-
Notifications
You must be signed in to change notification settings - Fork 24
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Forward function Robinson Linear example
- Loading branch information
1 parent
8cec7bf
commit 1e737cd
Showing
1 changed file
with
195 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,195 @@ | ||
| # Reproducing Abeysuriya 2015 outputs and BrainTrak equations with the forward function | ||
|
|
||
| # Importage: | ||
|
|
||
| # os stuff | ||
| import os | ||
| import sys | ||
| sys.path.append('..') | ||
|
|
||
| # whobpyt stuff | ||
| import whobpyt | ||
| from whobpyt.datatypes import Parameter as par | ||
| from whobpyt.models.robinson import RobinsonLinModel, RobinsonLinParams | ||
|
|
||
| # python stuff | ||
| import numpy as np | ||
| import pandas as pd | ||
| import scipy.io | ||
| import pickle | ||
| import warnings | ||
| warnings.filterwarnings('ignore') | ||
| import math | ||
| import numpy as np | ||
| #neuroimaging packages | ||
| import mne | ||
|
|
||
| # viz stuff | ||
| import matplotlib.pyplot as plt | ||
|
|
||
| def parameter_set(pars): | ||
| if pars == 'EC': | ||
| # Eyes closed | ||
| params = RobinsonLinParams( Gei = par(-4.11), | ||
| Gee = par(2.070), | ||
| Ges = par(0.77), | ||
| Gsn = par(8.10), | ||
| Gse = par(7.77), | ||
| Gsr = par(-3.3), | ||
| Grs = par(0.2), | ||
| Gre = par(0.66), | ||
| alpha = par(83), | ||
| beta = par(769), | ||
| gammae = par(116), | ||
| t0 = par(0.085), | ||
| re = par(0.086), | ||
| phin = par(1e-5), | ||
| EMG = par(0), | ||
| kmax = par(4), | ||
| k0 = par(10), | ||
| Lx = par(0.5) | ||
| ) | ||
|
|
||
| if pars == 'EO': | ||
| # Eyes open | ||
| params = RobinsonLinParams( Gei = par(-13.22), | ||
| Gee = par(10.50), | ||
| Ges = par(1.21), | ||
| Gsn = par(14.23), | ||
| Gse = par(5.78), | ||
| Gsr = par(-2.83), | ||
| Grs = par(0.25), | ||
| Gre = par(0.85), | ||
| alpha = par(83), | ||
| beta = par(769), | ||
| gammae = par(116), | ||
| t0 = par(0.085), | ||
| re = par(0.086), | ||
| phin = par(1e-5), | ||
| EMG = par(0), | ||
| kmax = par(4), | ||
| k0 = par(10), | ||
| Lx = par(0.5) | ||
| ) | ||
| if pars == 'REM': | ||
| # REM | ||
| params = RobinsonLinParams( Gei = par(-6.61), | ||
| Gee = par(5.87), | ||
| Ges = par(0.21), | ||
| Gsn = par(0.68), | ||
| Gse = par(0.66), | ||
| Gsr = par(-0.28), | ||
| Grs = par(4.59), | ||
| Gre = par(2.08), | ||
| alpha = par(45), | ||
| beta = par(185), | ||
| gammae = par(116), | ||
| t0 = par(0.085), | ||
| re = par(0.086), | ||
| phin = par(1e-5), | ||
| EMG = par(0), | ||
| kmax = par(4), | ||
| k0 = par(10), | ||
| Lx = par(0.5) | ||
| ) | ||
| if pars == 'S1': | ||
| # S1 | ||
| params = RobinsonLinParams( Gei = par(-8.30), | ||
| Gee = par(7.45), | ||
| Ges = par(0.31), | ||
| Gsn = par(3.90), | ||
| Gse = par(1.67), | ||
| Gsr = par(-0.40), | ||
| Grs = par(4.44), | ||
| Gre = par(7.47), | ||
| alpha = par(45), | ||
| beta = par(185), | ||
| gammae = par(116), | ||
| t0 = par(0.085), | ||
| re = par(0.086), | ||
| phin = par(1e-5), | ||
| EMG = par(0), | ||
| kmax = par(4), | ||
| k0 = par(10), | ||
| Lx = par(0.5) | ||
| ) | ||
| if pars == 'S2': | ||
| # S2 | ||
| params = RobinsonLinParams( Gei = par(-17.93), | ||
| Gee = par(16.8), | ||
| Ges = par(3.89), | ||
| Gsn = par(2.38), | ||
| Gse = par(0.07), | ||
| Gsr = par(-0.14), | ||
| Grs = par(8.33), | ||
| Gre = par(4.96), | ||
| alpha = par(45), | ||
| beta = par(185), | ||
| gammae = par(116), | ||
| t0 = par(0.085), | ||
| re = par(0.086), | ||
| phin = par(1e-5), | ||
| EMG = par(0), | ||
| kmax = par(4), | ||
| k0 = par(10), | ||
| Lx = par(0.5) | ||
| ) | ||
| if pars == 'SWS': | ||
| # SWS | ||
| params = RobinsonLinParams( Gei = par(-19.74), | ||
| Gee = par(19.52), | ||
| Ges = par(5.30), | ||
| Gsn = par(1.70), | ||
| Gse = par(0.22), | ||
| Gsr = par(-0.22), | ||
| Grs = par(1.35), | ||
| Gre = par(1.90), | ||
| alpha = par(45), | ||
| beta = par(185), | ||
| gammae = par(116), | ||
| t0 = par(0.085), | ||
| re = par(0.086), | ||
| phin = par(1e-5), | ||
| EMG = par(0), | ||
| kmax = par(4), | ||
| k0 = par(10), | ||
| Lx = par(0.5) | ||
| ) | ||
| if pars == 'Spindles': | ||
| # Spindles | ||
| params = RobinsonLinParams( Gei = par(-18.96), | ||
| Gee = par(18.52), | ||
| Ges = par(2.55), | ||
| Gsn = par(2.78), | ||
| Gse = par(0.73), | ||
| Gsr = par(-0.26), | ||
| Grs = par(16.92), | ||
| Gre = par(4.67), | ||
| alpha = par(45), | ||
| beta = par(185), | ||
| gammae = par(116), | ||
| t0 = par(0.085), | ||
| re = par(0.086), | ||
| phin = par(1e-5), | ||
| EMG = par(0), | ||
| kmax = par(4), | ||
| k0 = par(10), | ||
| Lx = par(0.5) | ||
| ) | ||
| return params | ||
|
|
||
| freq = np.linspace(1,60,200) | ||
| w1 = 2*math.pi*freq | ||
| options = ['EC','EO', 'REM', 'S1', 'S2', 'SWS', 'Spindles'] | ||
| for option in options: | ||
| params = parameter_set(option) | ||
| model = RobinsonLinModel(params) | ||
| P = model.forward(external=0, w1=w1) | ||
| plt.plot(freq,P/sum(P)) | ||
| plt.yscale("log") | ||
| plt.xscale("log") | ||
| plt.ylabel('Normalized Power (A.U.)') | ||
| plt.xlabel('Frequency (Hz)') | ||
| plt.legend(options) | ||
| plt.savefig('plot.png') | ||
| plt.title('Power spectra for different parameter sets') |