Compare the behavior of fftconvolve (with mode='same') to gaussian_filter (with mode='constant'):

import numpy as np
from scipy.signal import fftconvolve
from scipy.ndimage import gaussian_filter

x = np.linspace(-3, 3, 51)
y = np.sin(x)

blurring_kernel = np.zeros_like(x)
blurring_kernel[25] = 1
blurring_kernel = gaussian_filter(blurring_kernel, sigma=3)

a = fftconvolve(y, blurring_kernel, mode='same')
b = gaussian_filter(y, sigma=3, mode='constant')
print max(abs((a - b))) # a and b are identical
"""
You have to assume *something* outside the boundary.
This is probably what you want:
"""
c = gaussian_filter(y, sigma=3, mode='reflect')

You have to assume something outside the boundary of your signal. fftconvolve assumes zeros. gaussian_filter lets you choose from several different assumptions, and I find one of these is usually closer to my needs than assuming zeros.

For a quick fix, you could use gaussian_filter, or else pad your signal with something nonzero, to get the same effect at the boundary, perhaps using pad.

Use gaussian_filter instead of fftconvolve.

Compare the behavior of fftconvolve (with mode='same') to gaussian_filter (with mode='constant'):

import numpy as np
from scipy.signal import fftconvolve
from scipy.ndimage import gaussian_filter

x = np.linspace(-3, 3, 51)
y = np.sin(x)

blurring_kernel = np.zeros_like(x)
blurring_kernel[25] = 1
blurring_kernel = gaussian_filter(blurring_kernel, sigma=3)

a = fftconvolve(y, blurring_kernel, mode='same')
b = gaussian_filter(y, sigma=3, mode='constant')
print max(abs((a - b))) # a and b are identical
"""
You have to assume *something* outside the boundary.
This is probably what you want:
"""
c = gaussian_filter(y, sigma=3, mode='reflect')

You have to assume something outside the boundary of your signal. fftconvolve assumes zeros. gaussian_filter lets you choose from several different assumptions, and I find one of these is usually closer to my needs than assuming zeros.

For a quick fix, you could use gaussian_filter, or else pad your signal with something nonzero, to get the same effect at the boundary, perhaps using pad.