#X.shape
#(107284, 3)
#labels.shape
#(107284,)
#orderedPoints = np.column_stack((X, labels.T))
#o_fname =
#np.savetxt(o_fname, orderedPoints, delimiter=',', header='X, Y, Z, Label')
#from initial tests, 13% of epsilon in optics seems to work well for epsilon' (epsilon prime), ep
ep = eps * .13
startTime = time.time()
#Run DBSCAN to extract clusters from data ordered by OPTICS
print("Extracting clusters by running DBSCAN on points ordered by OPTICS. \n")
testtree.extract(epsilon_prime=ep, clustering='dbscan')
timeElapsed = time.time() - startTime
print(
"time elapsed after testtree.extract(epsilon_prime = {}, clustering='dbscan'): "
.format(ep), timeElapsed, "\n")
labels = testtree._cluster_id[:]
n_clusters_ = max(testtree._cluster_id)
print(
"Number of clusters from OPTICS parameters eps = {0}, min_samples = {1}, eps_prime = {2}: "
.format(eps, minNumSamples, ep), "\n", n_clusters_)
#Save output
#here
clusteredPoints = np.column_stack((X, labels.T))
#X.shape
#(107284, 3)
#labels.shape
#(107284,)
#orderedPoints = np.column_stack((X, labels.T))
#o_fname =
#np.savetxt(o_fname, orderedPoints, delimiter=',', header='X, Y, Z, Label')
ep = eps * eps_prime_perc
startTime = time.time()
#Run DBSCAN to extract clusters from data ordered by OPTICS
print("Extracting clusters by running testtree.extract(). \n")
testtree.extract(epsilon_prime = ep, clustering='auto')
timeElapsed = time.time() - startTime
print("time elapsed after testtree.extract(clustering='auto') with minPts {0}: ".format(minNumSamples), timeElapsed, "\n")
labels = testtree._cluster_id[:]
n_clusters_ = max(testtree._cluster_id)
print("Number of clusters from OPTICS extract_auto with parameters eps = {0}, min_samples = {1}, eps_prime_perc: {2}".format(eps, minNumSamples, eps_prime_perc), "\n", n_clusters_)
#Save output
#here
clusteredPoints = np.column_stack((X, labels.T))
o_fname = "OPTICS_extract_clustered_points_eps_{0}_min_samples_{1}_eps_prime_perc{2}.csv".format(eps, minNumSamples, eps_prime_perc)
np.savetxt(o_fname, clusteredPoints, delimiter=',', header='X, Y, Z, Label')
