annotate experiment-reverb/code/supervised_training_hmms_higher_orderpy @ 2:c87a9505f294 tip

Added LICENSE for code, removed .wav files
author Emmanouil Theofanis Chourdakis <e.t.chourdakis@qmul.ac.uk>
date Sat, 30 Sep 2017 13:25:50 +0100
parents 246d5546657c
children
rev   line source
e@0 1 #!/usr/bin/python2
e@0 2 # -*- coding: utf-8 -*-
e@0 3 """
e@0 4 Created on Thu Apr 23 11:53:17 2015
e@0 5
e@0 6 @author: mmxgn
e@0 7 """
e@0 8
e@0 9 # This file does the cluster estimation and the removal of outliers
e@0 10
e@0 11 from sys import argv, exit
e@0 12 from essentia.standard import YamlInput, YamlOutput
e@0 13 from essentia import Pool
e@0 14 from pca import *
e@0 15
e@0 16 from numpy import *
e@0 17 from sklearn import cluster
e@0 18 from sklearn.metrics import pairwise_distances
e@0 19 from sklearn.cluster import KMeans, MiniBatchKMeans
e@0 20 from matplotlib.pyplot import *
e@0 21 #from sklearn.mixture import GMM
e@0 22 from sklearn.naive_bayes import GaussianNB, MultinomialNB
e@0 23 from scipy.signal import decimate
e@0 24 from sklearn import cross_validation
e@0 25
e@0 26 #from hmmlearn import hmm
e@0 27 from hmmlearn.hmm import GMM
e@0 28 from hmmlearn import hmm
e@0 29 #from adpcm import adm, adm_reconstruct
e@0 30
e@0 31
e@0 32 mse = lambda A,B: ((array(A)-array(B)) ** 2).mean()
e@0 33
e@0 34
e@0 35 def smooth_matrix_1D(X):
e@0 36 window = scipy.signal.gaussian(51,4)
e@0 37 window = window/sum(window)
e@0 38 intermx = zeros((X.shape[0],X.shape[1]+100))
e@0 39 intermx[:, 50:-50] = X
e@0 40
e@0 41 for m in range(0, X.shape[0]):
e@0 42 # print intermx.shape
e@0 43 intermx[m,:] = convolve(ravel(intermx[m,:]), window,'same')
e@0 44
e@0 45 return intermx[:,50:-50]
e@0 46
e@0 47 def adm_reconstruct(codeword, h, dmin=.01, dmax=.28):
e@0 48 x = zeros((1, codeword.shape[1]))
e@0 49
e@0 50 delta1 = dmin
e@0 51 delta2 = dmin
e@0 52 Sum = h
e@0 53
e@0 54 x[0] = h
e@0 55 for i in range(0, codeword.shape[1]):
e@0 56 if codeword[0,i] == 0:
e@0 57 delta1 = dmin
e@0 58 delta2 = dmin
e@0 59
e@0 60 elif codeword[0,i] == 1:
e@0 61 delta2 = dmin
e@0 62 Sum += delta1
e@0 63 delta1 *= 2
e@0 64 if delta1 > dmax:
e@0 65 delta1 = dmax
e@0 66
e@0 67 elif codeword[0,i] == -1:
e@0 68 delta1 = dmin
e@0 69 Sum -= delta2
e@0 70 delta2 *= 2
e@0 71 if delta2 > dmax:
e@0 72 delta2 = dmax
e@0 73 x[0,i] = Sum
e@0 74 return x
e@0 75
e@0 76 def adm(x, dmin=.01, dmax=.28, tol=0.0001):
e@0 77
e@0 78 # Adaptive delta modulation adapted by code:
e@0 79 # (adeltamod.m)
e@0 80 #
e@0 81 # Adaptive Delta Modulator
e@0 82 # by Gandhar Desai (gdesai)
e@0 83 # BITS Pilani Goa Campus
e@0 84 # Date: 28 Sept, 2013
e@0 85
e@0 86 xsig = x
e@0 87
e@0 88 Lx = len(x)
e@0 89
e@0 90 ADMout = zeros((1, Lx))
e@0 91 codevec = zeros((1, Lx))
e@0 92
e@0 93
e@0 94 Sum = x[0]
e@0 95 delta1 = dmin
e@0 96 delta2 = dmin
e@0 97 mult1 = 2
e@0 98 mult2 = 2
e@0 99 for i in range(0, Lx):
e@0 100 #print abs(xsig[i] - Sum)
e@0 101 if (abs(xsig[i] - Sum) < tol):
e@0 102 bit = 0
e@0 103 delta2 = dmin
e@0 104 delta1 = dmin
e@0 105
e@0 106
e@0 107 elif (xsig[i] >= Sum):
e@0 108 bit = 1
e@0 109 delta2 = dmin
