2748

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Build # 2748

Build Type

Pull #1580

travis-ci

Committed by

kevinjos

Commit Message

<a href="https://github.com/mne-tools/mne-python/commit/<a class=hub.com/mne-tools/mne-python/commit/<a class="double-link" href="https://git"><a class=hub.com/mne-tools/mne-python/commit/34f5ba3aa63a238d8718ce81e4e046ada3fc9650">34f5ba3aa<a href="https://github.com/mne-tools/mne-python/commit/34f5ba3aa63a238d8718ce81e4e046ada3fc9650">&lt;a href=&quot;https://github.com/mne-tools/mne-python/commit/34f5ba3aa63a238d8718ce81e4e046ada3fc9650">&quot;&gt;Revert &amp;quot;Merge branch &amp;#39;master&amp;#39; into issue1537&amp;quot;

This reverts commit &lt;/a&gt;&lt;a class=&quot;double-link&quot; href=&quot;https://github.com/mne-tools/mne-python/commit/&lt;a class=&quot;double-link&quot; href=&quot;https://github.com/mne-tools/mne-python/commit/62e04f9722f6a8fde2b888d4d2aa68616f69aa78">62e04f972</a>">62e04f972</a><a href="https://github.com/mne-tools/mne-python/commit/34f5ba3aa63a238d8718ce81e4e046ada3fc9650">, reversing
changes made to </a><a class="double-link" href="https://github.com/mne-tools/mne-python/commit/<a class="double-link" href="https://github.com/mne-tools/mne-python/commit/18a3423ad75fa49957bfcfb94309d5a40718970b">18a3423ad">18a3423ad.

Pull Request Pull Request #1580: ICEauthority test failure, download sample data, vim/emacs to IDEs

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26.67

/mne/commands/mne_clean_eog_ecg.py

#!/usr/bin/env python
"""Clean a raw file from EOG and ECG artifacts with PCA (ie SSP)
"""
from __future__ import print_function

# Authors : Dr Engr. Sheraz Khan,  P.Eng, Ph.D.
#           Engr. Nandita Shetty,  MS.
#           Alexandre Gramfort, Ph.D.


import os
import sys

import mne


def clean_ecg_eog(in_fif_fname, out_fif_fname=None, eog=True, ecg=True,
                  ecg_proj_fname=None, eog_proj_fname=None,
                  ecg_event_fname=None, eog_event_fname=None, in_path='.'):
    """Clean ECG from raw fif file

    Parameters
    ----------
    in_fif_fname : string
        Raw fif File
    eog_event_fname : string
        name of EOG event file required.
    eog : bool
        Reject or not EOG artifacts.
    ecg : bool
        Reject or not ECG artifacts.
    ecg_event_fname : string
        name of ECG event file required.
    in_path :
        Path where all the files are.
    """
    if not eog and not ecg:
        raise Exception("EOG and ECG cannot be both disabled")

    # Reading fif File
    raw_in = mne.io.Raw(in_fif_fname)

    if in_fif_fname.endswith('_raw.fif') or in_fif_fname.endswith('-raw.fif'):
        prefix = in_fif_fname[:-8]
    else:
        prefix = in_fif_fname[:-4]

    if out_fif_fname is None:
        out_fif_fname = prefix + '_clean_ecg_eog_raw.fif'
    if ecg_proj_fname is None:
        ecg_proj_fname = prefix + '_ecg_proj.fif'
    if eog_proj_fname is None:
        eog_proj_fname = prefix + '_eog_proj.fif'
    if ecg_event_fname is None:
        ecg_event_fname = prefix + '_ecg-eve.fif'
    if eog_event_fname is None:
        eog_event_fname = prefix + '_eog-eve.fif'

    print('Implementing ECG and EOG artifact rejection on data')

    if ecg:
        ecg_events, _, _ = mne.preprocessing.find_ecg_events(raw_in)
        print("Writing ECG events in %s" % ecg_event_fname)
        mne.write_events(ecg_event_fname, ecg_events)

        print('Computing ECG projector')

        command = ('mne_process_raw --cd %s --raw %s --events %s --makeproj '
                   '--projtmin -0.08 --projtmax 0.08 --saveprojtag _ecg_proj '
                   '--projnmag 2 --projngrad 1 --projevent 999 --highpass 5 '
                   '--lowpass 35 --projmagrej 4000  --projgradrej 3000'
                   % (in_path, in_fif_fname, ecg_event_fname))
        st = os.system(command)

