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Optimize maximum filter #203

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Optimize maximum filter #203

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7 changes: 4 additions & 3 deletions dejavu/fingerprint.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
import numpy as np
import matplotlib.mlab as mlab
import matplotlib.pyplot as plt
from scipy.ndimage.filters import maximum_filter
from scipy.ndimage.filters import maximum_filter1d
from scipy.ndimage.morphology import (generate_binary_structure,
iterate_structure, binary_erosion)
import hashlib
Expand Down Expand Up @@ -93,9 +93,10 @@ def get_2D_peaks(arr2D, plot=False, amp_min=DEFAULT_AMP_MIN):
# http://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.iterate_structure.html#scipy.ndimage.iterate_structure
struct = generate_binary_structure(2, 1)
neighborhood = iterate_structure(struct, PEAK_NEIGHBORHOOD_SIZE)

# find local maxima using our filter shape
local_max = maximum_filter(arr2D, footprint=neighborhood) == arr2D
local_max = maximum_filter1d(arr2D, size=PEAK_NEIGHBORHOOD_SIZE*2+1, axis=0)
local_max = maximum_filter1d(local_max, size=PEAK_NEIGHBORHOOD_SIZE*2+1, axis=1)
local_max = local_max == arr2D
background = (arr2D == 0)
eroded_background = binary_erosion(background, structure=neighborhood,
border_value=1)
Expand Down