e@0 110 Sum += delta1
e@0 111 delta1 *= mult1
e@0 112 if delta1 > dmax:
e@0 113 delta1 = dmax
e@0 114
e@0 115
e@0 116 else:
e@0 117 bit = -1
e@0 118 delta1 = dmin
e@0 119 Sum -= delta2
e@0 120 delta2 *= mult2
e@0 121 if delta2 > dmax:
e@0 122 delta2 = dmax
e@0 123
e@0 124
e@0 125
e@0 126 ADMout[0, i] = Sum
e@0 127 codevec[0, i]= bit
e@0 128
e@0 129 return ADMout,codevec, x[0]
e@0 130
e@0 131 if __name__=="__main__":
e@0 132 if len(argv) != 2:
e@0 133 print "[EE] Wrong number of arguments"
e@0 134 print "[II] Correct syntax is:"
e@0 135 print "[II] \t%s <training_file>"
e@0 136 print "[II] where <training_file> is a .yaml file containing the"
e@0 137 print "[II] features of the dataset (try output2_stage/fulltraining-last.yaml)"
e@0 138 exit(-1)
e@0 139
e@0 140
e@0 141 n_clusters = 25
e@0 142 UpsamplingFactor = 10
e@0 143 dmin = 0.001
e@0 144 dmax = 0.28
e@0 145 tol = 0.001
e@0 146
e@0 147 infile = argv[1]
e@0 148
e@0 149 features_pool = YamlInput(filename = infile)()
e@0 150
e@0 151
e@0 152
e@0 153 feature_captions = features_pool.descriptorNames()
e@0 154 parameter_captions = []
e@0 155
e@0 156
e@0 157 for c in features_pool.descriptorNames():
e@0 158 if c.split('.')[0] == 'parameter':
e@0 159 parameter_captions.append(c)
e@0 160 if c.split('.')[0] == 'metadata' or c.split('.')[0] == 'parameter':
e@0 161 feature_captions.remove(c)
e@0 162
e@0 163
e@0 164
e@0 165 # close('all')
e@0 166
e@0 167 print "[II] Loaded training data from %s (%s) " % (infile, features_pool['metadata.date'][0])
e@0 168 print "[II] %d Features Available: " % len(feature_captions)
e@0 169
e@0 170
e@0 171
e@0 172 print str(feature_captions).replace("', ","\n").replace('[','').replace("'","[II]\t ")[:-7]
e@0 173
e@0 174 nfeatures_in = len(feature_captions)
e@0 175 nparameters_in = len(parameter_captions)
e@0 176 features_vector = zeros((nfeatures_in, len(features_pool[feature_captions[0]])))
e@0 177
e@0 178 parameters_vector = zeros((nparameters_in, len(features_pool[parameter_captions[0]])))
e@0 179
e@0 180
e@0 181 for i in range(0, nfeatures_in):
e@0 182 features_vector[i, :] = features_pool[feature_captions[i]].T
e@0 183 for i in range(0, nparameters_in):
e@0 184 parameters_vector[i, :] = features_pool[parameter_captions[0]].T
e@0 185
e@0 186 print "[II] %d parameters used:" % len(parameter_captions)
e@0 187 print str(parameter_captions).replace("', ","\n").replace('[','').replace("'","[II]\t ")[:-7].replace('parameter.','')
e@0 188
e@0 189 print "[II] Marking silent parts"
e@0 190
e@0 191 silent_parts = zeros((1, len(features_pool[feature_captions[i]].T)))
e@0 192
e@0 193 rms = features_vector[feature_captions.index('rms'), :]
e@0 194
e@0 195 # Implementing Hysteresis Gate -- High threshold is halfway between
e@0 196 # the mean and the max and Low is halfway between the mean dn the min
e@0 197
e@0 198 rms_threshold_mean = mean(rms)
e@0 199
e@0 200 rms_threshold_max = max(rms)
e@0 201 rms_threshold_min = min(rms)
e@0 202
e@0 203 rms_threshold_high = 0.1 * rms_threshold_mean
e@0 204 rms_threshold_low = 0.01 * rms_threshold_mean
e@0 205
