def get_features_from_one_signal(X, sample_rate=50):
assert X.ndim == 1, "Expected single signal in feature extraction"
mean = np.mean(X)
stdev = np.std(X)
abs_energy = fc.abs_energy(X)
sum_of_changes = fc.absolute_sum_of_changes(X)
autoc = fc.autocorrelation(X, sample_rate)
count_above_mean = fc.count_above_mean(X)
count_below_mean = fc.count_below_mean(X)
kurtosis = fc.kurtosis(X)
longest_above = fc.longest_strike_above_mean(X)
zero_crossing = fc.number_crossing_m(X, mean)
num_peaks = fc.number_peaks(X, int(sample_rate / 10))
sample_entropy = fc.sample_entropy(X)
spectral_density = fc.spkt_welch_density(X, [{
"coeff": 1
}, {
"coeff": 2
}, {
"coeff": 3
}, {
"coeff": 4
}, {
"coeff": 5
}, {
"coeff": 6
}])
c, v = zip(*spectral_density)
v = np.asarray(v)
return [
mean, stdev, abs_energy, sum_of_changes, autoc, count_above_mean,
count_below_mean, kurtosis, longest_above, zero_crossing, num_peaks,
sample_entropy, v[0], v[1], v[2], v[3], v[4], v[5]
]
def get_sta_features(self, data):
"""
Calculate the value of 9 kinds of selected statistical features
:param data:
:return:
"""
def _cal_trend(data):
time_list = np.arange(len(data))
# create linear regression object
regr = linear_model.LinearRegression()
regr.fit(time_list.reshape(-1, 1), np.array(data).reshape(-1, 1))
return regr.coef_[0][0]
E = ts.abs_energy(data)
S = ts.binned_entropy(data, max_bins=5)
ro = ts.autocorrelation(data, lag=4)
skewness = ts.skewness(data)
kurtosis = ts.kurtosis(data)
trend = _cal_trend(data)
mean = ts.mean(data)
min = ts.minimum(data)
max = ts.maximum(data)
return [E, S, ro, skewness, kurtosis, trend, mean, min, max]
def feature_extract(dt):
import tsfresh.feature_extraction.feature_calculators as fc
ft = {
'abs_energy': fc.abs_energy(dt),
'sum_values': fc.sum_values(dt),
'mean': fc.mean(dt),
'maximum': fc.maximum(dt),
'minimum': fc.minimum(dt),
'median': fc.median(dt),
'quantile_0.1': fc.quantile(dt, 0.1),
'quantile_0.2': fc.quantile(dt, 0.2),
'quantile_0.3': fc.quantile(dt, 0.3),
'quantile_0.4': fc.quantile(dt, 0.4),
'quantile_0.5': fc.quantile(dt, 0.5),
'quantile_0.6': fc.quantile(dt, 0.6),
'quantile_0.7': fc.quantile(dt, 0.7),
'quantile_0.8': fc.quantile(dt, 0.8),
'quantile_0.9': fc.quantile(dt, 0.9),
#
# TODO:
# Below functions dont works well -> need to be checked!!
#
#'fft_coefficient__coeff_0__attr_real': fc.fft_coefficient(dt {"coeff": 0, "attr": "real"}),
#'fft_coefficient__coeff_0__attr_imag': fc.fft_coefficient(dt {"coeff": 0, "attr": "imag"}),
#'fft_coefficient__coeff_0__attr_abs': fc.fft_coefficient(dt {"coeff": 0, "attr": "abs"}),
#'fft_coefficient__coeff_0__attr_angle': fc.fft_coefficient(dt {"coeff": 0, "attr": "angle"}),
#
#=> Mr. Huy just fix this issue with above function fft_ft !!
