[Mne_analysis] cwt and visualization

JR KING jeanremi.king at gmail.com
Fri Jul 15 14:13:14 EDT 2016
Search archives:

This is a matplotlib issue not an MNE one.

Look for the 'extent' parameter in plt.imshow or plt.matshow(), and set the
ticks with axis.set_xticks() axis.set_ticklabels()

HTH

JR

On 15 July 2016 at 14:04, Nico Adelhöfer <nico.adelhoefer at st.ovgu.de> wrote:

> Hello Jean-Rémi,
>
> thanks a lot! The code for cwt_morlet you provided worked. However,
> the y-axis labeling doesn't show the frequencies but the position of
> the analyzed frequency in the array. For example:
>
> when freqs = [0, 20, 60], then the y-axis will be labeled 0, 1, 2
> instead of 0, 20, 60.
>
> Is there a way around it? While at this issue, the x-axis shows
> seconds*sfreq, but I'd like to be labeled as seconds.
>
> In other words: Is there a way to change the axis labeling without
> changing the content?
>
> I hope you can help me with this one.
>
> Thanks,
> Nico
>
>
>
> Quoting JR KING <jeanremi.king at gmail.com>:
>
> > Hi Nico,
> >
> > You can check how to apply and plot time frequency analyses in this
> example:
> >
> http://martinos.org/mne/stable/auto_examples/time_frequency/plot_time_frequency_simulated.html
> >
> > The main function boils down to:
> >
> > import numpy as np
> > from mne.time_frequency import tfr_morlet
> > freqs = np.linspace(5, 45, 20)  # an array of floats
> > power = tfr_morlet(epochs, freqs=freqs, n_cycles=5, return_itc=False)
> > power.plot([0])
> >
> >
> > If you wish to use arrays directly, instead of mne `Epochs` objects as
> > above, you can indeed use cwt_morlet:
> >
> > import numpy as np
> > import matplotlib.pyplot as plt
> > from mne.time_frequency import cwt_morlet
> > n_signal, n_time = 10, 10000
> > X = np.random.rand(n_signal, n_time)
> > tfr = cwt_morlet(X, sfreq=1000, freqs = np.linspace(5, 45, 20), decim=10)
> > power = np.abs(tfr)
> > channel = 5
> > plt.matshow(power[channel], origin='lower', cmap='viridis',
> aspect='auto')
> > plt.show()
> >
> > Hope that helps,
> >
> > Best,
> >
> > Jean-Rémi
> >
> >
> > On 13 July 2016 at 13:36, Nico Adelhöfer <nico.adelhoefer at st.ovgu.de>
> wrote:
> >
> >> Hello,
> >>
> >> I'm new to this mailing list and to MNE. I think so far it is really
> great!
> >>
> >> I have a few questions concerning the usage of the cwt_morlet
> >> function; I want to plot a continuous wavelet transform from a single
> >> EEG channel. I have a raw multi-channel .fif file, approximately 300s
> >> long with a sampling frequency of 512 Hz. I'm interested in a
> >> frequency range of approximately 0-45 Hz. How can I achieve this in
> >> the simplest way possible? Specifically,
> >>
> >> 1. what datatype is the first parameter (X)? I tried the variable from
> >> read_raw_fif, but that gives me "'tuple' object has no attribute
> >> 'shape'". I also tried raw[4][0], which seems to work. But is this
> >> really the correct approach?
> >> 2. is freqs simply a list of integers with the frequencies of
> >> interest? If the length is > 1, I get a Value Error ("Maximum allowed
> >> size exceeded"). Does this mean I have to resample my raw data until
> >> it works?
> >> 3. when it worked, it created an np.ndarray with numbers with complex
> >> parts. Do I see it correctly that the complex parts show the phase
> >> while the real part shows the power value?
> >> 4. how can I visualize the result?
> >>
> >> Sorry for these basic questions. Help would be much appreciated!
> >>
> >> Nico
> >>
> >> _______________________________________________
> >> 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.
> >>
> >>
>
>
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20160715/1b3e8253/attachment.html 


More information about the Mne_analysis mailing list