e@0 206 for n in range(1, len(rms)):
e@0 207 prev = rms[n-1]
e@0 208 curr = rms[n]
e@0 209
e@0 210 if prev >= rms_threshold_high:
e@0 211 if curr < rms_threshold_low:
e@0 212 silent_parts[0,n] = 1
e@0 213 else:
e@0 214 silent_parts[0,n] = 0
e@0 215 elif prev <= rms_threshold_low:
e@0 216 if curr > rms_threshold_high:
e@0 217 silent_parts[0,n] = 0
e@0 218 else:
e@0 219 silent_parts[0,n] = 1
e@0 220 else:
e@0 221 silent_parts[0,n] = silent_parts[0,n-1]
e@0 222
e@0 223
e@0 224 if silent_parts[0,1] == 1:
e@0 225 silent_parts[0, 0] = 1
e@0 226
e@0 227
e@0 228
e@0 229 active_index = invert(silent_parts.flatten().astype(bool))
e@0 230
e@0 231 # Keep only active parts
e@0 232
e@0 233 # Uncomment this
e@0 234 features_vector = features_vector[:, active_index]
e@0 235
e@0 236 moments_vector = zeros((features_vector.shape[0], 2))
e@0 237
e@0 238 print "[II] Storing moments vector"
e@0 239 for i in range(0, features_vector.shape[0]):
e@0 240 mean_ = mean(features_vector[i,:])
e@0 241 std_ = std(features_vector[i,:], ddof=1)
e@0 242 moments_vector[i,0] = mean_
e@0 243 moments_vector[i,1] = std_
e@0 244
e@0 245 features_vector[i,:] = (features_vector[i,:] - mean_)/std_
e@0 246
e@0 247 features_vector_original = features_vector
e@0 248
e@0 249
e@0 250 print "[II] Extracting PCA configuration "
e@0 251
e@0 252 kernel, q, featurelist = extract_pca_configuration_from_data(features_vector)
e@0 253
e@0 254 print "[II] Optimal number of PCs to keep: %d" % q
e@0 255
e@0 256 feature_captions_array = array(feature_captions)
e@0 257
e@0 258 features_to_keep = list(feature_captions_array[featurelist])
e@0 259 print "[II] Decided to keep %d features:" % len(features_to_keep)
e@0 260 print str(features_to_keep).replace("', ","\n").replace('[','').replace("'","[II]\t ")[:-7]
e@0 261
e@0 262
e@0 263 features_kept_data = features_vector[featurelist,:]
e@0 264
e@0 265 features_vector = (kernel.T*features_kept_data)[0:q,:]
e@0 266
e@0 267 parameters_k_means = KMeans(init='k-means++', n_init=10, max_iter=300, tol=0.0000001, verbose = 0)
e@0 268
e@0 269 print "[II] Trying ADM-coded parameters"
e@0 270 print "[II] Upsampling features and parameters by a factor of %d" % UpsamplingFactor
e@0 271
e@0 272
e@0 273 # Upsampled features and parameters
e@0 274 features_vector_upsampled = smooth_matrix_1D(repeat(features_vector,UpsamplingFactor, axis=1))
e@0 275
e@0 276 # feature_labels_upsampled = repeat(features_clustering_labels,UpsamplingFactor, axis=0)
e@0 277 parameters_vector_upsampled = repeat(parameters_vector,UpsamplingFactor, axis=1)
e@0 278
e@0 279 # parameters_vector_upsampled = smooth_matrix_1D(parameters_vector_upsampled)
e@0 280
e@0 281 parameters_vector_upsampled_adm = matrix(zeros(shape(parameters_vector_upsampled)))
e@0 282 parameters_vector_upsampled_code = matrix(zeros(shape(parameters_vector_upsampled)))
e@0 283 parameters_vector_upsampled_firstval = matrix(zeros((parameters_vector_upsampled.shape[0],1)))
e@0 284
e@0 285 # Reconstructed parameters
e@0 286
e@0 287 parameters_vector_upsampled_reconstructed = matrix(zeros(shape(parameters_vector_upsampled)))
