actogram.py

import csv
import numpy as np
import matplotlib.pylab as plt
import matplotlib
from datetime import datetime


def import_data(filename, n_wheels):
    with open(filename) as fh:
        reader = csv.reader(fh, delimiter='\t')
        rows = [[r[0]] + list(map(int, r[1:])) for r in reader]

    data = np.zeros((len(rows), n_wheels))
    for i, row in enumerate(rows):
        data[i, :] = row[1:1 + n_wheels]
    return data.T, [r[0] for r in rows]


def plot_actogram(data, times, n_wheels, animals):
    if n_wheels != len(animals):
        raise Exception("Animals doesn't match n_wheels")

    N, T = data.shape
    data /= np.max(data)
    times = [datetime.strptime(t, '%m/%d/%y %H:%M') for t in times]
    times = matplotlib.dates.date2num(times)

    fig = plt.figure()
    ax = fig.add_subplot(1, 1, 1)
    for i in range(N):
        d = data[i, :] != 0
        plt.plot_date(times[d], data[i, d] + i, '.', markersize=2, xdate=True)

    plt.grid(which='both')

    major_ticks = np.arange(8) + .25
    minor_ticks = np.arange(32) * .25
    ax.set_yticks(major_ticks)
    ax.set_yticks(minor_ticks, minor=True)
    ax.set_yticklabels(animals)
    ax.grid(which='minor', alpha=0.4)

    vals = ax.get_xticks()
    minor = []
    for i, val in enumerate(vals):
        for t in range(4):
            minor.append(val + t / 4.)
    ax.set_xticks(minor, minor=True)
    ax.grid(which='minor', alpha=0.4)

    plt.tight_layout()
    plt.show()

if __name__ == '__main__':
    n_wheels = 8
    animals = ['1730', '1734', '1736', '1743', '1744', '1745', '1746', '1747']
    filename = r'E:\image j text.txt'
    data, t = import_data(filename, n_wheels)
    plot_actogram(data, t, n_wheels, animals)