why scipy.spatial.ckdtree runs slower than scipy.spatial.kdtree
Multi tool use
Clash Royale CLAN TAG#URR8PPPwhy scipy.spatial.ckdtree runs slower than scipy.spatial.kdtree
Normally,scipy.spatial.ckdtree runs much faster than scipy.spatial.kdtree.
But in my case,scipy.spatial.ckdtree runs slower than scipy.spatial.kdtree.
My code is as follows:
import numpy as np
from laspy.file import File
from scipy import spatial
from timeit import default_timer as timer
inFile = File("Toronto_Strip_01.las")
dataset = np.vstack([inFile.x, inFile.y, inFile.z]).transpose()
print(dataset.shape)
start=timer()
tree = spatial.cKDTree(dataset)
# balanced_tree = False
end=timer()
distance,index=tree.query(dataset[100,:],k=5)
print(distance,index)
print(end-start)
start=timer()
tree = spatial.KDTree(dataset)
end=timer()
dis,indices= tree.query(dataset[100,:],k=5)
print(dis,indices)
print(end-start)
dataset.shape is (2727891, 3),dataset.max() is 4834229.32
But, in a test case, scipy.spatial.ckdtree runs much faster than scipy.spatial.kdtree,the code is as follows:
import numpy as np
from timeit import default_timer as timer
from scipy import spatial
np.random.seed(0)
A = np.random.random((2000000,3))*2000000
start1 = timer()
kdt=spatial.KDTree(A)
end1 = timer()
distance,index = kdt.query(A[100,:],k=5)
print(distance,index)
print(end1-start1)
start2 = timer()
kdt = spatial.cKDTree(A) # cKDTree + outside construction
end2 = timer()
distance,index = kdt.query(A[100,:],k=5)
print(distance,index)
print(end2-start2)
Here is my problem: in my code,Do I need to process the dataset to speedup the cKDTree?
my scipy version is 1.1.0,cython is 0.28.4
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