File: utils.py

package info (click to toggle)
python-mne 0.13.1%2Bdfsg-3
  • links: PTS, VCS
  • area: main
  • in suites: stretch
  • size: 92,032 kB
  • ctags: 8,249
  • sloc: python: 84,750; makefile: 205; sh: 15
file content (389 lines) | stat: -rw-r--r-- 14,930 bytes parent folder | download
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
# 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)