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1 #!/usr/bin/python2
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2 # -*- coding: utf-8 -*-
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3 """
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4 Created on Thu Apr 23 11:53:17 2015
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5
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6 @author: mmxgn
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7 """
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8
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9 # This file does the cluster estimation and the removal of outliers
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10
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11 from sys import argv, exit
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12 from essentia.standard import YamlInput, YamlOutput
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13 from essentia import Pool
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14 from pca import *
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15
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16 from numpy import *
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17 from sklearn import cluster
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18 from sklearn.metrics import pairwise_distances
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19 from sklearn.cluster import KMeans, MiniBatchKMeans
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20 from matplotlib.pyplot import *
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21 #from sklearn.mixture import GMM
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22 from sklearn.naive_bayes import GaussianNB, MultinomialNB
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23 from scipy.signal import decimate
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24 from sklearn import cross_validation
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25
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26 #from hmmlearn import hmm
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27 from hmmlearn.hmm import GMM
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28 from hmmlearn import hmm
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29 #from adpcm import adm, adm_reconstruct
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30
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31
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32 mse = lambda A,B: ((array(A)-array(B)) ** 2).mean()
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33
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34
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35 def smooth_matrix_1D(X):
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36 window = scipy.signal.gaussian(51,4)
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37 window = window/sum(window)
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38 intermx = zeros((X.shape[0],X.shape[1]+100))
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39 intermx[:, 50:-50] = X
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40
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41 for m in range(0, X.shape[0]):
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42 # print intermx.shape
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43 intermx[m,:] = convolve(ravel(intermx[m,:]), window,'same')
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44
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45 return intermx[:,50:-50]
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46
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47 def adm_reconstruct(codeword, h, dmin=.01, dmax=.28):
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48 x = zeros((1, codeword.shape[1]))
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49
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50 delta1 = dmin
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51 delta2 = dmin
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52 Sum = h
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53
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54 x[0] = h
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55 for i in range(0, codeword.shape[1]):
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56 if codeword[0,i] == 0:
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57 delta1 = dmin
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58 delta2 = dmin
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59
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60 elif codeword[0,i] == 1:
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61 delta2 = dmin
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62 Sum += delta1
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63 delta1 *= 2
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64 if delta1 > dmax:
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65 delta1 = dmax
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66
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67 elif codeword[0,i] == -1:
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68 delta1 = dmin
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69 Sum -= delta2
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70 delta2 *= 2
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71 if delta2 > dmax:
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72 delta2 = dmax
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73 x[0,i] = Sum
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74 return x
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75
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76 def adm(x, dmin=.01, dmax=.28, tol=0.0001):
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77
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78 # Adaptive delta modulation adapted by code:
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79 # (adeltamod.m)
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80 #
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81 # Adaptive Delta Modulator
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82 # by Gandhar Desai (gdesai)
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83 # BITS Pilani Goa Campus
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84 # Date: 28 Sept, 2013
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85
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86 xsig = x
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87
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88 Lx = len(x)
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89
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90 ADMout = zeros((1, Lx))
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91 codevec = zeros((1, Lx))
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92
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93
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94 Sum = x[0]
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95 delta1 = dmin
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96 delta2 = dmin
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97 mult1 = 2
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98 mult2 = 2
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99 for i in range(0, Lx):
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100 #print abs(xsig[i] - Sum)
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101 if (abs(xsig[i] - Sum) < tol):
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102 bit = 0
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103 delta2 = dmin
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104 delta1 = dmin
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105
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106
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107 elif (xsig[i] >= Sum):
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108 bit = 1
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109 delta2 = dmin
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110 Sum += delta1
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111 delta1 *= mult1
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112 if delta1 > dmax:
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113 delta1 = dmax
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114
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115
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116 else:
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117 bit = -1
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118 delta1 = dmin