        if st != 0:
            print("Error while running : %s" % command)

    if eog:
        eog_events = mne.preprocessing.find_eog_events(raw_in)
        print("Writing EOG events in %s" % eog_event_fname)
        mne.write_events(eog_event_fname, eog_events)

        print('Computing EOG projector')

        command = ('mne_process_raw --cd %s --raw %s --events %s --makeproj '
                   '--projtmin -0.15 --projtmax 0.15 --saveprojtag _eog_proj '
                   '--projnmag 2 --projngrad 2 --projevent 998 --lowpass 35 '
                   '--projmagrej 4000  --projgradrej 3000'
                   % (in_path, in_fif_fname, eog_event_fname))

        print('Running : %s' % command)

        st = os.system(command)
        if st != 0:
            raise ValueError('Problem while running : %s' % command)

    if out_fif_fname is not None:
        # Applying the ECG EOG projector
        print('Applying ECG EOG projector')

        command = ('mne_process_raw --cd %s --raw %s '
                   '--proj %s --projoff --save %s --filteroff'
                   % (in_path, in_fif_fname, in_fif_fname, out_fif_fname))
        command += ' --proj %s --proj %s' % (ecg_proj_fname, eog_proj_fname)

        print('Command executed: %s' % command)

        st = os.system(command)

        if st != 0:
            raise ValueError('Pb while running : %s' % command)

        print('Done removing artifacts.')
        print("Cleaned raw data saved in: %s" % out_fif_fname)
        print('IMPORTANT : Please eye-ball the data !!')
    else:
        print('Projection not applied to raw data.')


def run():
    from mne.commands.utils import get_optparser

    parser = get_optparser(__file__)

    parser.add_option("-i", "--in", dest="raw_in",
                      help="Input raw FIF file", metavar="FILE")
    parser.add_option("-o", "--out", dest="raw_out",
                      help="Output raw FIF file", metavar="FILE",
                      default=None)
    parser.add_option("-e", "--no-eog", dest="eog", action="store_false",
                      help="Remove EOG", default=True)
    parser.add_option("-c", "--no-ecg", dest="ecg", action="store_false",
                      help="Remove ECG", default=True)

    options, args = parser.parse_args()

    if options.raw_in is None:
        parser.print_help()
        if is_main:
            sys.exit(1)
        return

    raw_in = options.raw_in
    raw_out = options.raw_out
    eog = options.eog
    ecg = options.ecg

    clean_ecg_eog(raw_in, raw_out, eog=eog, ecg=ecg)


is_main = (__name__ == '__main__')
if is_main:
    run()

