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# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
# Denis Egnemann <denis.engemann@gmail.com>
# License: BSD Style.
import os
import os.path as op
import shutil
import tarfile
import stat
import sys
from .. import __version__ as mne_version
from ..utils import get_config, set_config, _fetch_file, logger, warn, verbose
from ..externals.six import string_types
from ..externals.six.moves import input
_data_path_doc = """Get path to local copy of {name} dataset
Parameters
----------
path : None | str
Location of where to look for the {name} dataset.
If None, the environment variable or config parameter
{conf} is used. If it doesn't exist, the
"mne-python/examples" directory is used. If the {name} dataset
is not found under the given path (e.g., as
"mne-python/examples/MNE-{name}-data"), the data
will be automatically downloaded to the specified folder.
force_update : bool
Force update of the {name} dataset even if a local copy exists.
update_path : bool | None
If True, set the {conf} in mne-python
config to the given path. If None, the user is prompted.
download : bool
If False and the {name} dataset has not been downloaded yet,
it will not be downloaded and the path will be returned as
'' (empty string). This is mostly used for debugging purposes
and can be safely ignored by most users.
verbose : bool, str, int, or None
If not None, override default verbose level (see mne.verbose).
Returns
-------
path : str
Path to {name} dataset directory.
"""
_version_doc = """Get version of the local {name} dataset
Returns
-------
version : str | None
Version of the {name} local dataset, or None if the dataset
does not exist locally.
"""
_bst_license_text = """
License
-------
This tutorial dataset (EEG and MRI data) remains a property of the MEG Lab,
McConnell Brain Imaging Center, Montreal Neurological Institute,
McGill University, Canada. Its use and transfer outside the Brainstorm
tutorial, e.g. for research purposes, is prohibited without written consent
from the MEG Lab.
If you reference this dataset in your publications, please:
1) acknowledge its authors: Elizabeth Bock, Esther Florin, Francois Tadel
and Sylvain Baillet, and
2) cite Brainstorm as indicated on the website:
http://neuroimage.usc.edu/brainstorm
For questions, please contact Francois Tadel (francois.tadel@mcgill.ca).
"""
def _dataset_version(path, name):
"""Get the version of the dataset"""
ver_fname = op.join(path, 'version.txt')
if op.exists(ver_fname):
with open(ver_fname, 'r') as fid:
version = fid.readline().strip() # version is on first line
else:
# Sample dataset versioning was introduced after 0.3
# SPM dataset was introduced with 0.7
version = '0.3' if name == 'sample' else '0.7'
return version
def _get_path(path, key, name):
"""Helper to get a dataset path"""
# 1. Input
if path is not None:
if not isinstance(path, string_types):
raise ValueError('path must be a string or None')
return path
# 2. get_config(key)
# 3. get_config('MNE_DATA')
path = get_config(key, get_config('MNE_DATA'))
if path is not None:
return path
# 4. ~/mne_data (but use a fake home during testing so we don't
# unnecessarily create ~/mne_data)
logger.info('Using default location ~/mne_data for %s...' % name)
path = op.join(os.getenv('_MNE_FAKE_HOME_DIR',
op.expanduser("~")), 'mne_data')
if not op.exists(path):
logger.info('Creating ~/mne_data')
try:
os.mkdir(path)
except OSError:
raise OSError("User does not have write permissions "
"at '%s', try giving the path as an "
"argument to data_path() where user has "
"write permissions, for ex:data_path"
"('/home/xyz/me2/')" % (path))
return path
def _do_path_update(path, update_path, key, name):
"""Helper to update path"""
path = op.abspath(path)
if update_path is None:
if get_config(key, '') != path:
update_path = True
if '--update-dataset-path' in sys.argv:
answer = 'y'
else:
msg = ('Do you want to set the path:\n %s\nas the default '
'%s dataset path in the mne-python config [y]/n? '
% (path, name))
answer = input(msg)
if answer.lower() == 'n':
update_path = False
else:
update_path = False
if update_path is True:
set_config(key, path, set_env=False)
return path
def _data_path(path=None, force_update=False, update_path=True, download=True,
name=None, check_version=False, return_version=False,
archive_name=None):
"""Aux function
"""
key = {
'fake': 'MNE_DATASETS_FAKE_PATH',
'misc': 'MNE_DATASETS_MISC_PATH',
'sample': 'MNE_DATASETS_SAMPLE_PATH',
'spm': 'MNE_DATASETS_SPM_FACE_PATH',
'somato': 'MNE_DATASETS_SOMATO_PATH',
'brainstorm': 'MNE_DATASETS_BRAINSTORM_PATH',
'testing': 'MNE_DATASETS_TESTING_PATH',
'multimodal': 'MNE_DATASETS_MULTIMODAL_PATH',
}[name]
path = _get_path(path, key, name)
# To update the testing or misc dataset, push commits, then make a new
# release on GitHub. Then update the "releases" variable:
releases = dict(testing='0.25', misc='0.1')