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119 Sum -= delta2
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120 delta2 *= mult2
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121 if delta2 > dmax:
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122 delta2 = dmax
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123
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124
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125
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126 ADMout[0, i] = Sum
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127 codevec[0, i]= bit
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128
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129 return ADMout,codevec, x[0]
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130
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131 if __name__=="__main__":
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132 if len(argv) != 2:
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133 print "[EE] Wrong number of arguments"
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134 print "[II] Correct syntax is:"
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135 print "[II] \t%s <training_file>"
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136 print "[II] where <training_file> is a .yaml file containing the"
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137 print "[II] features of the dataset (try output2_stage/fulltraining-last.yaml)"
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138 exit(-1)
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139
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140
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141 n_clusters = 25
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142 UpsamplingFactor = 10
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143 dmin = 0.001
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144 dmax = 0.28
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145 tol = 0.001
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146
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147 infile = argv[1]
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148
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149 features_pool = YamlInput(filename = infile)()
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150
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151
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152
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153 feature_captions = features_pool.descriptorNames()
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154 parameter_captions = []
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155
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156
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157 for c in features_pool.descriptorNames():
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158 if c.split('.')[0] == 'parameter':
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159 parameter_captions.append(c)
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160 if c.split('.')[0] == 'metadata' or c.split('.')[0] == 'parameter':
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161 feature_captions.remove(c)
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162
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163
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164
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165 # close('all')
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166
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167 print "[II] Loaded training data from %s (%s) " % (infile, features_pool['metadata.date'][0])
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168 print "[II] %d Features Available: " % len(feature_captions)
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169
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170
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171
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172 print str(feature_captions).replace("', ","\n").replace('[','').replace("'","[II]\t ")[:-7]
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173
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174 nfeatures_in = len(feature_captions)
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175 nparameters_in = len(parameter_captions)
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176 features_vector = zeros((nfeatures_in, len(features_pool[feature_captions[0]])))
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177
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178 parameters_vector = zeros((nparameters_in, len(features_pool[parameter_captions[0]])))
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179
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180
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181 for i in range(0, nfeatures_in):
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182 features_vector[i, :] = features_pool[feature_captions[i]].T
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183 for i in range(0, nparameters_in):
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184 parameters_vector[i, :] = features_pool[parameter_captions[0]].T
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185
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186 print "[II] %d parameters used:" % len(parameter_captions)
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187 print str(parameter_captions).replace("', ","\n").replace('[','').replace("'","[II]\t ")[:-7].replace('parameter.','')
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188
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189 print "[II] Marking silent parts"
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190
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191 silent_parts = zeros((1, len(features_pool[feature_captions[i]].T)))
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192
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193 rms = features_vector[feature_captions.index('rms'), :]
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194
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195 # Implementing Hysteresis Gate -- High threshold is halfway between
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196 # the mean and the max and Low is halfway between the mean dn the min
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197
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198 rms_threshold_mean = mean(rms)
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199
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200 rms_threshold_max = max(rms)
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201 rms_threshold_min = min(rms)
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202
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203 rms_threshold_high = 0.1 * rms_threshold_mean
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204 rms_threshold_low = 0.01 * rms_threshold_mean
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205
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206 for n in range(1, len(rms)):
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207 prev = rms[n-1]
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208 curr = rms[n]
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209
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210 if prev >= rms_threshold_high:
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211 if curr < rms_threshold_low:
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212 silent_parts[0,n] = 1
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213 else:
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214 silent_parts[0,n] = 0
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215 elif prev <= rms_threshold_low:
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216 if curr > rms_threshold_high:
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217 silent_parts[0,n] = 0
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218 else:
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219 silent_parts[0,n] = 1
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220 else:
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221 silent_parts[0,n] = silent_parts[0,n-1]
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222
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223
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224 if silent_parts[0,1] == 1:
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225 silent_parts[0, 0] = 1
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226