e@0 288
e@0 289
e@0 290
e@0 291
e@0 292 def adm_matrix(X, dmin=0.001,dmax=0.28,tol=0.001):
e@0 293
e@0 294 out = matrix(zeros(shape(X)))
e@0 295 code = matrix(zeros(shape(X)))
e@0 296 firstval = matrix(zeros((X.shape[0], 1)))
e@0 297
e@0 298 for i in range(0, X.shape[0]):
e@0 299 out[i,:], code[i,:], firstval[i,0] = adm(X[i,:],dmin=dmin,dmax=dmax,tol=tol)
e@0 300
e@0 301 return out,code,firstval
e@0 302
e@0 303 # parameters_vector_upsampled_reconstructed[i,:] = adm_reconstruct(parameters_vector_upsampled_code[i,:],parameters_vector_upsampled_firstval[i,0], dmin=dmin,dmax=dmax)
e@0 304
e@0 305 def adm_matrix_reconstruct(code, firstval, dmin=0.001, dmax=0.28):
e@0 306 X = matrix(zeros(shape(code)))
e@0 307 for i in range(0, code.shape[0]):
e@0 308 X[i,:] = adm_reconstruct(code[i,:], firstval[i,0], dmin=dmin, dmax=dmax)
e@0 309
e@0 310 return X
e@0 311
e@0 312
e@0 313 parameters_vector_upsampled_adm, parameters_vector_upsampled_code, parameters_vector_upsampled_firstval = adm_matrix(parameters_vector_upsampled, dmin, dmax, tol)
e@0 314
e@0 315
e@0 316 def diff_and_pad(X):
e@0 317 return concatenate((
e@0 318 zeros((
e@0 319 shape(X)[0],
e@0 320 1
e@0 321 )),
e@0 322 diff(X, axis=1)),
e@0 323 axis=1)
e@0 324
e@0 325
e@0 326 print "[II] Clustering features."
e@0 327 #
e@0 328 features_clustering = GMM(n_components = n_clusters, covariance_type='diag')
e@0 329 #
e@0 330 features_clustering.fit( features_vector_upsampled.T, y=parameters_vector_upsampled_code)
e@0 331 #
e@0 332 features_clustering_means = features_clustering.means_
e@0 333 features_clustering_labels = features_clustering.predict(features_vector_upsampled.T)
e@0 334 features_clustering_sigmas = features_clustering.covars_
e@0 335 #
e@0 336 features_vector_upsampled_estimated = zeros(shape(features_vector_upsampled))
e@0 337 #
e@0 338 #
e@0 339 for n in range(0, len(features_vector_upsampled_estimated[0])):
e@0 340 features_vector_upsampled_estimated[:,n] = features_clustering_means[features_clustering_labels[n]]
e@0 341 #
e@0 342 #
e@0 343 print "[II] Features MSE for %d clusters: %.3f" % (n_clusters, mse(features_vector_upsampled, features_vector_upsampled_estimated))
e@0 344
e@0 345
e@0 346
e@0 347
e@0 348 def cross_validate_classification(data, classes, estimator):
e@0 349 print "[II] Crossvalidating... "
e@0 350 from copy import deepcopy
e@0 351 estimator_fulldata = deepcopy(estimator)
e@0 352 estimator_fulldata.fit(data, classes)
e@0 353
e@0 354 percents = arange(0.1,0.9,0.1)
e@0 355 MSEs = []
e@0 356 labels = estimator.predict(data)
e@0 357
e@0 358 print "[II] for full training-testing: %.2f" % (sum(array(classes==labels).astype(float))/len(labels))
e@0 359
e@0 360 for p in percents:
e@0 361 train,test,trainlabels,testlabels = cross_validation.train_test_split(data,classes,test_size=p,random_state=0)
e@0 362 estimator_ = deepcopy(estimator)
e@0 363 estimator_.fit(train, trainlabels)
e@0 364 labels = estimator.predict(test)
e@0 365 print "[II] for training(%.2f)-testing(%.2f): %.2f" % ((1-p),p,sum(array(testlabels==labels).astype(float))/len(labels))
e@0 366
