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Gudhi_benchmarks.py
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import numpy as np
import gudhi as gd
import time
dirr = 'Datasets/'
#######################################
### dragon
#######################################
#start = time.time()
#dataset = 'dragon'
#d1 = dirr+'dragon2000_locs.csv'
#
#data = np.loadtxt(d1, delimiter=',')
#
#print('Processing ', dataset)
#
#skeleton = gd.RipsComplex(
# points = data,
# max_edge_length = 1000
#)
#
#Rips_simplex_tree = skeleton.create_simplex_tree(max_dimension = 2)
#
#BarCodes_Rips0 = Rips_simplex_tree.persistence()
#
#vals = Rips_simplex_tree.persistence_intervals_in_dimension(1)
#np.savetxt(dirr+'/dragon_Gudhi_H1.csv', vals, delimiter=',')
#
#print('Time taken ', time.time() - start)
#
#######################################
#
#
#######################################
### fract
#######################################
#start = time.time()
#dataset = 'fract'
#d1 = dirr+'fractal_r_distmat.csv'
#
#data = np.loadtxt(d1, delimiter=',')
#
#print('Processing ', dataset)
#
#skeleton = gd.RipsComplex(
# distance_matrix = data,
# max_edge_length = 1000
#)
#
#Rips_simplex_tree = skeleton.create_simplex_tree(max_dimension = 3)
#
#BarCodes_Rips0 = Rips_simplex_tree.persistence()
#
#vals = Rips_simplex_tree.persistence_intervals_in_dimension(1)
#np.savetxt(dirr+'/fract_Gudhi_H1.csv', vals, delimiter=',')
#
#vals = Rips_simplex_tree.persistence_intervals_in_dimension(2)
#np.savetxt(dirr+'/fract_Gudhi_H2.csv', vals, delimiter=',')
#
#print('Time taken ', time.time() - start)
#
#######################################
######################################
## o3
######################################
start = time.time()
dataset = 'o3/'
d1 = dirr+dataset+'o3_8192.csv'
print('Processing ', dataset)
data = np.loadtxt(d1, delimiter=',')
skeleton = gd.RipsComplex(
points = data,
max_edge_length = 1
)
Rips_simplex_tree = skeleton.create_simplex_tree(max_dimension = 3)
BarCodes_Rips0 = Rips_simplex_tree.persistence()
vals = Rips_simplex_tree.persistence_intervals_in_dimension(1)
np.savetxt(dirr+'Gudhi_H1.csv', vals, delimiter=',')
vals = Rips_simplex_tree.persistence_intervals_in_dimension(2)
np.savetxt(dirr+'Gudhi_H2.csv', vals, delimiter=',')
print('Time taken ',time.time()-start)
exit()
######################################
## torus4
######################################
start = time.time()
dataset = 'torus4'
d1 = dirr+'torus4_locs.csv'
print('Processing ', dataset)
data = np.loadtxt(d1, delimiter=',')
skeleton = gd.RipsComplex(
points = data,
max_edge_length = 0.15
)
Rips_simplex_tree = skeleton.create_simplex_tree(max_dimension = 3)
BarCodes_Rips0 = Rips_simplex_tree.persistence()
vals = Rips_simplex_tree.persistence_intervals_in_dimension(1)
np.savetxt(dirr+'/torus4_Gudhi_H1.csv', vals, delimiter=',')
vals = Rips_simplex_tree.persistence_intervals_in_dimension(2)
np.savetxt(dirr+'/torus4_Gudhi_H2.csv', vals, delimiter=',')
finish = time.time()
print('Time taken ',time.time()-start)