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227
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228
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229 active_index = invert(silent_parts.flatten().astype(bool))
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230
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231 # Keep only active parts
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232
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233 # Uncomment this
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234 features_vector = features_vector[:, active_index]
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235
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236 moments_vector = zeros((features_vector.shape[0], 2))
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237
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238 print "[II] Storing moments vector"
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239 for i in range(0, features_vector.shape[0]):
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240 mean_ = mean(features_vector[i,:])
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241 std_ = std(features_vector[i,:], ddof=1)
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242 moments_vector[i,0] = mean_
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243 moments_vector[i,1] = std_
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244
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245 features_vector[i,:] = (features_vector[i,:] - mean_)/std_
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246
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247 features_vector_original = features_vector
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248
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249
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250 print "[II] Extracting PCA configuration "
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251
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252 kernel, q, featurelist = extract_pca_configuration_from_data(features_vector)
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253
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254 print "[II] Optimal number of PCs to keep: %d" % q
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255
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256 feature_captions_array = array(feature_captions)
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257
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258 features_to_keep = list(feature_captions_array[featurelist])
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259 print "[II] Decided to keep %d features:" % len(features_to_keep)
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260 print str(features_to_keep).replace("', ","\n").replace('[','').replace("'","[II]\t ")[:-7]
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261
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262
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263 features_kept_data = features_vector[featurelist,:]
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264
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265 features_vector = (kernel.T*features_kept_data)[0:q,:]
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266
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267 parameters_k_means = KMeans(init='k-means++', n_init=10, max_iter=300, tol=0.0000001, verbose = 0)
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268
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269 print "[II] Trying ADM-coded parameters"
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270 print "[II] Upsampling features and parameters by a factor of %d" % UpsamplingFactor
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271
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272
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273 # Upsampled features and parameters
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274 features_vector_upsampled = smooth_matrix_1D(repeat(features_vector,UpsamplingFactor, axis=1))
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275
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276 # feature_labels_upsampled = repeat(features_clustering_labels,UpsamplingFactor, axis=0)
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277 parameters_vector_upsampled = repeat(parameters_vector,UpsamplingFactor, axis=1)
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278
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279 # parameters_vector_upsampled = smooth_matrix_1D(parameters_vector_upsampled)
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280
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281 parameters_vector_upsampled_adm = matrix(zeros(shape(parameters_vector_upsampled)))
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282 parameters_vector_upsampled_code = matrix(zeros(shape(parameters_vector_upsampled)))
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283 parameters_vector_upsampled_firstval = matrix(zeros((parameters_vector_upsampled.shape[0],1)))
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284
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285 # Reconstructed parameters
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286
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287 parameters_vector_upsampled_reconstructed = matrix(zeros(shape(parameters_vector_upsampled)))
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288
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289
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290
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291
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292 def adm_matrix(X, dmin=0.001,dmax=0.28,tol=0.001):
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293
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294 out = matrix(zeros(shape(X)))
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295 code = matrix(zeros(shape(X)))
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296 firstval = matrix(zeros((X.shape[0], 1)))
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297
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298 for i in range(0, X.shape[0]):
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299 out[i,:], code[i,:], firstval[i,0] = adm(X[i,:],dmin=dmin,dmax=dmax,tol=tol)
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300
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301 return out,code,firstval
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302
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303 # parameters_vector_upsampled_reconstructed[i,:] = adm_reconstruct(parameters_vector_upsampled_code[i,:],parameters_vector_upsampled_firstval[i,0], dmin=dmin,dmax=dmax)
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304
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305 def adm_matrix_reconstruct(code, firstval, dmin=0.001, dmax=0.28):
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306 X = matrix(zeros(shape(code)))
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307 for i in range(0, code.shape[0]):
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308 X[i,:] = adm_reconstruct(code[i,:], firstval[i,0], dmin=dmin, dmax=dmax)
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309
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310 return X
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311
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312
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313 parameters_vector_upsampled_adm, parameters_vector_upsampled_code, parameters_vector_upsampled_firstval = adm_matrix(parameters_vector_upsampled, dmin, dmax, tol)
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314
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315
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316 def diff_and_pad(X):
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317 return concatenate((
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318 zeros((
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319 shape(X)[0],
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320 1
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321 )),
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322 diff(X, axis=1)),
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323 axis=1)
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324
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325
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326 print "[II] Clustering features."
