1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
|
import inspect
import numpy as np
from scipy import ndimage as ndi
from skimage.feature import peak_local_max
# Inspect signature to automatically handle API changes across versions.
# `indices` currently defaults to True, but will be removed in the future.
peak_kwargs = {}
parameters = inspect.signature(peak_local_max).parameters
if 'indices' in parameters and parameters['indices'].default:
peak_kwargs = {'indices': False}
class PeakLocalMaxSuite:
def setup(self):
mask = np.zeros([500, 500], dtype=bool)
x, y = np.indices((500, 500))
x_c = x // 20 * 20 + 10
y_c = y // 20 * 20 + 10
mask[(x - x_c) ** 2 + (y - y_c) ** 2 < 8**2] = True
# create a mask, label each disk,
self.labels, num_objs = ndi.label(mask)
# create distance image for peak searching
self.dist = ndi.distance_transform_edt(mask)
def time_peak_local_max(self):
peak_local_max(
self.dist,
labels=self.labels,
min_distance=20,
exclude_border=False,
**peak_kwargs,
)
|