}
ft.update(fft_ft(dt))
return ft
def ACEnergy(self,x):
x = self.butter_bandpass_filter(x, 0.1, 20, 200)
# n=len(frame)
# Y=fft(frame)/n
Y = abs(fft(x))
Y = Y / len(Y)
return fc.abs_energy(Y[range(1, len(Y))]) # ACEnergy
def time_series_abs_energy(x):
"""
:param x: the time series to calculate the feature of
:type x: pandas.Series
:return: the value of this feature
:return type: float
"""
return ts_feature_calculators.abs_energy(x)
def TS_features(signal):
energy = ts.abs_energy(signal)
abs_sum = ts.absolute_sum_of_changes(signal)
above_mean = ts.count_above_mean(signal)
below_mean = ts.count_below_mean(signal)
first_max_location = ts.first_location_of_maximum(signal)
first_min_location = ts.first_location_of_minimum(signal)
return energy, abs_sum, above_mean, below_mean, first_max_location, first_min_location
def abs_energy(mag):
"""Returns the absolute energy of the time series, defined to be the sum over the squared
values of the time-series.
rtype: float
"""
energy = ts.abs_energy(mag)
return energy
def time_series_abs_energy(x):
"""
Returns the absolute energy of the time series which is the sum over the squared values
.. math::
E = \\sum_{i=1,\ldots, n} x_i^2
:param x: the time series to calculate the feature of
:type x: pandas.Series
:return: the value of this feature
:return type: float
"""
return ts_feature_calculators.abs_energy(x)
def extract_feats(ts):
std = fc.standard_deviation(ts)
kurtosis = fc.kurtosis(ts)
skewness = fc.skewness(ts)
cam = fc.count_above_mean(ts)
cbm = fc.count_below_mean(ts)
lsam = fc.longest_strike_above_mean(ts)
lsbm = fc.longest_strike_below_mean(ts)
psd = fc.fourier_entropy(ts, bins=1000000)
energy = fc.abs_energy(ts)
return np.array(
[std, kurtosis, skewness, cam, cbm, lsam, lsbm, psd, energy])
def transform(self, value):
if value is None:
return None
# TODO: remove try-except and validate value in order to avoid exception
try:
return [
abs_energy(value),
kurtosis(value),
mean_abs_change(value),
skewness(value),
count_above_mean(value) / len(value),
count_below_mean(value) / len(value)
]
except:
return None
def abs_energy(self, x):
"""
As in tsfresh `abs_energy <https://github.com/blue-yonder/tsfresh/blob/master/tsfresh/feature_extraction/\
feature_calculators.py#L390>`_ \
Returns the absolute energy of the time series which is the sum over the squared values\
.. math::
E=\\sum_{i=1,\ldots, n}x_i^2
:param x: the time series to calculate the feature of
:type x: pandas.Series
:return: the value of this feature
:rtype: float
"""
_energy = feature_calculators.abs_energy(x)
logging.debug("abs energy by tsfresh calculated")
return _energy
def extract_features(data):
day = 24 * 60
return list(
numpy.nan_to_num(
numpy.array([
feature.symmetry_looking(data, [{
'r': 0.3
}])[0][1],
feature.variance_larger_than_standard_deviation(data).bool(),
feature.ratio_beyond_r_sigma(data, 2),
feature.has_duplicate_max(data),
feature.has_duplicate_min(data),
feature.has_duplicate(data),
feature.agg_autocorrelation(numpy.array(data.value),
[{
'f_agg': 'mean',
'maxlag': day
}])[0][1],
feature.partial_autocorrelation(data, [{
'lag': day
}])[0][1],
feature.abs_energy(numpy.array(data.value)),
feature.mean_change(data),
feature.mean_second_derivative_central(data),
feature.median(data),
float(feature.mean(data)),