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327 #
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328 features_clustering = GMM(n_components = n_clusters, covariance_type='diag')
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329 #
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330 features_clustering.fit( features_vector_upsampled.T, y=parameters_vector_upsampled_code)
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331 #
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332 features_clustering_means = features_clustering.means_
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333 features_clustering_labels = features_clustering.predict(features_vector_upsampled.T)
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334 features_clustering_sigmas = features_clustering.covars_
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335 #
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336 features_vector_upsampled_estimated = zeros(shape(features_vector_upsampled))
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337 #
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338 #
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339 for n in range(0, len(features_vector_upsampled_estimated[0])):
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340 features_vector_upsampled_estimated[:,n] = features_clustering_means[features_clustering_labels[n]]
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341 #
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342 #
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343 print "[II] Features MSE for %d clusters: %.3f" % (n_clusters, mse(features_vector_upsampled, features_vector_upsampled_estimated))
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344
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345
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346
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347
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348 def cross_validate_classification(data, classes, estimator):
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349 print "[II] Crossvalidating... "
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350 from copy import deepcopy
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351 estimator_fulldata = deepcopy(estimator)
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352 estimator_fulldata.fit(data, classes)
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353
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354 percents = arange(0.1,0.9,0.1)
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355 MSEs = []
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356 labels = estimator.predict(data)
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357
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358 print "[II] for full training-testing: %.2f" % (sum(array(classes==labels).astype(float))/len(labels))
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359
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360 for p in percents:
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361 train,test,trainlabels,testlabels = cross_validation.train_test_split(data,classes,test_size=p,random_state=0)
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362 estimator_ = deepcopy(estimator)
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363 estimator_.fit(train, trainlabels)
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364 labels = estimator.predict(test)
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365 print "[II] for training(%.2f)-testing(%.2f): %.2f" % ((1-p),p,sum(array(testlabels==labels).astype(float))/len(labels))
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366
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367 return MSEs
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368
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369 def cross_validate_clustering(data, estimator):
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370 print "[II] Crossvalidating... "
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371 estimator_fulldata = estimator
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372 estimator_fulldata.fit(data)
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373
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374 # labels = estimator_fulldata.predict(data)
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375 means = estimator_fulldata.means_
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376 # print means
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377
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378 percents = arange(0.1,0.6,0.1)
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379 MSEs = []
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380 reconstructed = zeros(shape(data))
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381 labels = estimator.predict(data)
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382 for n in range(0, len(reconstructed)):
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383 reconstructed[n,:] = means[labels[n]]
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384
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385 MSEs.append(mse(data,reconstructed))
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386 for p in percents:
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387 train,test = cross_validation.train_test_split(data,test_size=p,random_state=0)
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388 train = matrix(train)
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389 test = matrix(test)
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390
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391 estimator.fit(train)
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392 means = estimator.means_
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393 labels = estimator.predict(test)
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394 reconstructed = zeros(shape(test))
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395 for n in range(0, len(reconstructed)):
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396 reconstructed[n,:] = means[labels[n]]
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397
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398 m = mse(test,reconstructed)
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399
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400 print "[II] MSE for clustering crossvalidated data %.2f-%.2f: %.5f" % ((1-p), p, m)
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401 MSEs.append(m)
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402
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403 print "[II] Crossvalidation complete"
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404
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405 return MSEs
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406
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407
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408
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409
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410 # Construct parameters alphabet, each symbol is going to be a different column vector
|
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411 # in parameter code matrix
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412
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413
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414 def vector_to_states(X):
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415 """
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416 Input: a vector MxN with N samples and M variables
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417 Output: a codeword dictionary `parameters_alphabet',
|
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418 state_seq, inverse `parameters_alphabet_inv' """
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419
|
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420
|
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421 parameters_alphabet = {}
|
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422 n = 0
|
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423
|
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424 for i in range(0, X.shape[1]):
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425 vec = tuple(ravel(X[:,i]))
|
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426 if vec not in parameters_alphabet:
|
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427 parameters_alphabet[vec] = n
|
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428 n += 1
|
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429
|
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430 parameters_alphabet_inv = dict([(parameters_alphabet[m],m) for m in parameters_alphabet])
|
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431
|
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432 state_seq = array([parameters_alphabet[tuple(ravel(X[:,m]))] for m in range(0, parameters_vector_upsampled_code.shape[1])] )
|
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433
|
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434 return state_seq, parameters_alphabet, parameters_alphabet_inv
|
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|
435
|
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|
436
|
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|
437 def states_to_vector(predicted, parameters_alphabet_inv):
|
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|
438 estimated = matrix(zeros((len(parameters_alphabet_inv[0]), len(predicted))))
|
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439 for i in range(0, len(state_seq)):
|
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440 estimated[:, i] = matrix(parameters_alphabet_inv[predicted[i]]).T
|
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|
441
|
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|
442 return estimated
|
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|
443
|
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|
444 state_seq, parameters_alphabet, parameters_alphabet_inv = vector_to_states(parameters_vector_upsampled_code)
|
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|
445
|
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|
446
|
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|
447 parameters_change_variable = matrix(diff_and_pad(parameters_vector_upsampled)!=0).astype(int)
|
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|
448
|
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|
449 changes_state_seq, changes_parameters_alphabet, changes_parameters_alphabet_inv = vector_to_states(parameters_change_variable)
|
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|
450
|
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|
451
|
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|
452 # This is an hmm that just codes the changes"
|
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|
453 # We have only two states, change and stay the same.