e@0 367 return MSEs
e@0 368
e@0 369 def cross_validate_clustering(data, estimator):
e@0 370 print "[II] Crossvalidating... "
e@0 371 estimator_fulldata = estimator
e@0 372 estimator_fulldata.fit(data)
e@0 373
e@0 374 # labels = estimator_fulldata.predict(data)
e@0 375 means = estimator_fulldata.means_
e@0 376 # print means
e@0 377
e@0 378 percents = arange(0.1,0.6,0.1)
e@0 379 MSEs = []
e@0 380 reconstructed = zeros(shape(data))
e@0 381 labels = estimator.predict(data)
e@0 382 for n in range(0, len(reconstructed)):
e@0 383 reconstructed[n,:] = means[labels[n]]
e@0 384
e@0 385 MSEs.append(mse(data,reconstructed))
e@0 386 for p in percents:
e@0 387 train,test = cross_validation.train_test_split(data,test_size=p,random_state=0)
e@0 388 train = matrix(train)
e@0 389 test = matrix(test)
e@0 390
e@0 391 estimator.fit(train)
e@0 392 means = estimator.means_
e@0 393 labels = estimator.predict(test)
e@0 394 reconstructed = zeros(shape(test))
e@0 395 for n in range(0, len(reconstructed)):
e@0 396 reconstructed[n,:] = means[labels[n]]
e@0 397
e@0 398 m = mse(test,reconstructed)
e@0 399
e@0 400 print "[II] MSE for clustering crossvalidated data %.2f-%.2f: %.5f" % ((1-p), p, m)
e@0 401 MSEs.append(m)
e@0 402
e@0 403 print "[II] Crossvalidation complete"
e@0 404
e@0 405 return MSEs
e@0 406
e@0 407
e@0 408
e@0 409
e@0 410 # Construct parameters alphabet, each symbol is going to be a different column vector
e@0 411 # in parameter code matrix
e@0 412
e@0 413
e@0 414 def vector_to_states(X):
e@0 415 """
e@0 416 Input: a vector MxN with N samples and M variables
e@0 417 Output: a codeword dictionary `parameters_alphabet',
e@0 418 state_seq, inverse `parameters_alphabet_inv' """
e@0 419
e@0 420
e@0 421 parameters_alphabet = {}
e@0 422 n = 0
e@0 423
e@0 424 for i in range(0, X.shape[1]):
e@0 425 vec = tuple(ravel(X[:,i]))
e@0 426 if vec not in parameters_alphabet:
e@0 427 parameters_alphabet[vec] = n
e@0 428 n += 1
e@0 429
e@0 430 parameters_alphabet_inv = dict([(parameters_alphabet[m],m) for m in parameters_alphabet])
e@0 431
e@0 432 state_seq = array([parameters_alphabet[tuple(ravel(X[:,m]))] for m in range(0, parameters_vector_upsampled_code.shape[1])] )
e@0 433
e@0 434 return state_seq, parameters_alphabet, parameters_alphabet_inv
e@0 435
e@0 436
e@0 437 def states_to_vector(predicted, parameters_alphabet_inv):
e@0 438 estimated = matrix(zeros((len(parameters_alphabet_inv[0]), len(predicted))))
e@0 439 for i in range(0, len(state_seq)):
e@0 440 estimated[:, i] = matrix(parameters_alphabet_inv[predicted[i]]).T
e@0 441
e@0 442 return estimated
e@0 443
e@0 444 state_seq, parameters_alphabet, parameters_alphabet_inv = vector_to_states(parameters_vector_upsampled_code)
e@0 445
e@0 446
e@0 447 parameters_change_variable = matrix(diff_and_pad(parameters_vector_upsampled)!=0).astype(int)
e@0 448
e@0 449 changes_state_seq, changes_parameters_alphabet, changes_parameters_alphabet_inv = vector_to_states(parameters_change_variable)
e@0 450
e@0 451
e@0 452 # This is an hmm that just codes the changes"
e@0 453 # We have only two states, change and stay the same.
