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DcGA_kmeans_step2.py
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DcGA_kmeans_step2.py
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# -*- coding: utf-8 -*-
"""
Created on Mon Jul 27 09:53:37 2020
"""
# Used to connect and query the database
import sqlite3
# libs for array use, plots, etc.
import numpy as np
# lib containing the predefined K-MEANS in python
from sklearn.cluster import KMeans
# lib used to generate the possible permutation of N digits
from itertools import permutations
# lib to compute some statistics
# import statistics as st
# the cGA producing initial centroids
from cGA import cGA
# lib used to write on excel files
from xlwt import Workbook
# Given a vector reduces it, accumulating each n values in one (mean value)
def reduce_vector(v: list, n: int) -> list:
v2 = []
for i in range(0, len(v), n):
mean = 0
for j in range(i, i+n):
mean += v[j]
v2.append(mean/n)
return v2
# Return an array in which each position indicates the elements in cluster i
def get_sets(cluster, num):
s = []
for idx in range(num):
s.append(
set(
[i for i, e in enumerate(cluster) if e == idx]
)
)
return s
# distance between two clusters with an specific order
def distance_with_order(s1, s2, perm_comb):
dist = 0
for i in range(len(perm_comb)):
dist += len(s1[i].union(s2[perm_comb[i]])) - len(s1[i].intersection(s2[perm_comb[i]]))
return dist
# distance between two clustersing (it test all possible combinations)
def distance_clusters(cluster1, cluster2, cluster_num):
index_cluster_all = list(range(0, cluster_num)) # create an array with the indexes of clusters
perm = permutations(index_cluster_all) # stores the permutations
d = None
set_c1 = get_sets(cluster1, cluster_num)
set_c2 = get_sets(cluster2, cluster_num)
for perm_comb in perm: # browse the permutations
n_d = distance_with_order(set_c1, set_c2, perm_comb)
if not d or n_d < d:
d = n_d
return d
def clustering_step_2(cluster_num, verb,pop,it,pc,pm,NN,D):
print("***********************************************************************************************")
print(" THE PROCESSING OF THE SECOND STEP OF CLUSTERING HAS STARTED")
print("***********************************************************************************************")
# connect to the database
conn = sqlite3.connect('db-reduced.db')
c = conn.cursor()
# extract the series of info
series = c.execute('SELECT DISTINCT serie_name FROM data')
data_ser = series.fetchall()
# extract the locations
locations = c.execute('SELECT DISTINCT location_name FROM data')
data_loc = locations.fetchall()
# define the number of months considered in each clustering
months_considered = [1, 2, 3, 4, 6, 12] # 1 is for a clustering considering all the months (not mean of 12 months)
months_histogram = [0, 0, 0, 0, 0]
# display some information about the final data displayed
if verb == 1:
print("***********************************************************************************************")
print("IMPORTANT:")
print(" - The data displayed at the end of step II is a 1x33 array.")
print("- Each value in the array corresponds to the ideal number of months to consider for the clustering of "
"each series of information.")
print(" - The index of the value corresponds to the index of the serie of information to be used with.")
print(" - If a given value is Y months, then 15 x Y features will be considered in the clustering.")
print("- Technically speaking, 15 x 1 features will be considered since we will take the mean of Y months in "
"each of the 15 years.")
