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import numpy as np
import peakutils
from timeit import default_timer as timer
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
def benchit():
tests = [("Small - Low noise", make_data(200, 1.), 100),
("Small - High noise", make_data(200, 3.), 100),
("Big - Low noise", make_data(20000, 1), 5),
("Big - High noise", make_data(20000, 2.), 5),
("Plateaus", (0, np.insert(np.ones(20000-3), [1000, 10000, -1000], 3)), 5)]
for name, data, rep in tests:
begin = timer()
for _ in range(rep):
y = data[1] - peakutils.baseline(data[1])
if name == "Plateaus": y = data[1]
i = peakutils.indexes(y, thres=0.4, min_dist=y.size // 5)
end = timer()
each = (end - begin) / rep
print("*{}* test took {:.3f} seconds each rep".format(name, each))
if __name__ == '__main__':
np.random.seed(1997)
benchit()
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