Diff of /python/oversampling.py [000000] .. [4d064f]

Switch to unified view

a b/python/oversampling.py
1
#!/usr/bin/env python
2
3
"""
4
train_SVM.py
5
    
6
VARPA, University of Coruna
7
Mondejar Guerra, Victor M.
8
15 Dec 2017
9
"""
10
11
import os
12
import csv
13
import gc
14
import cPickle as pickle
15
import time
16
from imblearn.over_sampling import SMOTE, ADASYN
17
from imblearn.combine import SMOTEENN, SMOTETomek
18
import collections
19
from sklearn import svm
20
import numpy as np
21
22
cpu_threads = 7
23
24
# http://contrib.scikit-learn.org/imbalanced-learn/stable/auto_examples/combine/plot_comparison_combine.html#sphx-glr-auto-examples-combine-plot-comparison-combine-py
25
26
# Perform the oversampling method over the descriptor data
27
def perform_oversampling(oversamp_method, db_path, oversamp_features_name, tr_features, tr_labels):
28
    start = time.time()
29
    
30
    oversamp_features_pickle_name = db_path + oversamp_features_name + '_' + oversamp_method + '.p'
31
    print(oversamp_features_pickle_name)
32
33
    if True:
34
        print("Oversampling method:\t" + oversamp_method + " ...")
35
        # 1 SMOTE
36
        if oversamp_method == 'SMOTE':  
37
            #kind={'borderline1', 'borderline2', 'svm'}
38
            svm_model = svm.SVC(C=0.001, kernel='rbf', degree=3, gamma='auto', decision_function_shape='ovo')
39
            oversamp = SMOTE(ratio='auto', random_state=None, k_neighbors=5, m_neighbors=10, out_step=0.5, kind='svm', svm_estimator=svm_model, n_jobs=1)
40
41
            # PROBAR SMOTE CON OTRO KIND
42
43
        elif oversamp_method == 'SMOTE_regular_min':
44
            oversamp = SMOTE(ratio='minority', random_state=None, k_neighbors=5, m_neighbors=10, out_step=0.5, kind='regular', svm_estimator=None, n_jobs=1)
45
46
        elif oversamp_method == 'SMOTE_regular':
47
            oversamp = SMOTE(ratio='auto', random_state=None, k_neighbors=5, m_neighbors=10, out_step=0.5, kind='regular', svm_estimator=None, n_jobs=1)
48
  
49
        elif oversamp_method == 'SMOTE_border':
50
            oversamp = SMOTE(ratio='auto', random_state=None, k_neighbors=5, m_neighbors=10, out_step=0.5, kind='borderline1', svm_estimator=None, n_jobs=1)
51
                 
52
        # 2 SMOTEENN
53
        elif oversamp_method == 'SMOTEENN':    
54
            oversamp = SMOTEENN()
55
56
        # 3 SMOTE TOMEK
57
        # NOTE: http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.65.3904&rep=rep1&type=pdf
58
        elif oversamp_method == 'SMOTETomek':
59
            oversamp = SMOTETomek()
60
61
        # 4 ADASYN
62
        elif oversamp_method == 'ADASYN':
63
            oversamp = ADASYN(ratio='auto', random_state=None, k=None, n_neighbors=5, n_jobs=cpu_threads)
64
 
65
        tr_features_balanced, tr_labels_balanced  = oversamp.fit_sample(tr_features, tr_labels)
66
        # TODO Write data oversampled!
67
        print("Writing oversampled data at: " + oversamp_features_pickle_name + " ...")
68
        np.savetxt('mit_db/' + oversamp_features_name + '_DS1_labels.csv', tr_labels_balanced.astype(int), '%.0f') 
69
        f = open(oversamp_features_pickle_name, 'wb')
70
        pickle.dump(tr_features_balanced, f, 2)
71
        f.close
72
73
    end = time.time()
74
75
    count = collections.Counter(tr_labels_balanced)
76
    print("Oversampling balance")
77
    print(count)
78
    print("Time required: " + str(format(end - start, '.2f')) + " sec" )
79
80
    return tr_features_balanced, tr_labels_balanced