requesting support - Power Spectra Interactive model

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Pragha

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Aug 17, 2021, 9:33:45 AMAug 17
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Dear TVB user,
I tried to calculate the power spectrum for the simulated data. Please find the attachment of my code.  I guess that I have defined all the required parameters but I do get errors while executing. Could some help where I went wrong?

Thank you,
Pragha
PowerSpectrum.pdf

Julie Courtiol

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Aug 17, 2021, 12:14:35 PMAug 17
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Dear Pragha,

The error informs you there is a shape problem with your data. Indeed, the TimeSerieRegion requires data in TVB format, i.e., 4D:

TAVG = TAVG[:, numpy.newaxis,:,numpy.newaxis]

Then, you can define

tsr.data = TAVG

Best,
Julie


Dr. Julie Courtiol
Scientific Lab Manager
Brain Simulation Section 
Charité Universitätsmedizin Berlin

Le 17 août 2021 à 15:33, Pragha <praa...@gmail.com> a écrit :


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<PowerSpectrum.pdf>

Pragha

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Aug 19, 2021, 8:43:45 AMAug 19
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Thank you. But it is showing the same error after converting the data into 4d. Do I need to check something ?

Julie Courtiol

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Aug 19, 2021, 10:30:12 AMAug 19
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Hi Pragha,

Try with this:

psi = ps_int.PowerSpectraInteractive()
psi.time_series=tsr
psi.period=0.001 #s

Be careful, the tsr sampling period is in ms.

Also, I advise you to separate your code in several cells to debug it and see where the error is.

---
Best regards,

Julie Courtiol





Julie Courtiol

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Aug 19, 2021, 4:04:40 PMAug 19
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Dear Pragha,

I had a deeper look into the code and found why the function (psi.configure) returns an error. I will give you the correction below (and the file to replace in your tvb folder).

See also some comments on your code.

[4]: You don't need to define S, C and dS.
They were only defined for building the phase plane in the tutorial. Here, as you can see you are not using these variables.

[5] Úseless as you are already running the simulation in the previous cell (>> (time, data), = sim.run())

[14] The sampling period is wrong. It is also in ms!

#Create a tvb TimeSeries object
tsr = TimeSeriesRegion(connectivity=con,
                       data=tavg,
                       sample_period=sim.monitors[0].period)
tsr.configure()

Also, to identify the error easily, I advise you to separate your code lines in separated cells.

For psi, you need to define it as the TimeSeries above:

#Create and launch the interactive visualiser
psi = ps_int.PowerSpectraInteractive()
psi.time_series=tsr

For the psi.configure(), I have implemented some corrections in the code
line 159: convert the sampling period in second for further use 
lines 328 and 352: seg_tptsstarts and nfreq are float and need to be converted in integer

When you then run your notebook, you should obtain a similar figure

PS_Pragha.png

Best,
Julie
---
Best regards,

Julie Courtiol




power_spectra_interactive.py

Pragha

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Aug 20, 2021, 8:43:11 AMAug 20
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Dear Dr. Julie Courtiol,
Many thanks for the support. 

Best,
Pragha


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