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
|
#!/usr/bin/env python
r"""Create mne report for a folder.
Examples
--------
Before getting started with ``mne report``, make sure the files you want to
render follow the filename conventions defined by MNE:
.. highlight:: console
.. cssclass:: table-bordered
.. rst-class:: midvalign
============ ==============================================================
Data object Filename convention (ends with)
============ ==============================================================
raw -raw.fif(.gz), -raw_sss.fif(.gz), -raw_tsss.fif(.gz), _meg.fif
events -eve.fif(.gz)
epochs -epo.fif(.gz)
evoked -ave.fif(.gz)
covariance -cov.fif(.gz)
trans -trans.fif(.gz)
forward -fwd.fif(.gz)
inverse -inv.fif(.gz)
============ ==============================================================
To generate a barebones report from all the \*.fif files in the sample
dataset, invoke the following command in a system (e.g., Bash) shell::
$ mne report --path MNE-sample-data/ --verbose
On successful creation of the report, it will open the HTML in a new tab in
the browser. To disable this, use the ``--no-browser`` option.
TO generate a report for a single subject, give the ``SUBJECT`` name and
the ``SUBJECTS_DIR`` and this will generate the MRI slices (with BEM
contours overlaid on top if available)::
$ mne report --path MNE-sample-data/ --subject sample --subjects-dir \
MNE-sample-data/subjects --verbose
To properly render ``trans`` and ``covariance`` files, add the measurement
information::
$ mne report --path MNE-sample-data/ \
--info MNE-sample-data/MEG/sample/sample_audvis-ave.fif \
--subject sample --subjects-dir MNE-sample-data/subjects --verbose
To render whitened ``evoked`` files with baseline correction, add the noise
covariance file::
$ mne report --path MNE-sample-data/ \
--info MNE-sample-data/MEG/sample/sample_audvis-ave.fif \
--cov MNE-sample-data/MEG/sample/sample_audvis-cov.fif --bmax 0 \
--subject sample --subjects-dir MNE-sample-data/subjects --verbose
To generate the report in parallel::
$ mne report --path MNE-sample-data/ \
--info MNE-sample-data/MEG/sample/sample_audvis-ave.fif \
--subject sample --subjects-dir MNE-sample-data/subjects \
--verbose --jobs 6
For help on all the available options, do::
$ mne report --help
"""
import sys
import time
import mne
from mne.report import Report
from mne.utils import verbose, logger
@verbose
def log_elapsed(t, verbose=None):
"""Log elapsed time."""
logger.info('Report complete in %s seconds' % round(t, 1))
def run():
"""Run command."""
from mne.commands.utils import get_optparser, _add_verbose_flag
parser = get_optparser(__file__)
parser.add_option("-p", "--path", dest="path",
help="Path to folder who MNE-Report must be created")
parser.add_option("-i", "--info", dest="info_fname",
help="File from which info dictionary is to be read",
metavar="FILE")
parser.add_option("-c", "--cov", dest="cov_fname",
help="File from which noise covariance is to be read",
metavar="FILE")
parser.add_option("--bmin", dest="bmin",
help="Time at which baseline correction starts for "
"evokeds", default=None)
parser.add_option("--bmax", dest="bmax",
help="Time at which baseline correction stops for "
"evokeds", default=None)
parser.add_option("-d", "--subjects-dir", dest="subjects_dir",
help="The subjects directory")
parser.add_option("-s", "--subject", dest="subject",
help="The subject name")
parser.add_option("--no-browser", dest="no_browser", action='store_false',
help="Do not open MNE-Report in browser")
parser.add_option("--overwrite", dest="overwrite", action='store_false',
help="Overwrite html report if it already exists")
parser.add_option("-j", "--jobs", dest="n_jobs", help="Number of jobs to"
" run in parallel")
parser.add_option("-m", "--mri-decim", type="int", dest="mri_decim",
default=2, help="Integer factor used to decimate "
"BEM plots")
parser.add_option("--image-format", type="str", dest="image_format",
default='png', help="Image format to use "
"(can be 'png' or 'svg')")
_add_verbose_flag(parser)
options, args = parser.parse_args()
path = options.path
if path is None:
parser.print_help()
sys.exit(1)
info_fname = options.info_fname
cov_fname = options.cov_fname
subjects_dir = options.subjects_dir
subject = options.subject
image_format = options.image_format
mri_decim = int(options.mri_decim)
verbose = True if options.verbose is not None else False
open_browser = False if options.no_browser is not None else True
overwrite = True if options.overwrite is not None else False
n_jobs = int(options.n_jobs) if options.n_jobs is not None else 1
bmin = float(options.bmin) if options.bmin is not None else None
bmax = float(options.bmax) if options.bmax is not None else None
# XXX: this means (None, None) cannot be specified through command line
if bmin is None and bmax is None:
baseline = None
else:
baseline = (bmin, bmax)
t0 = time.time()
report = Report(info_fname, subjects_dir=subjects_dir,
subject=subject, baseline=baseline,
cov_fname=cov_fname, verbose=verbose,
image_format=image_format)
report.parse_folder(path, verbose=verbose, n_jobs=n_jobs,
mri_decim=mri_decim)
log_elapsed(time.time() - t0, verbose=verbose)
report.save(open_browser=open_browser, overwrite=overwrite)
mne.utils.run_command_if_main()
|