# And also update the "hashes['testing']" variable below.
# To update any other dataset, update the data archive itself (upload
# an updated version) and update the hash.
archive_names = dict(
misc='mne-misc-data-%s.tar.gz' % releases['misc'],
sample='MNE-sample-data-processed.tar.gz',
somato='MNE-somato-data.tar.gz',
spm='MNE-spm-face.tar.gz',
testing='mne-testing-data-%s.tar.gz' % releases['testing'],
multimodal='MNE-multimodal-data.tar.gz',
fake='foo.tgz',
)
if archive_name is not None:
archive_names.update(archive_name)
folder_names = dict(
brainstorm='MNE-brainstorm-data',
fake='foo',
misc='MNE-misc-data',
sample='MNE-sample-data',
somato='MNE-somato-data',
multimodal='MNE-multimodal-data',
spm='MNE-spm-face',
testing='MNE-testing-data',
)
urls = dict(
brainstorm='https://mne-tools.s3.amazonaws.com/datasets/'
'MNE-brainstorm-data/%s',
fake='https://github.com/mne-tools/mne-testing-data/raw/master/'
'datasets/%s',
misc='https://codeload.github.com/mne-tools/mne-misc-data/'
'tar.gz/%s' % releases['misc'],
sample="https://mne-tools.s3.amazonaws.com/datasets/%s",
somato='https://mne-tools.s3.amazonaws.com/datasets/%s',
spm='https://mne-tools.s3.amazonaws.com/datasets/%s',
testing='https://codeload.github.com/mne-tools/mne-testing-data/'
'tar.gz/%s' % releases['testing'],
multimodal='https://ndownloader.figshare.com/files/5999598',
)
hashes = dict(
brainstorm=None,
fake='3194e9f7b46039bb050a74f3e1ae9908',
misc='f0708d8914cf2692fee7b6c9f105e71c',
sample='1d5da3a809fded1ef5734444ab5bf857',
somato='f3e3a8441477bb5bacae1d0c6e0964fb',
spm='f61041e3f3f2ba0def8a2ca71592cc41',
testing='217aed43e361c86b622dc0363ae3cef4',
multimodal='26ec847ae9ab80f58f204d09e2c08367',
)
folder_origs = dict( # not listed means None
misc='mne-misc-data-%s' % releases['misc'],
testing='mne-testing-data-%s' % releases['testing'],
)
folder_name = folder_names[name]
archive_name = archive_names[name]
hash_ = hashes[name]
url = urls[name]
folder_orig = folder_origs.get(name, None)
if '%s' in url:
url = url % archive_name
folder_path = op.join(path, folder_name)
if name == 'brainstorm':
extract_path = folder_path
folder_path = op.join(folder_path, archive_names[name].split('.')[0])
rm_archive = False
martinos_path = '/cluster/fusion/sample_data/' + archive_name
neurospin_path = '/neurospin/tmp/gramfort/' + archive_name
if not op.exists(folder_path) and not download:
return ''
if not op.exists(folder_path) or force_update:
if name == 'brainstorm':
if '--accept-brainstorm-license' in sys.argv:
answer = 'y'
else:
answer = input('%sAgree (y/[n])? ' % _bst_license_text)
if answer.lower() != 'y':
raise RuntimeError('You must agree to the license to use this '
'dataset')
logger.info('Downloading or reinstalling '
'data archive %s at location %s' % (archive_name, path))
if op.exists(martinos_path):
archive_name = martinos_path
elif op.exists(neurospin_path):
archive_name = neurospin_path
else:
archive_name = op.join(path, archive_name)
rm_archive = True
fetch_archive = True
if op.exists(archive_name):
msg = ('Archive already exists. Overwrite it (y/[n])? ')
answer = input(msg)
if answer.lower() == 'y':
os.remove(archive_name)
else:
fetch_archive = False
if fetch_archive:
_fetch_file(url, archive_name, print_destination=False,
hash_=hash_)
if op.exists(folder_path):
def onerror(func, path, exc_info):
"""Deal with access errors (e.g. testing dataset read-only)"""