float(feature.standard_deviation(data)),
float(feature.longest_strike_below_mean(data)),
float(feature.longest_strike_above_mean(data)),
int(feature.number_peaks(data, 10)),
feature.linear_trend(numpy.array(data.value), [{
'attr': 'rvalue'
}])[0][1],
feature.c3(data, day),
float(feature.maximum(data)),
float(feature.minimum(data))
])))
def abs_energy(current_observation: pd.DataFrame, raw_key: str):
return tsf.abs_energy(current_observation[raw_key])
def create_features2(seg, ):
data_row = {}
xcz = des_filter(seg, high=CUTOFF)
zc = np.fft.fft(xcz)
zc = zc[:MAX_FREQ]
# FFT transform values
realFFT = np.real(zc)
imagFFT = np.imag(zc)
freq_bands = list(range(0, MAX_FREQ, FREQ_STEP))
magFFT = np.abs(zc)
phzFFT = np.angle(zc)
phzFFT[phzFFT == -np.inf] = -np.pi / 2.0
phzFFT[phzFFT == np.inf] = np.pi / 2.0
phzFFT = np.nan_to_num(phzFFT)
for freq in freq_bands:
data_row['FFT_Mag_01q%d' % freq] = np.quantile(magFFT[freq: freq + FREQ_STEP], 0.01)
data_row['FFT_Mag_10q%d' % freq] = np.quantile(magFFT[freq: freq + FREQ_STEP], 0.1)
data_row['FFT_Mag_90q%d' % freq] = np.quantile(magFFT[freq: freq + FREQ_STEP], 0.9)
data_row['FFT_Mag_99q%d' % freq] = np.quantile(magFFT[freq: freq + FREQ_STEP], 0.99)
data_row['FFT_Mag_mean%d' % freq] = np.mean(magFFT[freq: freq + FREQ_STEP])
data_row['FFT_Mag_std%d' % freq] = np.std(magFFT[freq: freq + FREQ_STEP])
data_row['FFT_Mag_max%d' % freq] = np.max(magFFT[freq: freq + FREQ_STEP])
data_row['FFT_Mag_min%d' % freq] = np.min(magFFT[freq: freq + FREQ_STEP])
data_row['FFT_Phz_mean%d' % freq] = np.mean(phzFFT[freq: freq + FREQ_STEP])
data_row['FFT_Phz_std%d' % freq] = np.std(phzFFT[freq: freq + FREQ_STEP])
data_row['FFT_Phz_max%d' % freq] = np.max(phzFFT[freq: freq + FREQ_STEP])
data_row['FFT_Phz_min%d' % freq] = np.min(phzFFT[freq: freq + FREQ_STEP])
data_row['FFT_Rmean'] = realFFT.mean()
data_row['FFT_Rstd'] = realFFT.std()
data_row['FFT_Rmax'] = realFFT.max()
data_row['FFT_Rmin'] = realFFT.min()
data_row['FFT_Imean'] = imagFFT.mean()
data_row['FFT_Istd'] = imagFFT.std()
data_row['FFT_Imax'] = imagFFT.max()
data_row['FFT_Imin'] = imagFFT.min()
data_row['FFT_Rmean_first_6000'] = realFFT[:6000].mean()
data_row['FFT_Rstd__first_6000'] = realFFT[:6000].std()
data_row['FFT_Rmax_first_6000'] = realFFT[:6000].max()
data_row['FFT_Rmin_first_6000'] = realFFT[:6000].min()
data_row['FFT_Rmean_first_18000'] = realFFT[:18000].mean()
data_row['FFT_Rstd_first_18000'] = realFFT[:18000].std()
data_row['FFT_Rmax_first_18000'] = realFFT[:18000].max()
data_row['FFT_Rmin_first_18000'] = realFFT[:18000].min()
del xcz
del zc
# gc.collect()
sigs = [seg]
for freq in range(0, MAX_FREQ + FREQ_STEP, FREQ_STEP):
if freq == 0:
xc_ = des_filter(seg, high=FREQ_STEP)
elif freq == MAX_FREQ:
xc_ = des_filter(seg, low=freq)
else:
xc_ = des_filter(seg, low=freq, high=freq + FREQ_STEP)
sigs.append(pd.Series(xc_))
for window in [50, 200, 1000]:
roll_mean = seg.rolling(window).mean().dropna()
roll_std = seg.rolling(window).std().dropna()
sigs.append(pd.Series(roll_mean))
sigs.append(pd.Series(roll_std))
for span in [30, 300, 3000]:
exp_mean = seg.ewm(span).mean().dropna()
exp_std = seg.ewm(span).std().dropna()
sigs.append(pd.Series(exp_mean))
sigs.append(pd.Series(exp_std))
for i, sig in enumerate(sigs):
data_row['mean_%d' % i] = sig.mean()
