def getFeatures(self, eegSegment, timeStampSegment, time_step, local_mu,
local_sigma):
targetBand = band(1, 12)
deltaBand = band(2.5, 3.5)
thetaBand = band(7.0, 8.0)
wideThetaBand = band(6.5, 8.0)
alphaBand = band(9.0, 9.5)
smallDelta = 0.000000001
#---------------
# compute power spectrum and sort it
powerSpect = np.abs(np.fft.fft(eegSegment))**2
freqs = np.fft.fftfreq(len(powerSpect), d=time_step)
idx = np.argsort(freqs)
sortedFreqs = freqs[idx]
sortedPowerSpect = powerSpect[idx]
# print(' ')
# print('in featureExtractorClassical.getFeaturesClassical():')
# print(' time_step = ' + str(time_step))
# print(' eegSegment = ' + str(eegSegment))
# print(' powerSpect = ' + str(powerSpect))
# print(' idx = ' + str(idx))
# print(' freqs = ' + str(freqs))
# print(' sortedFreqs = ' + str(sortedFreqs))
# print(' sortedPowerSpect = ' + str(sortedPowerSpect))
null = 0
cv = local_sigma / (np.abs(local_mu) + smallDelta)
# cv = local_sigma
integral = targetBand.getSumPower(sortedFreqs, sortedPowerSpect)
deltaPower = deltaBand.getSumPower(sortedFreqs, sortedPowerSpect)
thetaPower = thetaBand.getSumPower(sortedFreqs, sortedPowerSpect)
alphaPower = alphaBand.getSumPower(sortedFreqs, sortedPowerSpect)
wideThetaPower = wideThetaBand.getSumPower(sortedFreqs,
sortedPowerSpect)
deltaRatio = deltaPower / (deltaPower + thetaPower + alphaPower +
smallDelta)
thetaRatio = thetaPower / (deltaPower + smallDelta)
### return np.array([cv, integral, deltaRatio, deltaPower, alphaPower, thetaPower])
return np.array([
cv, integral, deltaRatio, deltaRatio, thetaRatio, deltaPower,
integral, alphaPower, thetaPower, thetaPower, integral
])
def __init__(self, paramDir='', paramFileName='', outputDir=''):
self.paramSetupType = 'directories'
pathFilePath = open('path.json')
p = json.load(pathFilePath)
self.pathPrefix = p['pathPrefix']
# print('self.pathPrefix = ', self.pathPrefix)
# directory and file name
if paramDir == '':
if paramFileName == '':
paramFilePath = self.pathPrefix + '/' + p[
'paramsDir'] + '/params.json'
else:
paramFilePath = self.pathPrefix + '/' + p[
'paramsDir'] + '/' + paramFileName
else:
paramFilePath = paramDir + '/' + paramFileName
print('in ParameterSetup, paramFilePath =', paramFilePath)
self.parameterFileHandler = open(paramFilePath)
d = json.load(self.parameterFileHandler)
if outputDir == '':
self.classifierDir = self.pathPrefix + '/' + d['classifierDir']
self.deepParamsDir = self.pathPrefix + '/' + d['deepParamsDir']
self.predDir = self.pathPrefix + '/' + d['predDir']
self.modelDirRoot = d['modelDirRoot']
else:
self.classifierDir = outputDir
self.deepParamsDir = outputDir
self.predDir = outputDir
self.modelDirRoot = outputDir
self.dataDir = self.pathPrefix + '/' + d['dataDir']
self.pickledDir = self.pathPrefix + '/' + d['pickledDir']
self.eegDir = self.pathPrefix + '/' + d['eegDir']
self.featureDir = self.pathPrefix + '/' + d['featureDir']
self.batchEvalDir = self.pathPrefix + '/' + d['batchEvalDir']
self.standardMiceDir = self.pathPrefix + '/' + d['standardMiceDir']
self.ksDir = self.pathPrefix + '/' + d['ksDir']
self.finalClassifierDir = self.pathPrefix + '/' + d[
'finalclassifierDir']
self.waveOutputDir = self.pathPrefix + '/' + d['wavesDir']
self.logDir = self.pathPrefix + '/' + d['logDir']
self.postDir = self.pathPrefix + '/' + d['postDir']
self.classifierPrefix = d['classifierPrefix']
self.label4withEMG = d['label4withEMG']