|
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|
454
|
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|
455
|
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|
456 parameters_state, parameter_state_alphabet, parameter_state_alphabet_inv = vector_to_states(parameters_vector_upsampled)
|
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|
457
|
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|
458
|
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|
459 print "[II] Testing Gaussian Naive Bayes Classifier"
|
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|
460 gnb = GaussianNB()
|
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|
461 gnb.fit(features_vector_upsampled.T, parameters_state)
|
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|
462
|
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|
463 parameters_state_estimated = gnb.predict(features_vector_upsampled.T)
|
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|
464
|
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|
465 output = states_to_vector(parameters_state_estimated, parameter_state_alphabet_inv)
|
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|
466
|
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|
467 figure()
|
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|
468 subplot(211)
|
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|
469 plot(parameters_vector_upsampled.T)
|
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|
470 title('Parameter value upsampled by a factor of %d' % UpsamplingFactor)
|
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|
471 ylabel('value')
|
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|
472 xlabel('frame #')
|
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|
473 subplot(212)
|
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|
474 #plot(smooth_matrix_1D(output).T)
|
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|
475 plot(output.T)
|
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|
476 ylabel('value')
|
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|
477 xlabel('frame #')
|
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|
478 cross_validate_classification(features_vector_upsampled.T, parameters_state, gnb)
|
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|
479
|
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|
480 print "[II] Trying Multinomial HMM"
|
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|
481
|
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|
482 # In order to do classification with HMMs, we need to:
|
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|
483 # 1. Split the parameters into classes
|
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|
484 # 2. Train one model per class
|
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|
485 # 3. Feed our data to all the models
|
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|
486 # 4. Check which has a better score and assig,n to M
|
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|
487
|
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|
488
|
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|
489 class HmmClassifier:
|
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|
490 def __init__(self, N=2, n_components = 1):
|
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|
491 self.n_components = n_components
|
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|
492 self.chain_size = N
|
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|
493 self.hmms_ = []
|
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|
494 self.N = N
|
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|
495
|
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|
496 def fit(self, X, states):
|
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|
497 self.n_states = len(unique(states))
|
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|
498
|
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|
499 for n in range(0, self.n_states):
|
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|
500 hmm_ = hmm.GaussianHMM(n_components = self.n_components, covariance_type = 'full')
|
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|
501
|
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|
502 # Get training data for each class
|
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|
503 vector = X[states == n,:]
|
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|
504
|
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|
505 # Fit the HMM
|
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|
506 # print vector
|
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|
507 hmm_.fit([vector])
|
