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d-v-b/forCaroline.py

Created July 17, 2020 18:47
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forCaroline.py
from scipy.ndimage.filters import gaussian_filter
import numpy as np
def generate_mask(array, sigma, percentile, percentile_downsampling=100, threshold=.4):
smoothed = gaussian_filter(array, sigma=sigma, mode='nearest')
lower = np.percentile(smoothed.ravel()[::percentile_downsampling], percentile)
mean = smoothed.mean()
level = lower + (threshold * (mean - lower))
mask = (smoothed > level).astype(array.dtype)
return mask
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