data_row['std_%d' % i] = sig.std()
data_row['max_%d' % i] = sig.max()
data_row['min_%d' % i] = sig.min()
data_row['mean_change_abs_%d' % i] = np.mean(np.diff(sig))
data_row['mean_change_rate_%d' % i] = np.mean(np.nonzero((np.diff(sig) / sig[:-1]))[0])
data_row['abs_max_%d' % i] = np.abs(sig).max()
data_row['abs_min_%d' % i] = np.abs(sig).min()
data_row['std_first_50000_%d' % i] = sig[:50000].std()
data_row['std_last_50000_%d' % i] = sig[-50000:].std()
data_row['std_first_10000_%d' % i] = sig[:10000].std()
data_row['std_last_10000_%d' % i] = sig[-10000:].std()
data_row['avg_first_50000_%d' % i] = sig[:50000].mean()
data_row['avg_last_50000_%d' % i] = sig[-50000:].mean()
data_row['avg_first_10000_%d' % i] = sig[:10000].mean()
data_row['avg_last_10000_%d' % i] = sig[-10000:].mean()
data_row['min_first_50000_%d' % i] = sig[:50000].min()
data_row['min_last_50000_%d' % i] = sig[-50000:].min()
data_row['min_first_10000_%d' % i] = sig[:10000].min()
data_row['min_last_10000_%d' % i] = sig[-10000:].min()
data_row['max_first_50000_%d' % i] = sig[:50000].max()
data_row['max_last_50000_%d' % i] = sig[-50000:].max()
data_row['max_first_10000_%d' % i] = sig[:10000].max()
data_row['max_last_10000_%d' % i] = sig[-10000:].max()
data_row['max_to_min_%d' % i] = sig.max() / np.abs(sig.min())
data_row['max_to_min_diff_%d' % i] = sig.max() - np.abs(sig.min())
data_row['count_big_%d' % i] = len(sig[np.abs(sig) > 500])
data_row['sum_%d' % i] = sig.sum()
data_row['mean_change_rate_first_50000_%d' % i] = np.mean(
np.nonzero((np.diff(sig[:50000]) / sig[:50000][:-1]))[0])
data_row['mean_change_rate_last_50000_%d' % i] = np.mean(
np.nonzero((np.diff(sig[-50000:]) / sig[-50000:][:-1]))[0])
data_row['mean_change_rate_first_10000_%d' % i] = np.mean(
np.nonzero((np.diff(sig[:10000]) / sig[:10000][:-1]))[0])
data_row['mean_change_rate_last_10000_%d' % i] = np.mean(
np.nonzero((np.diff(sig[-10000:]) / sig[-10000:][:-1]))[0])
for p in [1, 5, 10, 25, 50, 75, 90, 95, 99]:
data_row['percentile_p{}_{}'.format(p, i)] = np.percentile(sig, p)
data_row['abd_percentile_p{}_{}'.format(p, i)] = np.percentile(np.abs(sig), p)
data_row['trend_%d' % i] = add_trend_feature(sig)
data_row['abs_trend_%d' % i] = add_trend_feature(sig, abs_values=True)
data_row['abs_mean_%d' % i] = np.abs(sig).mean()
data_row['abs_std_%d' % i] = np.abs(sig).std()
data_row['mad_%d' % i] = sig.mad()
data_row['kurt_%d' % i] = sig.kurtosis()
data_row['skew_%d' % i] = sig.skew()
data_row['med_%d' % i] = sig.median()
# data_row['Hilbert_mean_%d' % i] = np.abs(hilbert(sig)).mean()
data_row['Hann_window50_%d' % i] = (convolve(sig, hann(50), mode='same') / sum(hann(50))).mean()
data_row['Hann_window500_%d' % i] = (convolve(sig, hann(500), mode='same') / sum(hann(500))).mean()
data_row['classic_sta_lta0_mean_%d' % i] = classic_sta_lta(sig, 50, 1000).mean()
data_row['classic_sta_lta1_mean_%d' % i] = classic_sta_lta(sig, 500, 10000).mean()
data_row['classic_sta_lta2_mean_%d' % i] = classic_sta_lta(sig, 5000, 100000).mean()
data_row['classic_sta_lta3_mean_%d' % i] = classic_sta_lta(sig, 3333, 6666).mean()
data_row['classic_sta_lta4_mean_%d' % i] = classic_sta_lta(sig, 10000, 25000).mean()
no_of_std = 2
for w in [10, 100, 500]:
signal_mean = sig.rolling(window=w).mean()
signal_std = sig.rolling(window=w).std()