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|
508
|
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|
509 # And append to the list
|
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|
510 self.hmms_.append(hmm_)
|
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|
511
|
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|
512 def predict(self,X):
|
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|
513 labels = zeros((X.shape[0],))
|
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|
514 N = self.N
|
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|
515
|
e@0
|
516 m = 0
|
e@0
|
517
|
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|
518 scores = zeros((1, self.n_states))
|
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|
519
|
e@0
|
520
|
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|
521 while m*N < X.shape[0]:
|
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|
522 if (m+1)*N > X.shape[0]:
|
e@0
|
523 testdata = X[m*N:,:]
|
e@0
|
524 else:
|
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|
525 testdata = X[m*N:(m+1)*N,:]
|
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|
526
|
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|
527 # print testdata
|
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|
528
|
e@0
|
529 for i in range(0, self.n_states):
|
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|
530 scores[0,i] = self.hmms_[i].score(testdata)
|
e@0
|
531
|
e@0
|
532 if (m+1)*N > X.shape[0]:
|
e@0
|
533 labels[m*N:] = argmax(scores)
|
e@0
|
534 else:
|
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|
535 labels[m*N:(m+1)*N] = argmax(scores)
|
e@0
|
536
|
e@0
|
537 m+= 1
|
e@0
|
538
|
e@0
|
539 return labels
|
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|
540
|
e@0
|
541 N = 150
|
e@0
|
542 n_components = 1
|
e@0
|
543
|
e@0
|
544 hmmc = HmmClassifier(N = N, n_components = n_components)
|
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|
545 hmmc.fit(features_vector_upsampled.T, parameters_state)
|
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|
546
|
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|
547 cross_validate_classification(features_vector_upsampled.T, parameters_state, hmmc)
|
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|
548
|
e@0
|
549
|
e@0
|
550
|
e@0
|
551
|
e@0
|
552 # hmms_ = []
|
e@0
|
553 #
|
e@0
|
554 # for n in range(0, len(parameter_state_alphabet)):
|
e@0
|
555 # #hmm_ = hmm.GMMHMM(n_components = 1, n_mix = 2)
|
e@0
|
556 # hmm_ = hmm.GaussianHMM(n_components = 1,covariance_type = 'full')
|
e@0
|
557 #
|
e@0
|
558 # # Get training data for each class
|
e@0
|
559 # vector = features_vector_upsampled[:,parameters_state == n]
|
e@0
|
560 #
|
e@0
|
561 # #if vector.shape[1] < n_clusters:
|
e@0
|
562 # # hmms_.append(None)
|
e@0
|
563 # #else:
|
e@0
|
564 #
|
e@0
|
565 # hmm_.fit([vector.T])
|
e@0
|
566 #
|
e@0
|
567 # # Append to the list
|
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|
568 #
|
e@0
|
569 # hmms_.append(hmm_)
|
e@0
|
570 #
|
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|
571 # labels = zeros((features_vector_upsampled.shape[1],))
|
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|
572 #
|
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|
573 # N = 20
|
e@0
|
574 # m = 0
|
e@0
|
575 #
|
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|
576 # while m*N < features_vector_upsampled.shape[1]:
|
e@0
|
577 #
|
e@0
|
578 # scores = zeros((1, len(parameter_state_alphabet)))
|
e@0
|
579 #
|
e@0
|
580 # if (m+1)*N > features_vector_upsampled.shape[1]:
|
e@0
|
581 # testdata = features_vector_upsampled[:,m*N:]
|
e@0
|
582 # else:
|
e@0
|
583 # testdata = features_vector_upsampled[:,m*N:(m+1)*N]
|
e@0
|
584 #
|
e@0
|
585 # for i in range(0, len(parameter_state_alphabet)):
|
e@0
|
586 # if hmms_[i] is not None:
|
e@0
|
587 # scores[0,i] = hmms_[i].score(testdata.T)
|
e@0
|
588 # else:
|
e@0
|
589 # scores[0,i] = -100000 # Very large negative score
|
e@0
|
590 # if (m+1)*N >= features_vector_upsampled.shape[1]:
|
e@0
|
591 # labels[m*N:] = argmax(scores)
|
e@0
|
592 # else:
|
e@0
|
593 # labels[m*N:(m+1)*N] = argmax(scores)
|
e@0
|
594 #
|
e@0
|
595 # m += 1
|
e@0
|
596
|
e@0
|
597
|
e@0
|
598 # figure()
|
e@0
|
599 #plot(labels.T)
|
e@0
|
600
|
e@0
|
601
|
e@0
|
602 labels = hmmc.predict(features_vector_upsampled.T)
|
e@0
|
603 estimated = states_to_vector(labels,parameter_state_alphabet_inv)
|
e@0
|
604 plot(estimated.T,'r--')
|
e@0
|
605
|
e@0
|
606 title('Estimated parameter values')
|
e@0
|
607 legend(['Naive Bayes Classifier', 'HMM chain size %d (%.1fms)' % (N, float(N)/UpsamplingFactor*23.0)])
|
e@0
|
608
|
e@0
|
609 ylabel('value')
|
e@0
|
610 xlabel('frame #') |