[Mne_analysis] mn.time_frequency.tfr_array_stockwell
Paul Fishback
fishbacp at mail.gvsu.edu
Thu Jul 9 16:47:39 EDT 2020
External Email - Use Caution
Thanks again. Now, a different message appears:
Warning (from warnings module):
File "/Users/fishbacp/Desktop/Python_Sabbatical/plot_stockwell.py", line
188
st_power, itc, freqs = mn.time_frequency.tfr_array_stockwell(signal,Fs,
fmin=min_freq, fmax=max_freq)
RuntimeWarning: The input signal is shorter (123200) than "n_fft" (131072).
Applying zero padding.
This warning message comes from the function, _check_input_st.
I looked at this function separately and, while n_times is correct, n_fft
is larger, even if I simply use the default value
in mn.time_frequency.tfr_array_stockwell.
Eventually, mn.time_frequency.tfr_array_stockwell runs and I return to the
shell (in Idle); however I inserted a line to print st_power and freqs,
which came back empty
Paul
On Thu, Jul 9, 2020 at 3:21 PM Eric Larson <larson.eric.d at gmail.com> wrote:
> External Email - Use Caution
>
> For now you can work around it by doing `data = data[np.newaxis]` to make
> it of shape `(n_epochs, n_channels, n_times)` (which appears to be what the
> function actually wants). Can you open an issue on the MNE-Python issue
> tracker so that we don't forget to fix this? It should really just operate
> along the last dimension and not assume that's 2.
>
> Eric
>
>
> On Thu, Jul 9, 2020 at 3:18 PM Paul Fishback <fishbacp at mail.gvsu.edu>
> wrote:
>
>> External Email - Use Caution
>>
>> Hi Alex,
>>
>> Thanks so much for responding to my message. I tried what you suggested,
>> but I'm still getting an error:
>>
>> raw=mn.io.read_raw_edf('/Users/fishbacp/Desktop/11.edf', preload=True)
>> Fs=raw.info['sfreq']
>>
>> data,times=raw[:,:]
>> print('data: '+str(data.shape)) #This indicates the data shape is
>> 46-by-123200, which makes sense for my recording: 46 channels, 10 minute
>> time length, and sampling frequency 200 Hz.
>>
>> signal = data[[0]]
>> print('signal: '+str(signal.shape)) # This produces 1-by-123200 for
>> this channel
>> min_freq = 5
>> max_freq = 100
>> st_power, itc, freqs = mn.time_frequency.tfr_array_stockwell(signal,Fs,
>> fmin=min_freq, fmax=max_freq)
>>
>> This is the error message:
>>
>> Traceback (most recent call last):
>> File "/Users/fishbacp/Desktop/Python_Sabbatical/plot_stockwell.py",
>> line 145, in <module>
>> st_power, itc, freqs =
>> mn.time_frequency.tfr_array_stockwell(signal,Fs, fmin=min_freq,
>> fmax=max_freq)
>> File
>> "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/mne/time_frequency/_stockwell.py",
>> line 172, in tfr_array_stockwell
>> n_out = data.shape[2] // decim + bool(data.shape[2] % decim)
>> IndexError: tuple index out of range
>>
>> Lines-171-173 in the script, located at
>> https://github.com/mne-tools/mne-python/blob/maint/0.20/mne/time_frequency/_stockwell.py#L101-L199 are
>> as follows:
>>
>> [image: image.png]
>>
>> I don't see how data.shape[2] could even be defined if data lacks a third
>> dimension.
>>
>> I'm not wed to using this implementation of the stockwell transform. I
>> tried it first because I enjoy using MNE, but if you know of other good
>> implementations, I would enjoy hearing about them.
>>
>> Many, many thanks.
>>
>> Best,
>>
>> Paul
>>
>> On Thu, Jul 9, 2020 at 10:38 AM Alexandre Gramfort <
>> alexandre.gramfort at inria.fr> wrote:
>>
>>> External Email - Use Caution
>>>
>>> hi Paul,
>>>
>>> try:
>>>
>>> import numpy as np
>>> import mne
>>>
>>> raw = mne.io.read_raw_edf('/Users/fishbacp/Desktop/EEG_file.edf',
>>> preload=True)
>>> Fs = raw.info['sfreq']
>>> data, times=raw[:, :]
>>> signal = data[[0]]
>>> min_freq = 5
>>> max_freq = 100
>>> st_power, itc, freqs = mne.time_frequency.tfr_array_stockwell(signal,
>>> Fs, fmin=min_freq, fmax=max_freq)
>>>
>>> --
>>>
>>> signal must be a 2d array with dimensions: channel x time
>>>
>>> Alex
>>>
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>>> Mne_analysis mailing list
>>> Mne_analysis at nmr.mgh.harvard.edu
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>>>
>>
>>
>> --
>> Professor of Mathematics, Grand Valley State University
>>
>> 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
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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