def find_peaks(self):
width = self.peak_minimum_sample_distance
indices = peakutils.indexes(self.filtered_data, min_dist=width)
final_idxs = []
fits = []
for idx in indices:
w = width
if idx - width < 0:
w = idx
if idx + w > len(self.t):
w = len(self.t) - idx
ti = np.array(self.t)[idx - w:idx + w]
datai = np.array(self.filtered_data)[idx - w:idx + w]
try:
params = peakutils.gaussian_fit(ti, datai, center_only=False)
y = [peakutils.gaussian(x, *params) for x in ti]
# ax.plot(ti, y)
ssr = np.sum(np.power(np.subtract(y, datai), 2.0))
sst = np.sum(np.power(np.subtract(y, datai), 2.0))
r2 = 1 - (ssr / sst)
fits.append(r2)
if params[2] < self.gaussian_cutoff:
final_idxs.append(idx)
except RuntimeError:
pass
return final_idxs, fits
def test_est_hr():
import os.path
import sys
sys.path.append(
os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir))
from est_hr import est_hr
import peakutils
import numpy as np
# Simulate Data with Peaks and Noise
# Assume 75 bpm -> 1.25/second
delta_t = 0.01 # seconds
signal_choice = 3 # Both ECG and PP combined
x = np.linspace(0, 10, 10 / delta_t)
x_ind = np.array(range(len(x)))
centers = (1 / delta_t, 1.8 / delta_t, 2.6 / delta_t, 3.4 / delta_t,
4.2 / delta_t, 5 / delta_t, 5.8 / delta_t, 6.6 / delta_t)
tmp = np.zeros(len(x_ind))
for i in range(len(centers)):
tmp = tmp + (peakutils.gaussian(x_ind, 5, centers[i], 5))
ECG_data = tmp + np.random.rand(x_ind.size)
PP_data = tmp + np.random.rand(x_ind.size)
inst_HR = est_hr(ECG_data, PP_data, delta_t, signal_choice)
eps = 5 # Range of 5 bpm accepted for accuracy
assert (inst_HR > (75 - eps / 2) and inst_HR < (75 + eps / 2))
def find_peaks_simplified(data, t, width=5, gaussian_cutoff=10.0):
indices = peakutils.indexes(data, min_dist=width)
final_idxs = []
fits = []
for idx in indices:
w = width
if idx - width < 0:
w = idx
if idx + w > len(t):
w = len(t) - idx
ti = np.array(t)[idx - w:idx + w]
datai = np.array(data)[idx - w:idx + w]
try:
params = peakutils.gaussian_fit(ti, datai, center_only=False)
y = [peakutils.gaussian(x, *params) for x in ti]
# ax.plot(ti, y)
ssr = np.sum(np.power(np.subtract(y, datai), 2.0))
sst = np.sum(np.power(np.subtract(y, datai), 2.0))
r2 = 1 - (ssr / sst)
fits.append(r2)
if params[2] < gaussian_cutoff:
final_idxs.append(idx)
except RuntimeError:
pass
return final_idxs, fits
def test_gaussian_fit(self):
params = np.array([0.5, 6, 2])
x = np.arange(10)
y = peakutils.gaussian(x, *params)
self.assertAlmostEqual(peakutils.gaussian_fit(x, y), params[1])
res = peakutils.gaussian_fit(x, y, center_only=False)
np.testing.assert_allclose(res, params)
def test_gaussian_fit(self):
params = np.array([0.5, 6, 2])
x = np.arange(10)
y = peakutils.gaussian(x, *params)
self.assertAlmostEqual(peakutils.gaussian_fit(x, y), params[1])
res = peakutils.gaussian_fit(x, y, center_only=False)
np.testing.assert_allclose(res, params)
def aux_test_peaks(self, dtype):
'''(3 peaks + baseline + noise)'''
x = numpy.linspace(0, 100, 1000)
centers = (20, 40, 70)
y = (1000 * (peakutils.gaussian(x, 1, centers[0], 3) +
peakutils.gaussian(x, 2, centers[1], 5) +
peakutils.gaussian(x, 3, centers[2], 1) +
numpy.random.random(x.size) * 0.2)).astype(dtype)
filtered = scipy.signal.savgol_filter(y, 51, 3).astype(dtype)
idx = peakutils.indexes(filtered, thres=0.3, min_dist=100)
peaks = peakutils.interpolate(x, y, idx, width=30)
self.assertEqual(idx.size, len(centers))
self.assertEqual(peaks.size, len(centers))
# interpolation should work!
for i in range(peaks.size):
self.assertAlmostEqual(peaks[i], centers[i], delta=0.5)
def test_peaks(self):
'''(3 peaks + baseline + noise)'''
x = numpy.linspace(0, 100, 1000)
centers = (20, 40, 70)
y = (peakutils.gaussian(x, 1, centers[0], 3) +
peakutils.gaussian(x, 2, centers[1], 5) +
peakutils.gaussian(x, 3, centers[2], 1) +
numpy.random.random(x.size) * 0.2)
filtered = scipy.signal.savgol_filter(y, 51, 3)
idx = peakutils.indexes(filtered, thres=0.3, min_dist=100)
peaks = peakutils.interpolate(x, y, idx, width=30)
self.assertEqual(idx.size, len(centers))
self.assertEqual(peaks.size, len(centers))
