[Mne_analysis] trouble filtering ECG channel data
Jon Houck
jhouck at mrn.org
Fri Apr 22 16:24:05 EDT 2016
Hi Megan,
Notch_filter will only filter the MEG/EEG channels unless you specify some
channels using picks. You could do something like:
picks = mne.pick_types(raw.info, ecg=True)
raw.notch_filter(freqs = np.arange(60, 241, 60), picks=picks )
which will then find and filter the ECG data. I think if you added that to
your notch_filter and added the picks lines for EEG and ECG in your if
statement, you'd be good to go.
Jon
On Fri, Apr 22, 2016 at 11:49 AM, Megan Schendel <mschendel at mrn.org> wrote:
> Hello all,
> I have written a little script that pulls the ECG channel data out of the
> fif file and writes a text file to pass to QRSTool (free external software).
>
> But I have some fif files with the ECG data on channel EEG063 and some on
> ECG063. My script works on the channel labeled EEG063, but it fails for
> the ECG063. Specifically, I use raw.pick to get the channel I want. I can
> plot it fine, it returns type mne.io.fiff.raw.RawFIF, but when I try to
> filter using raw.notch_filter, I get a weird error. See below for the
> relevant snippets of code and outputs.
>
> I just discovered the raw.set_channel_types method and wonder if that
> could help, but I'm having trouble getting the syntax right...
>
> (also, btw, mne.sys.info() gives me an error... so I can't tell what mne
> version I'm running. I did attempt git pull master origin and I'm still
> having the problem with raw.filter.)
>
> Thanks much in advance,
> Megan
>
> [mschendel at XXXX ~]$ ipython
> Python 3.5.1 |Anaconda 2.5.0 (64-bit)| (default, Dec 7 2015, 11:16:01)
> In [1]: import mne
> In [2]: mne.sys.info()
> ---------------------------------------------------------------------------
> AttributeError Traceback (most recent call last)
> <ipython-input-2-aa9bd53b86f1> in <module>()
> ----> 1 mne.sys.info()
>
> AttributeError: module 'mne' has no attribute 'sys'
>
> #
> # Here is my io.Raw command... no trouble there...
> #
>
> In [21]: raw = io.Raw(infile, preload=True, verbose=None)
> # Cut all the io reporting...
>
> In [22]: if 'EEG063' in raw.ch_names:
> ....: raw_bits = raw.pick_channels(['EEG063'])
> ....: print ('Found EEG063 ')
> ....: elif 'ECG063' in raw.ch_names:
> ....: raw_bits = raw.pick_channels(['ECG063'])
> ....: print ('Found ECG063 ')
> ....:
> Found EEG063
>
> In [23]: raw.notch_filter(freqs = numpy.arange(60, 241, 60) )
> ---------------------------------------------------------------------------
> RuntimeError Traceback (most recent call last)
> <ipython-input-13-f5e5440dff87> in <module>()
> ----> 1 raw.notch_filter(freqs = numpy.arange(60, 241, 60) )
>
> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/lib/python3.5/site-packages/mne/io/base.py
> in notch_filter(self, freqs, picks, filter_length, notch_widths,
> trans_bandwidth, n_jobs, method, iir_params, mt_bandwidth, p_value, verbose)
>
> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/lib/python3.5/site-packages/mne/utils.py
> in verbose(function, *args, **kwargs)
> 549 finally:
> 550 set_log_level(old_level)
> --> 551 return function(*args, **kwargs)
> 552
> 553
>
> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/lib/python3.5/site-packages/mne/io/base.py
> in notch_filter(self, freqs, picks, filter_length, notch_widths,
> trans_bandwidth, n_jobs, method, iir_params, mt_bandwidth, p_value, verbose)
> 932 # let's be safe.
> 933 if len(picks) < 1:
> --> 934 raise RuntimeError('Could not find any valid
> channels for '
> 935 'your Raw object. Please
> contact the '
> 936 'MNE-Python developers.')
>
> RuntimeError: Could not find any valid channels for your Raw object.
> Please contact the MNE-Python developers.
>
> #
> # Try to remap channel to EEG type...
> #
> In [30]: raw_bits.set_channel_types(mapping = {'ECG063': ‘eeg’})
> File "<ipython-input-30-1c0e7f2a2c6d>", line 1
> raw_bits.set_channel_types(mapping = {'ECG063': ‘eeg’})
> ^
> SyntaxError: invalid character in identifier
>
>
>
> #
> # If I do the same with data that has channel labeled as EEG ...
> #
> In [5]: if 'EEG063' in raw.ch_names:
> raw_bits = raw.pick_channels(['EEG063'])
> print ('Found EEG063 ')
> elif 'ECG063' in raw.ch_names:
> raw_bits = raw.pick_channels(['ECG063'])
> print ('Found ECG063 ')
> ...:
> Found EEG063
> In [6]: raw_bits.notch_filter(freqs = numpy.arange(60, 241, 60) )
>
> In [7]: raw_bits.notch_filter(freqs = numpy.arange(60, 241, 60) )
> # no complaints...
>
>
>
> MEG Technician
> The Mind Research Network
> 1101 Yale Blvd. NE
> Albuquerque, New Mexico 87106
> 505-272-3304
>
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
--
Jon M. Houck, Ph.D.
Assistant Professor of Translational Neuroscience
Mind Research Network
1101 Yale Blvd. NE
Albuquerque, NM 87106
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20160422/d87378d8/attachment-0001.html
More information about the Mne_analysis
mailing list