print("***********************************************************************************************")
# ============================================== PERFORM CLUSTERING ACCORDING TO 6 CONFIGURATIONS ==================
i = 0 # index to count down the series having been processed ("i" will be only used for displaying information)
wb = Workbook() # open a new workbood
sh = wb.add_sheet('data') # add a new sheet
for tuple1 in data_ser: # browse series
i = i + 1 # increment the index of the serie each time one is browsed
cluster_labels = np.zeros(52) # will store the number of the cluster to whome each city belongs
if verb == 1:
print("-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=")
print("Information n° %i being processed: " % i, tuple1[0])
print("-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=")
for ind in months_considered: # browse the number of months considered:2, 3, 4, 6 and 12
data_x_months = np.zeros(15*12//ind) # stores the data of 15 years x 12/ind values (The mean of ind months)
for tuple2 in data_loc: # browse locations
# print(tuple2[0]) # uncomment to know which city you are browsing
# ====== RETRIEVE THE RECORDS OF THE GIVEN SERIE FOR THE PROCESSED CITY ===============================
records = c.execute('SELECT * FROM data WHERE serie_name = ? AND location_name = ? ',
(tuple1[0][:], tuple2[0][:]))
data_rec = records.fetchall()
data_mat = [] # the matrix contains the records of a city for a given series, year and period
for tuple3 in data_rec:
# print(tuple3) # uncomment to know the tuple of info being displayed
data_mat = np.append(data_mat, tuple3[5]) # append the records
# ===== build-up the matrix of records that will undergo clustering, lines: cities, columns:
data_mat = reduce_vector(data_mat, ind)
# records of the cities =========
data_x_months = np.vstack((data_x_months, data_mat))
# ====================== PERFORM THE K-MEANS CLUSTERING ========================
data_x_months = np.delete(data_x_months, 0, 0) # delete the first row of unuseful zeros (see above)
# print(len(data_all_months[0])) # uncomment to check the number of records
# print(len(data_all_months)) # uncomment to check the number of cities
# ====================== compute initial centroids using GA ========================
dim = len(data_x_months[:,0]) # extract the number of cities = size of te GA's individual
# compute the initial centroids via GA
centro = cluster_num - 1;
centroids = cGA(pop,dim,it,pc,pm,data_x_months,centro,NN,D)
# ============= PERFORM K-MEANS CLUSTERING USING K CENTROIDS FOUND IN STEP I ===========================
# perform the K-means clustering: info about parameters can be found in
# https://scikit-learn.org/stable/modules/generated/sklearn.cluster.KMeans.html
clust = KMeans(n_clusters=cluster_num, init=centroids, n_init=10, max_iter=300, tol=0.0001, verbose=0,
random_state=None, copy_x=True, algorithm='auto').fit(data_x_months)
# print(clust.labels_) # uncomment to observe the labels of the clusters to which belong each city
# print(clust.inertia_) # uncomment to observe the value of dispertion: sum of squared distances
cluster_labels = np.vstack((cluster_labels, clust.labels_)) # append the result of the clustering
cluster_labels = np.delete(cluster_labels, 0, 0) # delete the unuseful set of zeros at the begining
# print(len(cluster_labels)) # uncomment to know the number of feature configurations considered
# print(len(cluster_labels[0])) # uncomment to know the number of cities considered
# print(cluster_labels) # uncomment to print the result of clustering in each of the 6 feature configurations
# ======== COMPUTE DISTANCE BETWEEN CLUSTERING USING 15x12 FEATURES CONFIGURATIONS AND 15 x 1 FEATURES =========
distance_clustering = [] # will contain the distances between the clustering
# compute the distance between the clustering
index_feat = 0
for ind_config in range(1, len(months_considered)):
distance = distance_clusters(cluster_labels[0][:], cluster_labels[ind_config][:], cluster_num)
# display the distance between the clustering
if verb == 1:
print(f"The distance between a clustering with 180 features and the one with "
f"{12//months_considered[ind_config] * 15} features considering {months_considered[ind_config]}"
f" months) is: {distance}")
# append the distance between the clustering of 180 features and the processed clustering
distance_clustering.append(distance)
sh.write((i-1),index_feat,distance) # write down the distance in excel file
index_feat = index_feat + 1
min_dist = min(distance_clustering)
for j in range(len(distance_clustering)):
if distance_clustering[j] == min_dist:
months_histogram[j] += 1
if verb == 1:
for i, e in enumerate(months_histogram):
print(f"{months_considered[i+1]} months: {e}")
features_number = months_considered[
len(months_histogram) - months_histogram[::-1].index(max(months_histogram))
]
sh.write(40,0,features_number) #" write down the ideal number of features to be considered
wb.save('step2_data.xls') # save the wokbook
if verb == 1:
print("***********************************************************************************************")
print("Ideal # of months to to be used for the clustering:", features_number)
print("***********************************************************************************************")
print("***********************************************************************************************")
print(" THE PROCESSING OF THE SECOND STEP OF CLUSTERING HAS FINISHED")
print("***********************************************************************************************")
return features_number