self.label4withoutEMG = d['label4withoutEMG']
# for signal processing
self.windowSizeInSec = d[
'windowSizeInSec'] # size of window in time for estimating the state
self.samplingFreq = d['samplingFreq'] # sampling frequency of data
if 'graphUpdateFreqInHz' in d:
self.graphUpdateFreqInHz = d['graphUpdateFreqInHz']
else:
self.graphUpdateFreqInHz = 1
if 'terminalConfigDefaultValue' in d:
self.terminal_config_default_value = d[
'terminalConfigDefaultValue']
else:
self.terminal_config_default_value = 'RSE'
if 'channelIDs' in d:
self.channelIDs = d['channelIDs']
else:
self.channelIDs = [1, 0]
self.writeWholeWaves = d[
'writeWholeWaves'] # sampling frequency of data
self.computeKS = d['computeKS']
# for using history
self.preContextSize = d[
'preContextSize'] # number of time windows in EEG to look back in time
self.postContextSize = d[
'postContextSize'] # number of time windows in EEG to look back in time
self.pastStageLookUpNum = d[
'pastStageLookUpNum'] # number of stage labels to look back in time
# for wavelets
self.waveletWidths = d['waveletWidths']
# for using EMG
self.useEMG = d['useEMG']
self.emgTimeFrameNum = d['emgTimeFrameNum']
# for making a histogram
self.wholeBand = band(d['bandMin'], d['bandMax'])
self.binWidth4freqHisto = d[
'binWidth4freqHisto'] # bin width in the frequency domain for visualizing spectrum as a histogram
# file prefix
self.eegFilePrefix = d['eegFilePrefix']
self.trainDataFilePrefix = d['trainDataFilePrefix']
self.featureFilePrefix = d['featureFilePrefix']
self.classifierFilePrefix = d['classifierFilePrefix']
# feature extractor
self.extractorType = d['extractorType']
self.lightPeriodStartTime = d['lightPeriodStartTime']
# classifier
self.classifierType = d['classifierType']
self.networkType = d['networkType']
# print('&%&%&%&% in ParameterSetup, self.networkType =', self.networkType)
self.classifierParams = d['classifierParams']
if self.useEMG:
label4EMG = self.label4withEMG
else:
label4EMG = self.label4withoutEMG
self.classifierName = self.classifierPrefix + '.' + label4EMG
self.sampleClassLabels = d['sampleClassLabels']
self.subsampleRatios = d['subsampleRatios']
self.supersample = d['supersample']
self.predict_by_batch = d['predict_by_batch']
# self.replacesWWWRtoWWWW = d['replacesWWWRtoWWWW']
self.numOfConsecutiveWsThatProhibitsR = d[
'numOfConsecutiveWsThatProhibitsR']
# stride size used for prediction
self.timeWindowStrideInSec = d['timeWindowStrideInSec']
# self.lookBackTimeWindowNum = d['lookBackTimeWindowNum']
self.useRawData = d['useRawData']
self.useFreqHisto = d['useFreqHisto']
self.useTime = d['useTime']
if 'useSTFT' in d:
self.useSTFT = d['useSTFT']
else:
self.useSTFT = 0
# parameters for the optimzer
self.optimizerType = d['optimizerType']
self.adam_learningRate = d['adam_learningRate']
self.sgd_learningRate = d['sgd_learningRate']
self.sgd_decay = np.float(d['sgd_decay'])
self.sgd_momentum = d['sgd_momentum']
# optimization parameters for deep learning
self.deep_epochs = d['deep_epochs']
self.deep_steps_per_epoch = d['deep_steps_per_epoch']
self.deep_batch_size = d['deep_batch_size']
# network structure for deep learning
if 'torch_loss_function' in d:
self.torch_loss_function = d['torch_loss_function']
else:
self.torch_loss_function = 'cross_entropy'
self.torch_filter_nums = d['torch_filter_nums']
self.torch_kernel_sizes = d['torch_kernel_sizes']
