ivneuro.delta_coherence
A module with delta_coherence function.
Functions
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Calculate the coherence between 2 signals at a experimental interval of time of interest (exp_interval), at a baseline interval of time (baseline), and the difference betrween the spectral at the experimental interval and the baseline. |
Module Contents
- ivneuro.delta_coherence.delta_coherence(contvar, exp_interval, baseline, lowest_freq=0, highest_freq=500, sample_subsamples=None, sampling_rate=None, nperseg=500, noverlap=400, nfft=2000)
Calculate the coherence between 2 signals at a experimental interval of time of interest (exp_interval), at a baseline interval of time (baseline), and the difference betrween the spectral at the experimental interval and the baseline.
This function is based on the coherence function of scipy.signal, wich uses Welch’s method. exp_interval and baseline must be lists of slices of the same lenght, when when the lists have more than one element each, the results are the averages across intervals (either coherence at exp_interval, coherence at baseline, or their difference). To calculate the difference of coherence between experimental interval and baseline, the function subtracts the coherence at baseline from the coherence at exp_interval, for each frequency and trial (pair of elements in interval and baseline).
- Parameters:
contvar (pandas.DataFrame) – Dataframe with continuous variables in each column, and timestamps as index.
exp_interval (list) – List of slices corresponding to experimental intervals to calculate coherence.
baseline (list) – List of slices corresponding to baseline intervals to calculate coherence.
lowest_freq (int or float, optional) – The lowest frequency to include in the coherence spectral. The default is 0.
highest_freq (int or float, optional) – The highest freq to include in the coherence spectral. The default is 500.
sample_subsamples (dict or None, optional) – When a dict, key must be sample names and values must be lists of subsample names, e.g.: {‘sample_A’:[‘subsample_A1’,’subsample_A2’…’subsample_An’], ‘sample_B’:[‘subsample_B1’,’subsample_B2’…’subsample_Bn’]…}. Coherences and coeherence differences will be averaged across pairs of subsamples corresponding to the same samples pair. It must only be used when contvar contains multiple replicates for each observation (e.g., local field potentials recorded with multiple wires of the same tetrode). If None, each column of contvar is treated as an independent sample, and therefore the results contain coherences for every pair of contvar columns. The default is None.
sampling_rate (int or float or None, optional) – Sampling rate of the continuous variables, wich is used in signal.coherence() function of the scipy package. If None, the sampling_rate is calculated using the inverse of the median difference between consecutive timestamps of the contvar’s index. The default is None.
nperseg (int, optional) – The nperseg parameter to enter to signal.coherence() function of the scipy package. Refer to scipy.signal.coherence in scipy manual for more information. The default is 500.
noverlap (int, optional) – The noverlap parameter to enter to signal.coherence() function of the scipy package. Refer to scipy.signal.coherence in scipy manual for more information. The default is 400.
nfft (int, optional) – The nfft parameter to enter to signal.coherence() function of the scipy package. Refer to scipy.signal.coherence in scipy manual for more information. The default is 2000.
- Returns:
coherence_exp_interval (pandas.DataFrame) – Coherence for each pair of variables (or pair of samples if sample_subsamples != None), at the experimental interval. Variable names (or sample names) as 2-levels columns (one level for each member of the pair) and frequency as index.
power_baseline (pandas.DataFrame) – Coherence for each pair of variables (or pair of samples if sample_subsamples != None), at the baseline interval. Variable names (or sample names) as 2-levels columns (one level for each member of the pair) and frequency as index.
delta_coherence (pandas.DataFrame) – Difference of coherence between experimental interval and baseline interval, for each pair of variables (or pair of samples if sample_subsamples != None). Variable names (or sample names) as 2-levels columns (one level for each member of the pair) and frequency as index.
Examples
Create event, intervals and signals.
>>> import ivneuro as ivn >>> import pandas as pd >>> event = [*range(30,300, 30)] # Events >>> # Make intervals >>> exp_interval = ivn.make_intervals(event, 0, 2) # Experimental interval >>> baseline = ivn.make_intervals(event, -6, -4) #Baseline interval >>> # Create signals >>> signal1 = ivn.generate_signal(300, event, 30, burst_amplitude=0.06, seed=15) >>> signal2 = ivn.generate_signal(300, event, 30.2, burst_amplitude=0.13, seed = 30) >>> signal3 = ivn.generate_signal(300, event, 80, burst_amplitude=0.05, seed = 50) >>> signals = pd.concat([signal1, signal2, signal3], axis = 1)
Calculate coherence and delta coherence between intervals with delta_coherence function.
>>> exp_coh, baseline_coh, delta_coh = ivn.delta_coherence(signals, exp_interval, baseline) >>> delta_coh.head() Signal 30Hz Signal 30.2Hz Signal 30.2Hz Signal 80Hz Signal 80Hz 0.0 -0.079927 -0.024874 0.068144 0.5 -0.045909 -0.058171 0.043984 1.0 -0.019668 -0.081587 0.025753 1.5 -0.015086 -0.076264 0.023711 2.0 -0.016446 -0.059058 0.025952
Set signal1 and signal2 as replicates of sample1, and signal3 as sample2.
>>> # Make dictionary to group replicates of each sample >>> sample_subsamples = {'sample1' : ['Signal 30Hz', 'Signal 30.2Hz'], 'sample2':['Signal 80Hz']} >>> # Calculate coherence and delta coherence >>> exp_coh, baseline_coh, delta_coh = ivn.delta_coherence(signals, exp_interval, baseline, sample_subsamples = sample_subsamples) >>> delta_coh.head() sample1 sample1 sample2 0.0 -0.079927 0.021635 0.5 -0.045909 -0.007093 1.0 -0.019668 -0.027917 1.5 -0.015086 -0.026276 2.0 -0.016446 -0.016553