e@0 454
e@0 455
e@0 456 parameters_state, parameter_state_alphabet, parameter_state_alphabet_inv = vector_to_states(parameters_vector_upsampled)
e@0 457
e@0 458
e@0 459 print "[II] Testing Gaussian Naive Bayes Classifier"
e@0 460 gnb = GaussianNB()
e@0 461 gnb.fit(features_vector_upsampled.T, parameters_state)
e@0 462
e@0 463 parameters_state_estimated = gnb.predict(features_vector_upsampled.T)
e@0 464
e@0 465 output = states_to_vector(parameters_state_estimated, parameter_state_alphabet_inv)
e@0 466
e@0 467 figure()
e@0 468 subplot(211)
e@0 469 plot(parameters_vector_upsampled.T)
e@0 470 title('Parameter value upsampled by a factor of %d' % UpsamplingFactor)
e@0 471 ylabel('value')
e@0 472 xlabel('frame #')
e@0 473 subplot(212)
e@0 474 #plot(smooth_matrix_1D(output).T)
e@0 475 plot(output.T)
e@0 476 ylabel('value')
e@0 477 xlabel('frame #')
e@0 478 cross_validate_classification(features_vector_upsampled.T, parameters_state, gnb)
e@0 479
e@0 480 print "[II] Trying Multinomial HMM"
e@0 481
e@0 482 # In order to do classification with HMMs, we need to:
e@0 483 # 1. Split the parameters into classes
e@0 484 # 2. Train one model per class
e@0 485 # 3. Feed our data to all the models
e@0 486 # 4. Check which has a better score and assig,n to M
e@0 487
e@0 488
e@0 489 class HmmClassifier:
e@0 490 def __init__(self, N=2, n_components = 1):
e@0 491 self.n_components = n_components
e@0 492 self.chain_size = N
e@0 493 self.hmms_ = []
e@0 494 self.N = N
e@0 495
e@0 496 def fit(self, X, states):
e@0 497 self.n_states = len(unique(states))
e@0 498
e@0 499 for n in range(0, self.n_states):
e@0 500 hmm_ = hmm.GaussianHMM(n_components = self.n_components, covariance_type = 'full')
e@0 501
e@0 502 # Get training data for each class
e@0 503 vector = X[states == n,:]
e@0 504
e@0 505 # Fit the HMM
e@0 506 # print vector
e@0 507 hmm_.fit([vector])
e@0 508
e@0 509 # And append to the list
e@0 510 self.hmms_.append(hmm_)
e@0 511
e@0 512 def predict(self,X):
e@0 513 labels = zeros((X.shape[0],))
e@0 514 N = self.N
e@0 515
e@0 516 m = 0
e@0 517
e@0 518 scores = zeros((1, self.n_states))
e@0 519
e@0 520
e@0 521 while m*N < X.shape[0]:
e@0 522 if (m+1)*N > X.shape[0]:
e@0 523 testdata = X[m*N:,:]
e@0 524 else:
e@0 525 testdata = X[m*N:(m+1)*N,:]
e@0 526
e@0 527 # print testdata
e@0 528
e@0 529 for i in range(0, self.n_states):
e@0 530 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:
e@0 535 labels[m*N:(m+1)*N] = argmax(scores)
e@0 536
e@0 537 m+= 1
e@0 538
e@0 539 return labels
e@0 540
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)
e@0 545 hmmc.fit(features_vector_upsampled.T, parameters_state)
e@0 546
e@0 547 cross_validate_classification(features_vector_upsampled.T, parameters_state, hmmc)
e@0 548
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
e@0 568 #
e@0 569 # hmms_.append(hmm_)
e@0 570 #
e@0 571 # labels = zeros((features_vector_upsampled.shape[1],))
e@0 572 #
e@0 573 # N = 20
e@0 574 # m = 0
e@0 575 #
e@0 576 # 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 #')