data_row['high_bound_mean_win{}_{}'.format(w, i)] = (signal_mean + no_of_std * signal_std).mean()
data_row['low_bound_mean_win{}_{}'.format(w, i)] = (signal_mean - no_of_std * signal_std).mean()
data_row['range_inf_4000_%d' % i] = feature_calculators.range_count(sig, -np.inf, -4000)
data_row['range_4000_inf_%d' % i] = feature_calculators.range_count(sig, 4000, np.inf)
for l, h in [[-4000, -2000], [-2000, 0], [0, 2000], [2000, 4000]]:
data_row['range_{}_{}_{}'.format(np.abs(l), np.abs(h), i)] = feature_calculators.range_count(sig, l, h)
data_row['iqr0_%d' % i] = np.subtract(*np.percentile(sig, [75, 25]))
data_row['iqr1_%d' % i] = np.subtract(*np.percentile(sig, [95, 5]))
data_row['ave10_%d' % i] = stats.trim_mean(sig, 0.1)
data_row['num_cross_0_%d' % i] = feature_calculators.number_crossing_m(sig, 0)
data_row['ratio_value_number_%d' % i] = feature_calculators.ratio_value_number_to_time_series_length(sig)
# data_row['var_larger_than_std_dev_%d' % i] = feature_calculators.variance_larger_than_standard_deviation(sig)
data_row['ratio_unique_values_%d' % i] = feature_calculators.ratio_value_number_to_time_series_length(sig)
data_row['abs_energy_%d' % i] = feature_calculators.abs_energy(sig)
data_row['abs_sum_of_changes_%d' % i] = feature_calculators.absolute_sum_of_changes(sig)
data_row['count_above_mean_%d' % i] = feature_calculators.count_above_mean(sig)
data_row['count_below_mean_%d' % i] = feature_calculators.count_below_mean(sig)
data_row['mean_abs_change_%d' % i] = feature_calculators.mean_abs_change(sig)
data_row['mean_change_%d' % i] = feature_calculators.mean_change(sig)
data_row['first_loc_min_%d' % i] = feature_calculators.first_location_of_minimum(sig)
data_row['first_loc_max_%d' % i] = feature_calculators.first_location_of_maximum(sig)
data_row['last_loc_min_%d' % i] = feature_calculators.last_location_of_minimum(sig)
data_row['last_loc_max_%d' % i] = feature_calculators.last_location_of_maximum(sig)
data_row['long_strk_above_mean_%d' % i] = feature_calculators.longest_strike_above_mean(sig)
data_row['long_strk_below_mean_%d' % i] = feature_calculators.longest_strike_below_mean(sig)
# data_row['cid_ce_0_%d' % i] = feature_calculators.cid_ce(sig, 0)
# data_row['cid_ce_1_%d' % i] = feature_calculators.cid_ce(sig, 1)
for j in [10, 50, ]:
data_row['peak_num_p{}_{}'.format(j, i)] = feature_calculators.number_peaks(sig, j)
for j in [1, 10, 50, 100]:
data_row['spkt_welch_density_coeff{}_{}'.format(j, i)] = \
list(feature_calculators.spkt_welch_density(sig, [{'coeff': j}]))[0][1]
for j in [5, 10, 100]:
data_row['c3_c{}_{}'.format(j, i)] = feature_calculators.c3(sig, j)
for j in [5, 10, 50, 100, 1000]:
data_row['autocorrelation_auto{}_{}'.format(j, i)] = feature_calculators.autocorrelation(sig, j)
for j in [10, 100, 1000]:
data_row['time_rev_asym_stat_t{}_{}'.format(j, i)] = feature_calculators.time_reversal_asymmetry_statistic(
sig, j)
for j in range(1, 5):
data_row['kstat_k{}_{}'.format(j, i)] = stats.kstat(sig, j)
data_row['moment_m{}_{}'.format(j, i)] = stats.moment(sig, j)
for j in range(1, 3):
data_row['kstatvar_k{}_{}'.format(j, i)] = stats.kstatvar(sig, j)
for j in [5, 10, 50, 100]:
data_row['binned_entropy_b{}_{}'.format(j, i)] = feature_calculators.binned_entropy(sig, j)
return data_row
def main():
dirname = os.path.realpath('.')
