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Note Filter Example

Import streaming EEG data into Python using read_block
Filter around behavioral events that were timestamped by the user using the Run-time Notes feature in Synapse, using epoc_filter
Plot each occurrence in a subplot organized by Note type
Good for sleep scoring and behavioral discrimination

Housekeeping

Import the tdt package and other python packages we care about

# magic for Jupyter
%matplotlib inline

import matplotlib.pyplot as plt  # standard Python plotting library
import numpy as np

import tdt

Importing the Data

This example uses our example data sets. To import your own data, replace BLOCK_PATH with the full path to your own data block.

In Synapse, you can find the block path in the database. Go to Menu → History. Find your block, then Right-Click → Copy path to clipboard.

tdt.download_demo_data()
BLOCK_PATH = 'data/Subject1-180426-120951'

demo data ready

Set up the variables for the data you want to extract.

We will extract channel 1 from the EEG1 stream data store.

STORE = 'EEG1'
CHANNEL = 1
ONSET = [-3] # relative onset, in seconds, from the note timestamp

Now read the specified data from our block into a Python structure

data = tdt.read_block(BLOCK_PATH, channel=CHANNEL)

Found Synapse note file: data/Subject1-180426-120951\Notes.txt
read from t=0s to t=31.81s

All user notes are stored in a special epoc event called 'Note'

# find all the unique note values
notes, counts = np.unique(data.epocs.Note.notes, return_counts=True)

# find the highest number of occurrences (to inform our plot)
maxOccur = np.max(counts)

Loop through the notes for plotting

# some useful variables
num_notes = len(notes)
fs = data.streams[STORE].fs

fig = plt.figure(figsize=(14, 8))
for ind, note in enumerate(notes,1):

    print('Reading note:', note)

    # look at only the data around this note type
    filtered = tdt.epoc_filter(data, 'Note', values=note, t=ONSET)

    # for each note occurrence, plot the data from
    # the note onset to the next note onset
    n = len(filtered.streams[STORE].filtered)
    for j in range(n):
        plotInd = j * num_notes + ind
        ax = fig.add_subplot(maxOccur, num_notes, plotInd)

        # x-axis is the valid time ranges, in seconds
        len_wav = len(filtered.streams[STORE].filtered[j])
        ts = filtered.time_ranges[0,j] + np.linspace(1, len_wav, len_wav) / fs

        # plot the snippet, in microvolts
        y = np.transpose(1e6 * filtered.streams[STORE].filtered[j])
        trace1 = ax.plot(ts, y, lw=1, color='cornflowerblue')

        # if we specified an ONSET, draw the vertical line at the note onset
        if ONSET != 0:
            trace2 = ax.axvline(x = (ts[0]-ONSET),
                                color='slategray',
                                linewidth=3)

        # plot labels
        if j == 0:
            ax.set_title(note,fontsize=14)
        elif j == (n-1):
            if ind == 1:
                ax.set_ylabel('\u03BCV',fontsize=12)
                ax.set_xlabel('Time (s)',fontsize=12)

fig.tight_layout()

Reading note: grooming
Reading note: moving
Reading note: sleep

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