[DOC] Example for spectral connectivity methods comparing epochs and time

examples/spectral_connectivity_epoch_vs_time_simulated_data.py

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+"""
+======================================================================
+Contrasting the methods to calculate connectivity over epochs and time using simulated data
+======================================================================
+
+This example shows how to use the spectral connectivity measures using simulated data.
+
+Spectral connectivity is generally used to caculate connectivity between electrodes or regions in
+different frequency bands
+
+When there are multiple epochs for a session, like ERP data, the spectral_connectivity_epochs
+method can be used to infer the connectivity structure between channels across the epochs. It
+will return the connectivity over time estimated from all the epochs.
+
+When the connectivity is to be calculated on a single trial basis across the channels,
+the spectral_connectivity_time can be used.
+"""
+# Author: Divyesh Narayanan <divyesh.narayanan@gmail.com>
+#
+# License: BSD (3-clause)
+
+import numpy as np
+import mne
+from mne_connectivity import spectral_connectivity_epochs, spectral_connectivity_time
+from matplotlib import pyplot as plt
+print(__doc__)
+
+###############################################################################
+
+# Generate some data
+n_epochs = 2
+n_channels = 3
+n_samples = 1000
+sfreq = 250
+time = np.arange(n_samples)/sfreq
+# 4 secs
+
+# Things I tried
+# 1 epoch - all connectivity values give 1
+# Should serve as useful warning. All give 1 when the channels values are different but there is
+# only one epoch
+
+# multiple epochs - over epochs returns 1 when the connectivity between 2 channels are 1 in all
+# the epochs. Otherwise it is some form of estimate across the epochs. Not exactly the average of
+# the single epoch connectivity values.
+
+# Simulating data
+rng = np.random.RandomState(0)
+x1 = rng.rand(1, 1, n_samples)
+x2 = np.sin(2*np.pi*10*time)
+x3 = np.sin(2*np.pi*15*time)
+
+data = np.zeros((n_epochs,n_channels,n_samples))
+data[0,0,:] = x1
+data[0,1,:] = x2
+data[0,2,:] = x2 # x3
+
+# Same value for each channel in all the epochs
+# for i in range(n_epochs):
+#     data[i] = data[0]
+
+# Different values in different epochs
+data[1,0,:] = x1
+data[1,1,:] = x3
+data[1,2,:] = x3
+
+# Create epochs object for mne compatibility
+ch_names = ["T1","T2","T3"] # random names
+info = mne.create_info(ch_names, sfreq, ch_types="eeg")
+data_epoch = mne.EpochsArray(data,info)
+
+# Visualize the data
+data_epoch.plot(scalings=2)
+
+# Calculate coh over epochs/trials
+con_Epoch = spectral_connectivity_epochs(data_epoch, method="coh",
+    mode="cwt_morlet", sfreq=sfreq, cwt_freqs=np.array([10]))
+
+c_ep = con_Epoch.get_data(output='dense').squeeze(2) # squeezing freq ind since only one freq
+# average over time
+print(c_ep.mean(2))
+
+con_epoch = con_Epoch.get_data(output="raveled")
+plt.plot(con_epoch.squeeze(1).T)
+plt.show()
+
+# Calculating time-resolved spectral connectivity for each epoch
+con_Time = spectral_connectivity_time(data_epoch, method="coh",
+    mode="cwt_morlet", sfreq=sfreq, freqs=10)
+
+con_time = con_Time.get_data("raveled")
+con_time = con_time.squeeze(2) # removing the freq axis
+c_t1 = con_time[0]
+plt.plot(c_t1.T)
+plt.show()
+
+c_t2 = con_time[1]
+plt.plot(c_t2.T)
+plt.show()
+
+c_ti = con_Time.get_data('dense')
+c_ti = c_ti.squeeze(3)
+a = c_ti[0]
+b = c_ti[1]
+print(a.mean(2))
+print(b.mean(2))
+
+# other testing to compare with epochs method
+print((a+b).mean(2)/2)
+print((a.mean(2)+b.mean(2))/2)
+
+print()