self.torch_strides = d['torch_strides']
self.torch_skip_by = d['torch_skip_by']
self.torch_patience = d['torch_patience']
if 'torch_lstm_length' in d:
self.torch_lstm_length = d['torch_lstm_length']
if 'torch_lstm_num_layers' in d:
self.torch_lstm_num_layers = d['torch_lstm_num_layers']
if 'torch_lstm_hidden_size' in d:
self.torch_lstm_hidden_size = d['torch_lstm_hidden_size']
if 'torch_lstm_inputDim' in d:
self.torch_lstm_inputDim = d['torch_lstm_inputDim']
if 'torch_lstm_bidirectional' in d:
self.torch_lstm_bidirectional = d['torch_lstm_bidirectional']
self.torch_resnet_layer_nums = d['torch_resnet_layer_nums']
self.torch_resnet_conv_channels = d['torch_resnet_conv_channels']
self.torch_resnet_output_channels_coeffs = d[
'torch_resnet_output_channels_coeffs']
self.torch_resnet_output_channels_coeffs = d[
'torch_resnet_output_channels_coeffs']
self.torch_resnet_resblock_stride_nums = d[
'torch_resnet_resblock_stride_nums']
self.torch_resnet_avg_pool_size = d['torch_resnet_avg_pool_size']
self.deep_FCN_node_nums_by_layers = d['deep_FCN_node_nums_by_layers']
self.deep_CNN_filter_nums_by_layers = d[
'deep_CNN_filter_nums_by_layers']
self.deep_CNN_kernel_sizes_by_layers = d[
'deep_CNN_kernel_sizes_by_layers']
self.deep_CNN_kernel_stride_sizes_by_layers = d[
'deep_CNN_kernel_stride_sizes_by_layers']
self.deep_skipConnectionLayerNum = d['deep_skipConnectionLayerNum']
# dropoutRate
self.dropoutRate = d['dropoutRate']
# feature downsampling
self.downsample_outputDim = d['downsample_outputDim']
# features used in rawDataWithFreqHistoWithTime
self.additionalFeatureDim = d['additionalFeatureDim']
# markov order
self.markovOrderForTraining = d['markovOrderForTraining']
self.markovOrderForPrediction = d['markovOrderForPrediction']
# number of stages to consider
self.maximumStageNum = d['maximumStageNum']
# maximum number of samples to be params_used
self.maxSampleNum = d['maxSampleNum']
if 'showCh2' in d:
self.showCh2 = d['showCh2']
else:
self.showCh2 = True
# replace R to W if EMG or some other motion indicator is larger
# by this factor, when compared to the segment having the smallest value
# of the indicator among all past segments.
if 'useCh2ForReplace' in d:
self.useCh2ForReplace = d['useCh2ForReplace']
else:
self.useCh2ForReplace = True
self.ch2_thresh_default = d['ch2_thresh_default']
if 'ch2IntensityFunc' in d:
self.ch2IntensityFunc = d['ch2IntensityFunc']
else:
self.ch2IntensityFunc = 'max_mean'
if 'stft_time_bin_in_seconds' in d:
self.stft_time_bin_in_seconds = d['stft_time_bin_in_seconds']
else:
self.stft_time_bin_in_seconds = 1
if 'outputDim_cnn_for_stft' in d:
self.outputDim_cnn_for_stft = d['outputDim_cnn_for_stft']
else:
self.outputDim_cnn_for_stft = 8 * 3 * 2
# label correction (dictionary)
# self.classLabels = ['S', 'W', 'R']
self.labelCorrectionDict = {
'S': 'n',
'W': 'w',
'R': 'r',
'RW': 'w',
'M': 'm',
'P': 'P',
'F2': 'F2',
'?': '?',
'-': '-'
}
### self.stageLabel2stageID = {'W': 0, 'S': 1, 'R': 2, 'M': 3, 'P': 4, 'RW': 5, 'F2' : 6}
# self.stageLabels = ['W', 'S', 'R', 'M']
# self.stageLabels4evaluation = ['W', 'S', 'R', 'M']
self.capitalize_for_writing_prediction_to_file = {
'n': '1',
'w': 'W',
'r': 'R',
'RW': 'RW',
'm': 'M',
'p': 'P',
'F2': 'F2',
'?': '?'
}
self.capitalize_for_display = {
'n': 'NREM',
'w': 'Wake',
'r': 'REM',
'RW': 'RW',
'm': 'M',
'p': 'P',
'F2': 'F2',
'?': '?'