1	#!/usr/bin/env python
2	"""Clean a raw file from EOG and ECG artifacts with PCA (ie SSP)	5✔
3	"""
4	from __future__ import print_function	5✔
5
6	# Authors : Dr Engr. Sheraz Khan, P.Eng, Ph.D.
7	# Engr. Nandita Shetty, MS.
8	# Alexandre Gramfort, Ph.D.
9
10
11	import os	5✔
12	import sys	5✔
13
14	import mne	5✔
15
16
17	def clean_ecg_eog(in_fif_fname, out_fif_fname=None, eog=True, ecg=True,	5✔
18	ecg_proj_fname=None, eog_proj_fname=None,
19	ecg_event_fname=None, eog_event_fname=None, in_path='.'):
20	"""Clean ECG from raw fif file
21
22	Parameters
23	----------
24	in_fif_fname : string
25	Raw fif File
26	eog_event_fname : string
27	name of EOG event file required.
28	eog : bool
29	Reject or not EOG artifacts.
30	ecg : bool
31	Reject or not ECG artifacts.
32	ecg_event_fname : string
33	name of ECG event file required.
34	in_path :
35	Path where all the files are.
36	"""
37	if not eog and not ecg:	×
38	raise Exception("EOG and ECG cannot be both disabled")	×
39
40	# Reading fif File
41	raw_in = mne.io.Raw(in_fif_fname)	×
42
43	if in_fif_fname.endswith('_raw.fif') or in_fif_fname.endswith('-raw.fif'):	×
44	prefix = in_fif_fname[:-8]	×
45	else:
46	prefix = in_fif_fname[:-4]	×
47
48	if out_fif_fname is None:	×
49	out_fif_fname = prefix + '_clean_ecg_eog_raw.fif'	×
50	if ecg_proj_fname is None:	×
51	ecg_proj_fname = prefix + '_ecg_proj.fif'	×
52	if eog_proj_fname is None:	×
53	eog_proj_fname = prefix + '_eog_proj.fif'	×
54	if ecg_event_fname is None:	×
55	ecg_event_fname = prefix + '_ecg-eve.fif'	×
56	if eog_event_fname is None:	×
57	eog_event_fname = prefix + '_eog-eve.fif'	×
58
59	print('Implementing ECG and EOG artifact rejection on data')	×
60
61	if ecg:	×
62	ecg_events, _, _ = mne.preprocessing.find_ecg_events(raw_in)	×
63	print("Writing ECG events in %s" % ecg_event_fname)	×
64	mne.write_events(ecg_event_fname, ecg_events)	×
65
66	print('Computing ECG projector')	×
67
68	command = ('mne_process_raw --cd %s --raw %s --events %s --makeproj '	×
69	'--projtmin -0.08 --projtmax 0.08 --saveprojtag _ecg_proj '
70	'--projnmag 2 --projngrad 1 --projevent 999 --highpass 5 '
71	'--lowpass 35 --projmagrej 4000 --projgradrej 3000'
72	% (in_path, in_fif_fname, ecg_event_fname))
73	st = os.system(command)	×
74
75	if st != 0:	×
76	print("Error while running : %s" % command)	×
77
78	if eog:	×
79	eog_events = mne.preprocessing.find_eog_events(raw_in)	×
80	print("Writing EOG events in %s" % eog_event_fname)	×
81	mne.write_events(eog_event_fname, eog_events)	×
82
83	print('Computing EOG projector')	×
84
85	command = ('mne_process_raw --cd %s --raw %s --events %s --makeproj '	×
86	'--projtmin -0.15 --projtmax 0.15 --saveprojtag _eog_proj '
87	'--projnmag 2 --projngrad 2 --projevent 998 --lowpass 35 '
88	'--projmagrej 4000 --projgradrej 3000'
89	% (in_path, in_fif_fname, eog_event_fname))
90
91	print('Running : %s' % command)	×
92
93	st = os.system(command)	×
94	if st != 0:	×
95	raise ValueError('Problem while running : %s' % command)	×
96
97	if out_fif_fname is not None:	×
98	# Applying the ECG EOG projector
99	print('Applying ECG EOG projector')	×
100
101	command = ('mne_process_raw --cd %s --raw %s '	×
102	'--proj %s --projoff --save %s --filteroff'
103	% (in_path, in_fif_fname, in_fif_fname, out_fif_fname))
104	command += ' --proj %s --proj %s' % (ecg_proj_fname, eog_proj_fname)	×
105
106	print('Command executed: %s' % command)	×
107
108	st = os.system(command)	×
109
110	if st != 0:	×
111	raise ValueError('Pb while running : %s' % command)	×
112
113	print('Done removing artifacts.')	×
114	print("Cleaned raw data saved in: %s" % out_fif_fname)	×
115	print('IMPORTANT : Please eye-ball the data !!')	×
116	else:
117	print('Projection not applied to raw data.')	×
118
119
120	def run():	5✔
121	from mne.commands.utils import get_optparser	5✔
122
123	parser = get_optparser(__file__)	5✔
124
125	parser.add_option("-i", "--in", dest="raw_in",	5✔
126	help="Input raw FIF file", metavar="FILE")
127	parser.add_option("-o", "--out", dest="raw_out",	5✔
128	help="Output raw FIF file", metavar="FILE",
129	default=None)
130	parser.add_option("-e", "--no-eog", dest="eog", action="store_false",	5✔
131	help="Remove EOG", default=True)
132	parser.add_option("-c", "--no-ecg", dest="ecg", action="store_false",	5✔
133	help="Remove ECG", default=True)
134
135	options, args = parser.parse_args()	5✔
136
137	if options.raw_in is None:	5✔
138	parser.print_help()	5✔
139	if is_main:	5✔
140	sys.exit(1)	×
141	return	5✔
142
143	raw_in = options.raw_in	×
144	raw_out = options.raw_out	×
145	eog = options.eog	×
146	ecg = options.ecg	×
147
148	clean_ecg_eog(raw_in, raw_out, eog=eog, ecg=ecg)	×
149
150
151	is_main = (__name__ == '__main__')	5✔
152	if is_main:	5✔
153	run()	×

mne-tools / mne-python / 2748

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