[Mne_analysis] help
czx
chenzx_cqu at 163.com
Tue Dec 22 00:35:05 EST 2020
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> 1. Re: n_fft option for tfr_array_stockwell {Disarmed}
> (Alexandre Gramfort)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 21 Dec 2020 15:42:03 +0100
> From: Alexandre Gramfort <alexandre.gramfort at inria.fr>
> Subject: Re: [Mne_analysis] n_fft option for tfr_array_stockwell
> {Disarmed}
> To: Discussion and support forum for the users of MNE Software
> <mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
> <CADeotZrJBEVQY97NvJzK3GX=0zkiDv3tK6r3FOsW0MLePp9Y+w at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
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> hi,
>
> here are the lines that generate this behavior.
>
> https://secure-web.cisco.com/19bmNMoYnXLOkU_iFnakp_XeteNEgsBBxfAGwS0rF2CpZNdLrEeQ2Q7gkaBm6CPlzSZf0ojCFXZ9hmC1DsZAEgb0US11kbgMbsLoCOjXYEOf-NN97XCe29r1vUCh20gEOZLm2BIVUjGq3PJnp4npGEOWbrB5lG3fytl7LKURPdRZnu695xfBaNgSLPXjQqDRJ6MW6-NU8lSF9eSsZErLm6Xs_wM9LU9iGRhhtFMZfRgwj_W4Z4Ug6Ds8xnaQsostgCuEzh10kChT37jmHmXJKlQ/https%3A%2F%2Fgithub.com%2Fmne-tools%2Fmne-python%2Fblob%2Fmaster%2Fmne%2Ftime_frequency%2F_stockwell.py%23L26
>
> I read that "n_fft cannot be smaller than signal size".
>
> maybe simply the doc needs to be updated?
>
> HTH
> Alex
>
>
>> On Sun, Dec 20, 2020 at 6:32 PM Paul Fishback <fishbacp at mail.gvsu.edu>
>> wrote:
>> External Email - Use Caution
>> Alex,
>> I'm so sorry I left that out. Here's a snippet that includes that info as
>> well as plots the results. I set n_fft=500, but still received the warning,
>> RuntimeWarning: The input signal is shorter (5001) than "n_fft" (8192).
>> Applying zero padding..
>> import numpy as np
>> from scipy.signal import chirp
>> import matplotlib.pyplot as plt
>> from mne.time_frequency import tfr_array_stockwell
>> Nt=5000
>> time_length=10
>> t = np.linspace(0, time_length, Nt+1)
>> w = chirp(t, f0=12.5, f1=2.5, t1=10, method='linear')
>> y = np.expand_dims(w, axis=[0,1])
>> fmin = 0 # Hz
>> fmax = 25 # Hz
>> Fs = int(np.ceil(Nt/time_length))
>> st_power, itc,
>> freqs=tfr_array_stockwell(y,sfreq=Fs,fmin=fmin,fmax=fmax,n_fft=500)
>> extent = (t[0], t[-1], fmin, fmax)
>> fig, ax = plt.subplots(2, 1, sharex=True)
>> ax[0].plot(t, w)
>> ax[0].set(ylabel='amplitude')
>> ax[1].imshow(np.abs(st_power[0,:,:]), origin='lower', extent=extent)
>> ax[1].axis('tight')
>> ax[1].set(xlabel='time (s)', ylabel='frequency (Hz)')
>> plt.show()
>> On Sun, Dec 20, 2020 at 12:06 PM Alexandre Gramfort <
>> alexandre.gramfort at inria.fr> wrote:
>>> External Email - Use Caution
>>> hi Paul,
>>> can you share a full code snippet?
>>> Nt and time_length not defined
>>> Alex
>>> On Sat, Dec 19, 2020 at 9:42 PM Paul Fishback <fishbacp at mail.gvsu.edu>
>>> wrote:
>>>> External Email - Use Caution
>>>> Hello,
>>>> I'm interested in computing the Stockwell Transform of a simple
>>>> univariate time series. Because I already use MNE, I thought I'd
>>>> perform this task with the aid of the
>>>> tfr_array_stockwell command. However, I'm having a problem changing the
>>>> window length, n_fft.
>>>> As a simple "toy example," here's a chirp signal, where the frequency
>>>> decreases linearly from 12.5 to 2.5 Hz over a 10 second period:
>>>> from scipy.signal import chirp
>>>> from mne.time_frequency import tfr_array_stockwell
>>>> t = np.linspace(0, 10, 5001)
>>>> w = chirp(t, f0=12.5, f1=2.5, t1=10, method='linear')
>>>> y = np.expand_dims(w, axis=[0,1]) # Add dimensions to signal in order
>>>> to make a valid input for tfr_array_stockwell
>>>> fmin = 0
>>>> fmax = 25
>>>> Fs = int(np.ceil(Nt/time_length))
>>>> st_power, itc, freqs=tfr_array_stockwell(y,sfreq=Fs,fmin=fmin,fmax=fmax)
>>>> This works fine and the plotted results look great, but I do receive a
>>>> warning message indicating zero padding is being used. This is because the
>>>> signal length (5001)
>>>> is less than the default n_fft, which is 8192 in my case. (Since
>>>> 2^(12)=4096 < 5001 < 2^(13)=8192 )
>>>> However, if I change the default n_fft to something else, e.g. insert
>>>> n_fft=500 above, I still receive the same warning message.
>>>> Perhaps I'm missing something simple?
>>>> Thanks
>>>> Paul Fishback
>>>> --
>>>> Professor of Mathematics, Grand Valley State University
>>>> Past-President, Pi Mu Epsilon National Honorary Mathematics Society, Inc.
>>>> Department of Mathematics (MAK C-2-408)
>>>> Grand Valley State University
>>>> 1 Campus Dr.
>>>> Allendale, MI 49401
>>>> fishbacp at mail.gvsu.edu
>>>> 616.331.2040
>>>> 616.331.3120 (fax)
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>> --
>> Professor of Mathematics, Grand Valley State University
>> Past-President, Pi Mu Epsilon National Honorary Mathematics Society, Inc.
>> Department of Mathematics (MAK C-2-408)
>> Grand Valley State University
>> 1 Campus Dr.
>> Allendale, MI 49401
>> fishbacp at mail.gvsu.edu
>> 616.331.2040
>> 616.331.3120 (fax)
>> _______________________________________________
>> Mne_analysis mailing list
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