notebook.community

Edit and run 





In [1]:



    


import PyHdbscan
import numpy as np
import math
import sys



    











In [2]:



    


def readFile(filename):
	dataset = np.genfromtxt(filename, delimiter=',')
	r,c = dataset.shape
	
	if math.isnan(dataset[0][c-1]):
		dataset = np.delete(dataset, -1, axis=1)
	print("rows = ", r, " coloumns = ", c)
	return dataset



    











In [3]:



    


def printLabels(labels):
	print("\nCluster labels = [")
	for l in labels:
		print(str(l) + " ", end="")
	print("]\n")



    











In [4]:



    


def getClusterMap(labels):
	dmap = {}
	for i in range(len(labels)):
		key = labels[i]
		if key in dmap:
			dmap[key].append(i)
		else:
			dmap[key] = [i]
	return dmap



    











In [5]:



    


def main(fname):
	print("Opening file : ", fname)	
	dataset = readFile(fname)
	
	scan = PyHdbscan.PyHdbscan(6)
		
	print("\n***********************************************************************************\n")
	for i in range(3, 4):
		if i == 3:
			print("Clustering for dataset with minPts =", 3)
			scan.run(dataset)
		else:
			print("\nRe-Clustering for dataset with minPts =", i)
			scan.rerun(i)
			
		printLabels(scan.labels)
		print(set(scan.labels))
		dmap = getClusterMap(scan.labels) 
		
		for key in dmap:
			print(key, ":", dmap[key])
		print(getClusterMap(scan.labels))
		print("\n***********************************************************************************\n")



    











In [6]:



    


main("/home/junior/programming/phd/hdbscan/test_datasets/mydata.csv")



    


















    






Opening file :  /home/junior/programming/phd/hdbscan/test_datasets/mydata.csv
rows =  3354  coloumns =  65

***********************************************************************************

Clustering for dataset with minPts = 3

Cluster labels = [
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2 : [1851, 2053, 2144, 2151, 2216, 2488]
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13 : [2738, 2803, 2876, 2877, 2925, 3138]
15 : [2930, 3135, 3139, 3174, 3197, 3271, 3273, 3279, 3291, 3313, 3316]
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3145, 3146, 3164, 3191, 3244], 45: [45, 79, 100, 116, 132, 135, 148, 149, 188, 193, 204, 234, 241, 319, 326, 330, 789], 37: [47, 54, 483, 628, 1273, 1498, 2207, 2965, 3056], 39: [53, 203, 232, 245, 391, 935, 1234], 17: [274, 545, 648, 652, 747, 757, 760, 792, 995, 1045, 1050, 1097, 1203, 1217, 1258, 1276, 1329, 1378, 1494, 1531, 1633, 1643, 1670, 1721, 1722, 1847, 1939, 2092, 2171, 2246], 8: [386, 484, 570, 661, 916, 1002, 1028, 1047, 1052, 1073, 1236, 1264, 1305, 1418, 1421, 1551, 1659, 1719, 2084, 2104, 2172, 2270, 2645, 2749, 2768, 2904], 33: [510, 843, 972, 1017, 1051, 1300, 1380, 1689, 1732, 1785, 1811, 1819, 1822, 1877, 2030, 2102, 2299, 2475, 2547, 2676, 2784, 3002, 3013, 3137], 34: [527, 690, 808, 1275, 1287, 1385, 2065, 2303], 41: [607, 1229, 1239, 1308, 1429, 2929], 43: [673, 716, 922, 1064, 1070, 1266, 1426, 1504, 1545, 1549, 1582, 1583, 1595, 1605, 1701, 1813, 1828, 1831, 1887, 1966, 1991, 1996, 2060, 2133, 2166, 2220, 2345, 2372, 2456, 2525, 2527, 2642, 2855, 2897, 3348], 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[2533, 2587, 2837, 2845, 2924, 2935, 3011, 3080, 3103, 3110, 3116, 3132, 3152, 3253], 13: [2738, 2803, 2876, 2877, 2925, 3138], 15: [2930, 3135, 3139, 3174, 3197, 3271, 3273, 3279, 3291, 3313, 3316]}

***********************************************************************************


















In [7]:



    


main("/home/junior/Dropbox/business/Itron/Test-2000.csv")



    


















    






Opening file :  /home/junior/Dropbox/business/Itron/Test-2000.csv
rows =  2000  coloumns =  4

***********************************************************************************

Clustering for dataset with minPts = 3

Cluster labels = [
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