# Is the error an access error ?
do = False
if not os.access(path, os.W_OK):
perm = os.stat(path).st_mode | stat.S_IWUSR
os.chmod(path, perm)
do = True
if not os.access(op.dirname(path), os.W_OK):
dir_perm = (os.stat(op.dirname(path)).st_mode |
stat.S_IWUSR)
os.chmod(op.dirname(path), dir_perm)
do = True
if do:
func(path)
else:
raise
shutil.rmtree(folder_path, onerror=onerror)
logger.info('Decompressing the archive: %s' % archive_name)
logger.info('(please be patient, this can take some time)')
for ext in ['gz', 'bz2']: # informed guess (and the only 2 options).
try:
if name != 'brainstorm':
extract_path = path
tf = tarfile.open(archive_name, 'r:%s' % ext)
tf.extractall(path=extract_path)
tf.close()
break
except tarfile.ReadError as err:
logger.info('%s is %s trying "bz2"' % (archive_name, err))
if folder_orig is not None:
shutil.move(op.join(path, folder_orig), folder_path)
if rm_archive:
os.remove(archive_name)
path = _do_path_update(path, update_path, key, name)
path = op.join(path, folder_name)
# compare the version of the dataset and mne
data_version = _dataset_version(path, name)
try:
from distutils.version import LooseVersion as LV
except:
warn('Could not determine %s dataset version; dataset could '
'be out of date. Please install the "distutils" package.'
% name)
else: # 0.7 < 0.7.git shoud be False, therefore strip
if check_version and LV(data_version) < LV(mne_version.strip('.git')):
warn('The {name} dataset (version {current}) is older than '
'mne-python (version {newest}). If the examples fail, '
'you may need to update the {name} dataset by using '
'mne.datasets.{name}.data_path(force_update=True)'.format(
name=name, current=data_version, newest=mne_version))
return (path, data_version) if return_version else path
def _get_version(name):
"""Helper to get a dataset version"""
if not has_dataset(name):
return None
return _data_path(name=name, return_version=True)[1]
def has_dataset(name):
"""Helper for dataset presence"""
endswith = {
'brainstorm': 'MNE_brainstorm-data',
'fake': 'foo',
'misc': 'MNE-misc-data',
'sample': 'MNE-sample-data',
'somato': 'MNE-somato-data',
'spm': 'MNE-spm-face',
'testing': 'MNE-testing-data',
}[name]
archive_name = None
if name == 'brainstorm':
archive_name = dict(brainstorm='bst_raw')
dp = _data_path(download=False, name=name, check_version=False,
archive_name=archive_name)
return dp.endswith(endswith)
@verbose
def _download_all_example_data(verbose=True):
"""Helper to download all datasets used in examples and tutorials"""
# This function is designed primarily to be used by CircleCI. It has
# verbose=True by default so we get nice status messages
# Consider adding datasets from here to CircleCI for PR-auto-build
from . import (sample, testing, misc, spm_face, somato, brainstorm, megsim,
eegbci, multimodal)
sample.data_path()
testing.data_path()
misc.data_path()
spm_face.data_path()
somato.data_path()
multimodal.data_path()
sys.argv += ['--accept-brainstorm-license']
try:
brainstorm.bst_raw.data_path()
brainstorm.bst_auditory.data_path()
brainstorm.bst_phantom_elekta.data_path()
brainstorm.bst_phantom_ctf.data_path()
finally:
sys.argv.pop(-1)
megsim.load_data(condition='visual', data_format='single-trial',
data_type='simulation', update_path=True)
megsim.load_data(condition='visual', data_format='raw',
data_type='experimental', update_path=True)
megsim.load_data(condition='visual', data_format='evoked',
data_type='simulation', update_path=True)
url_root = 'http://www.physionet.org/physiobank/database/eegmmidb/'
eegbci.data_path(url_root + 'S001/S001R06.edf', update_path=True)
eegbci.data_path(url_root + 'S001/S001R10.edf', update_path=True)
eegbci.data_path(url_root + 'S001/S001R14.edf', update_path=True)
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