# interpolation should work!
for i in range(peaks.size):
self.assertAlmostEqual(peaks[i], centers[i], delta=0.5)
def find_peaks(filename, ax, fs):
data_dir = r"C:\Users\kevin\Desktop\Active Projects\Video Magnification Videos\\"
t, data = np.transpose(np.load(data_dir + filename))
ax.plot(t, data)
width = 5
order = 3
cutoff = 1.0
data = butter_lowpass_filter(data, cutoff, fs, order)
indices = peakutils.indexes(data, min_dist=width)
peak_ts = np.take(t, indices)
peak_ds = np.take(data, indices)
ax.plot(t, data)
ax.scatter(peak_ts, peak_ds, c='r', alpha=0.5)
final_idxs = []
post_gaussian = []
for idx in indices:
w = width
if idx - width < 0:
w = idx
if idx + w > len(t):
w = len(t) - idx
ti = t[idx - w:idx + w]
datai = data[idx - w:idx + w]
# ax.plot(ti, datai)
try:
params = peakutils.gaussian_fit(ti, datai, center_only=False)
y = [peakutils.gaussian(x, *params) for x in ti]
# ax.plot(ti, y)
ssr = np.sum(np.power(np.subtract(y, datai), 2.0))
sst = np.sum(np.power(np.subtract(y, datai), 2.0))
r2 = 1 - (ssr / sst)
post_gaussian.append(idx)
if params[2] < 10.0:
final_idxs.append(idx)
print('idx={0}, r2={1}, params={2}'.format(idx, r2, params))
except RuntimeError:
pass
peak_ts = np.take(t, post_gaussian)
peak_ds = np.take(data, post_gaussian)
ax.scatter(peak_ts, peak_ds, c='g', alpha=0.75)
peak_ts = np.take(t, final_idxs)
peak_ds = np.take(data, final_idxs)
ax.scatter(peak_ts, peak_ds, c='b', alpha=1.0)
for i, txt in enumerate(final_idxs):
ax.annotate(str(txt), (peak_ts[i], peak_ds[i]))
def gaussian(a, w, x, c):
return pe.gaussian(x, a, c, w)
def someData():
centers = (30.5, 72.3)
x = np.linspace(0, 120, 121)
y = (peakutils.gaussian(x, 5, centers[0], 3) +
peakutils.gaussian(x, 7, centers[1], 10) + np.random.rand(x.size))
return [x, y]
def gaussian(a, w, x, c):
return pe.gaussian(x, a, c, w)
def make_data(n, noise):
x = np.linspace(0, 100, n)
y = peakutils.gaussian(x, 5, 20, 10) + \
peakutils.gaussian(x, 8, 70, 3) + \
noise*np.random.rand(x.size) + np.polyval([3, 2], x)
return x, y
import numpy as np
import peakutils
from peakutils.plot import plot as pplt
from matplotlib import pyplot as plt
from smooth import smooth
centers = (30.5, 72.3)
x = np.linspace(0, 120, 121)
y = (peakutils.gaussian(x, 5, centers[0], 3) +
peakutils.gaussian(x, 7, centers[1], 10) +
np.random.rand(x.size))
plt.figure(figsize=(10,6))
plt.plot(x, y)
plt.title("Data with noise")
y=smooth(y, 10, 'bartlett')
plt.figure(figsize=(10,6))
plt.plot(y)
plt.title("Smoothing test")
dx = x[1]-x[0]
dydx = np.gradient(y,1)
d2ydx2 = np.gradient(dydx,1)
print dydx
indexes = peakutils.indexes(y, thres=0.5, min_dist=30)
print(indexes)
print(x[indexes], y[indexes])
plt.figure(figsize=(10,6))
pplt(x, y, indexes)
plt.title('First estimate')
def make_data(n, noise):
x = np.linspace(0, 100, n)
y = peakutils.gaussian(x, 5, 20, 10) + \
peakutils.gaussian(x, 8, 70, 3) + \
noise * np.random.rand(x.size) + np.polyval([3, 2], x)
return x, y
import numpy
import peakutils
from peakutils.plot import plot as pplot
from matplotlib import pyplot
centers = (30.5, 72.3)
x = numpy.linspace(0, 120, 121)
y = peakutils.gaussian(x, 5, centers[0], 3) + peakutils.gaussian(x, 7, centers[1], 10) + numpy.random.rand(x.size)
pyplot.figure(figsize=(10, 6))
pyplot.plot(x, y)
pyplot.title("Data with noise")
indexes = peakutils.indexes(y, thres=0.5, min_dist=30)
print(indexes)
print(x[indexes], y[indexes])
pyplot.figure(figsize=(10, 6))
pplot(x, y, indexes)
pyplot.title("First estimate")
pyplot.show()