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import numpy as np
from sklearn.metrics import pairwise_distances
import os
import gudhi as gd
import sys
sys.path.append("../sktda/")
from clustering import *
X = np.loadtxt("human")
print("Mapper computation with point cloud")
mapper = MapperComplex(inp="point cloud",
filters=X[:,[2,0]],
filter_bnds=np.array([[np.nan,np.nan],[np.nan,np.nan]]),
resolutions=np.array([np.nan,np.nan]), gains=np.array([0.33,0.33]),
colors=X[:,2:3],
).fit(X)
f = open("mapper_pc", "w")
f.write("%s\n%s\n%s\n%f %f\n%d %d\n" % ("human", "coord2-0", "coord2", 10, 0.33, len(mapper.mapper_.get_skeleton(0)), len([edge for (edge,f) in mapper.mapper_.get_skeleton(1) if len(edge)==2])))
for (vertex,_) in mapper.mapper_.get_skeleton(0):
f.write(str(vertex[0]) + " " + str(mapper.node_info_[vertex[0]]["colors"][0]) + " " + str(mapper.node_info_[vertex[0]]["size"]) + "\n")
for (edge,_) in mapper.mapper_.get_skeleton(1):
if len(edge) == 2:
f.write(str(edge[0]) + " " + str(edge[1]) + "\n")
f.close()
os.system("python3 ~/Git/gudhi-devel/src/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py -f ~/Git/gudhi-devel/src/cython/example/mapper_pc")
os.system("rm ~/Git/gudhi-devel/src/cython/example/mapper_pc")
dgms = mapper.compute_persistence_diagrams()
plot = gd.plot_persistence_diagram(dgms[0])
plot.show()
distrib = mapper.compute_distribution(X, N=10)
print("Distance threshold associated to confidence 90 percent is " + str(distrib[int(np.floor(0.9 * len(distrib)))]))
print("Mapper computation with pairwise distances only")
X = pairwise_distances(X)
mapper = MapperComplex(inp="distance matrix",
filters=X[:,[2,0]],
filter_bnds=np.array([[np.nan,np.nan],[np.nan,np.nan]]),
resolutions=np.array([np.nan,np.nan]), gains=np.array([0.33,0.33]),
colors=np.max(X, axis=1)[:,np.newaxis],
).fit(X)
f = open("mapper_dm", "w")
f.write("%s\n%s\n%s\n%f %f\n%d %d\n" % ("human", "coord2-0", "coord2", 10, 0.33, len(mapper.mapper_.get_skeleton(0)), len([edge for (edge,f) in mapper.mapper_.get_skeleton(1) if len(edge)==2])))
for (vertex,_) in mapper.mapper_.get_skeleton(0):
f.write(str(vertex[0]) + " " + str(mapper.node_info_[vertex[0]]["colors"][0]) + " " + str(mapper.node_info_[vertex[0]]["size"]) + "\n")
for (edge,_) in mapper.mapper_.get_skeleton(1):
if len(edge) == 2:
f.write(str(edge[0]) + " " + str(edge[1]) + "\n")
f.close()
os.system("python3 ~/Git/gudhi-devel/src/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py -f ~/Git/gudhi-devel/src/cython/example/mapper_dm")
os.system("rm ~/Git/gudhi-devel/src/cython/example/mapper_dm")
dgms = mapper.compute_persistence_diagrams()
plot = gd.plot_persistence_diagram(dgms[0])
plot.show()
distrib = mapper.compute_distribution(X, N=10)
print("Distance threshold associated to confidence 90 percent is " + str(distrib[int(np.floor(0.9 * len(distrib)))]))
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