}
self.capitalize_for_graphs = {
'n': 'S',
'w': 'W',
'r': 'R',
'RW': 'RW',
'm': 'M',
'p': 'P',
'F2': 'F2',
'?': '?'
}
# for reading data files
self.metaDataLineNumUpperBound4eeg = 100
self.metaDataLineNumUpperBound4stage = 100
self.cueWhereEEGDataStarts = 'Time'
# self.cueWhereStageDataStarts = 'No.,Epoch'
self.cueWhereStageDataStarts = ',,,%,%,uV^2,,uV^2'
# ID for the classifierp
# self.classifierID = ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
orig_stageLabels = ['S', 'W', 'R', 'RW', 'M', 'P', 'F2', '?', '-']
self.stagesByDepth = ['r', 'n', 'w', '?']
self.stageLabel2stageID = {
stage: stageID
for stage, stageID in zip(orig_stageLabels[:self.maximumStageNum],
range(self.maximumStageNum))
}
self.correctedLabel2depthID = {
stage: stageID
for stage, stageID in zip(self.stagesByDepth,
range(len(self.stagesByDepth)))
}
### self.stageLabels4evaluation = [key for key in self.stageLabel2stageID.keys()]
self.stageLabels4evaluation = orig_stageLabels[:self.maximumStageNum]
self.ch2_mean_init = d['ch2_mean_init']
self.ch2_variance_init = d['ch2_variance_init']
self.ch2_oldTotalSampleNum_init = d['ch2_oldTotalSampleNum_init']
# used in statistics.py to set the range of past signal used for computing mean and std
if 'standardization_max_storage_window_num' in d:
self.standardization_max_storage_window_num = d[
'standardization_max_storage_window_num']
else:
self.standardization_max_storage_window_num = 5000
if 'standardization_trigger_interval' in d:
self.standardization_trigger_interval = d[
'standardization_trigger_interval']
else:
self.standardization_trigger_interval = 500
if 'standardization_early_trigger' in d:
self.standardization_early_trigger = d[
'standardization_early_trigger']
else:
self.standardization_early_trigger = [
10, 20, 30, 40, 50, 100, 150, 200, 300, 400
]
metaDataLineNum4stage = 100
cueWhereEEGDataStarts = "Time"
cueWhereStageDataStarts = "No.,Epoch"
# for signal processing
wsizeInSec = 10 # size of window in time for estimating the state
samplingFreq = 128 # sampling frequency of data
# for training / test data extraction
# if trainWindowNumOrig = 0, all data is used for training.
### trainWindowNumOrig = 1500
### trainWindowNumOrig = 500
trainWindowNumOrig = 0
# for feature extraction
deltaBand = band(1, 4)
thetaBand = band(6, 9)
targetBands = (deltaBand, thetaBand)
lookBackWindowNum = 6
# for drawing spectrum
wholeBand = band(0, 16)
binWidth4freqHisto = 1 # bin width in the frequency domain for visualizing spectrum as a histogram
voltageRange = (-300, 300)
powerRange = (0, 2 * 10**8)
binnedPowerRange = (0, 2 * 10**9)
stage2color = {
'W': 'b',
'R': 'r',
'S': 'k',
'2': 'm',
metaDataLineNum4stage = 100
cueWhereEEGDataStarts = "Time"
cueWhereStageDataStarts = "No.,Epoch"
# for signal processing
windowSizeInSec = params.windowSizeInSec # size of window in time for estimating the state
samplingFreq = params.samplingFreq # sampling frequency of data
# for training / test data extraction
# if trainWindowNumOrig = 0, all data is used for training.
### trainWindowNumOrig = 1500
### trainWindowNumOrig = 500
trainWindowNumOrig = 0
# for feature extraction
deltaBand = band(1, 4)
thetaBand = band(6, 9)
targetBands = (deltaBand, thetaBand)
lookBackWindowNum = 6
# for drawing spectrum
wholeBand = params.wholeBand
binWidth4freqHisto = params.binWidth4freqHisto # bin width in the frequency domain for visualizing spectrum as a histogram
voltageRange = (-300, 300)
powerRange = (0, 2 * 10**8)
binnedPowerRange = (0, 2 * 10**9)
stage2color = {
'W': 'b',
'R': 'r',
'S': 'k',