x)) for x in ('mne', 'examples', 'doc')):
root_dir = op.abspath(up_dir)
return root_dir
def _get_numpy_libs():
bad_lib = 'unknown linalg bindings'
try:
from threadpoolctl import threadpool_info
except Exception as exc:
return bad_lib + f' (threadpoolctl module not found: {exc})'
pools = threadpool_info()
rename = dict(
openblas='OpenBLAS',
mkl='MKL',
)
for pool in pools:
if pool['internal_api'] in ('openblas', 'mkl'):
return (
f'{rename[pool["internal_api"]]} '
f'{pool["version"]} with '
f'{pool["num_threads"]} thread{_pl(pool["num_threads"])}')
return bad_lib
_gpu_cmd = """\
from pyvista import GPUInfo; \
gi = GPUInfo(); \
print(gi.version); \
print(gi.renderer)"""
def _get_gpu_info():
# Once https://github.com/pyvista/pyvista/pull/2250 is merged and PyVista
# does a release, we can triage based on version > 0.33.2
proc = subprocess.run(
[sys.executable, '-c', _gpu_cmd], check=False, capture_output=True)
out = proc.stdout.decode().strip().replace('\r', '').split('\n')
if proc.returncode or len(out) != 2:
return None, None
return out
def sys_info(fid=None, show_paths=False, *, dependencies='user'):
"""Print the system information for debugging.
This function is useful for printing system information
to help triage bugs.
Parameters
----------
fid : file-like | None
The file to write to. Will be passed to :func:`print()`.
Can be None to use :data:`sys.stdout`.
show_paths : bool
If True, print paths for each module.
dependencies : 'user' | 'developer'
Show dependencies relevant for users (default) or for developers
(i.e., output includes additional dependencies).
.. versionadded:: 0.24
Examples
--------
Running this function with no arguments prints an output that is
useful when submitting bug reports::
>>> import mne
>>> mne.sys_info() # doctest: +SKIP
Platform: Linux-4.15.0-1067-aws-x86_64-with-glibc2.2.5
Python: 3.8.1 (default, Feb 2 2020, 08:37:37) [GCC 8.3.0]
Executable: /usr/local/bin/python
CPU: : 36 cores
Memory: 68.7 GB
mne: 0.21.dev0
numpy: 1.19.0 {blas=openblas, lapack=openblas}
scipy: 1.5.1
matplotlib: 3.2.2 {backend=Qt5Agg}
sklearn: 0.23.1
numba: 0.50.1
nibabel: 3.1.1
nilearn: 0.7.0
dipy: 1.1.1
cupy: Not found
pandas: 1.0.5
pyvista: 0.25.3 {pyvistaqt=0.1.1, OpenGL 3.3 (Core Profile) Mesa 18.3.6 via llvmpipe (LLVM 7.0, 256 bits)}
vtk: 9.0.1
qtpy: 2.0.1 {PySide6=6.2.4}
pyqtgraph: 0.12.4
pooch: v1.5.1
""" # noqa: E501
_validate_type(dependencies, str)
_check_option('dependencies', dependencies, ('user', 'developer'))
ljust = 21 if dependencies == 'developer' else 18
platform_str = platform.platform()
if platform.system() == 'Darwin' and sys.version_info[:2] < (3, 8):
# platform.platform() in Python < 3.8 doesn't call
# platform.mac_ver() if we're on Darwin, so we don't get a nice macOS
# version number. Therefore, let's do this manually here.
macos_ver = platform.mac_ver()[0]
macos_architecture = re.findall('Darwin-.*?-(.*)', platform_str)
if macos_architecture:
macos_architecture = macos_architecture[0]
platform_str = f'macOS-{macos_ver}-{macos_architecture}'
del macos_ver, macos_architecture
out = partial(print, end='', file=fid)
out('Platform:'.ljust(ljust) + platform_str + '\n')
out('Python:'.ljust(ljust) + str(sys.version).replace('\n', ' ') + '\n')
out('Executable:'.ljust(ljust) + sys.executable + '\n')
out('CPU:'.ljust(ljust) + f'{platform.processor()}: ')
try:
import multiprocessing
except ImportError:
out('number of processors unavailable '
'(requires "multiprocessing" package)\n')
else:
out(f'{multiprocessing.cpu_count()} cores\n')
out('Memory:'.ljust(ljust))
try:
import psutil
except ImportError:
out('Unavailable (requires "psutil" package)')
else:
out(f'{psutil.virtual_memory().total / float(2 ** 30):0.1f} GB\n')
out('\n')
libs = _get_numpy_libs()
use_mod_names = ('mne', 'numpy', 'scipy', 'matplotlib', '', 'sklearn',
'numba', 'nibabel', 'nilearn', 'dipy', 'openmeeg', 'cupy',
'pandas', 'pyvista', 'pyvistaqt', 'ipyvtklink', 'vtk',
'qtpy', 'ipympl', 'pyqtgraph', 'pooch', '', 'mne_bids',
'mne_nirs', 'mne_features', 'mne_qt_browser',
'mne_connectivity', 'mne_icalabel')
if dependencies == 'developer':
use_mod_names += (
'', 'sphinx', 'sphinx_gallery', 'numpydoc', 'pydata_sphinx_theme',
'pytest', 'nbclient')
for mod_name in use_mod_names:
if mod_name == '':
out('\n')
continue
out(f'{mod_name}:'.ljust(ljust))
try:
mod = __import__(mod_name)
except Exception:
out('Not found\n')
else:
if mod_name == 'vtk':
vtk_version = mod.vtkVersion()
# 9.0 dev has VersionFull but 9.0 doesn't
for attr in ('GetVTKVersionFull', 'GetVTKVersion'):
if hasattr(vtk_version, attr):
version = getattr(vtk_version, attr)()
if version != '':
out(version)
break
else:
out('unknown')
else:
out(mod.__version__)
if mod_name == 'numpy':
out(f' {{{libs}}}')
elif mod_name == 'qtpy':
version, api = _check_qt_version(return_api=True)
out(f' {{{api}={version}}}')
elif mod_name == 'matplotlib':
out(f' {{backend={mod.get_backend()}}}')
elif mod_name == 'pyvista':
version, renderer = _get_gpu_info()
if version is None:
out(' {OpenGL could not be initialized}')
else:
out(f' {{OpenGL {version} via {renderer}}}')
if show_paths:
out(f'\n{" " * ljust}•{op.dirname(mod.__file__)}')
out('\n')
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