excelF = dirname + '\\Summary.xlsx'
myworkbook = openpyxl.load_workbook(excelF)
worksheet = myworkbook['SummaryPatients']
file = 1
for filename in glob.glob(dirname + "\*.txt"):
data = open(filename, 'r')
totalData = {}
time = []
totalForceL = []
totalForceR = []
id = []
for line in data:
tempForce = line.split()
id.append(1)
time.append(float(tempForce[0]))
totalForceL.append(float(tempForce[17]))
totalForceR.append(float(tempForce[18]))
totalData["id"] = id
totalData["time"] = time
totalData["totalForceL"] = totalForceL
totalData["totalForceR"] = totalForceR
dataPandas = pd.DataFrame.from_dict(totalData)
extracted_features = {}
#extract_featuresL = extract_features(dataPandas, column_id="id", column_kind=None, column_value=None)
worksheet['A' + str(file + 1)] = file
if 'Pt' in filename:
worksheet['B' + str(file + 1)] = 1
else:
worksheet['B' + str(file + 1)] = 0
worksheet['C' + str(file + 1)] = tf.abs_energy(
totalData["totalForceL"])
worksheet['D' + str(file + 1)] = tf.abs_energy(
totalData["totalForceR"])
worksheet['E' + str(file + 1)] = tf.kurtosis(totalData["totalForceL"])
worksheet['F' + str(file + 1)] = tf.kurtosis(totalData["totalForceR"])
worksheet['G' + str(file + 1)] = tf.skewness(totalData["totalForceL"])
worksheet['H' + str(file + 1)] = tf.skewness(totalData["totalForceR"])
worksheet['I' + str(file + 1)] = tf.median(totalData["totalForceL"])
worksheet['J' + str(file + 1)] = tf.median(totalData["totalForceR"])
worksheet['K' + str(file + 1)] = tf.mean(totalData["totalForceL"])
worksheet['L' + str(file + 1)] = tf.mean(totalData["totalForceR"])
worksheet['M' + str(file + 1)] = tf.variance(totalData["totalForceL"])
worksheet['N' + str(file + 1)] = tf.variance(totalData["totalForceR"])
temp = tf.fft_aggregated(totalData["totalForceL"],
[{
"aggtype": "centroid"
}, {
"aggtype": "variance"
}, {
"aggtype": "skew"
}, {
"aggtype": "kurtosis"
}])
int = 0
for list in temp:
if int == 0:
worksheet['O' + str(file + 1)] = list[1]
if int == 1:
worksheet['P' + str(file + 1)] = list[1]
if int == 2:
worksheet['Q' + str(file + 1)] = list[1]
if int == 3:
worksheet['R' + str(file + 1)] = list[1]
int += 1
temp2 = tf.fft_aggregated(totalData["totalForceR"],
[{
"aggtype": "centroid"
}, {
"aggtype": "variance"
}, {
"aggtype": "skew"
}, {
"aggtype": "kurtosis"
}])
int = 0
for list in temp2:
if int == 0:
worksheet['S' + str(file + 1)] = list[1]
if int == 1:
worksheet['T' + str(file + 1)] = list[1]
if int == 2:
worksheet['U' + str(file + 1)] = list[1]
if int == 3:
worksheet['V' + str(file + 1)] = list[1]
int += 1
file += 1
myworkbook.save(excelF)
def features(self, x, prefix):
feature_dict = dict()
# create features here
# numpy
feature_dict[prefix + '_' + 'mean'] = np.mean(x)
feature_dict[prefix + '_' + 'max'] = np.max(x)
feature_dict[prefix + '_' + 'min'] = np.min(x)
feature_dict[prefix + '_' + 'std'] = np.std(x)
feature_dict[prefix + '_' + 'var'] = np.var(x)
feature_dict[prefix + '_' + 'ptp'] = np.ptp(x)
feature_dict[prefix + '_' + 'percentile_10'] = np.percentile(x, 10)
feature_dict[prefix + '_' + 'percentile_20'] = np.percentile(x, 20)
feature_dict[prefix + '_' + 'percentile_30'] = np.percentile(x, 30)
feature_dict[prefix + '_' + 'percentile_40'] = np.percentile(x, 40)
feature_dict[prefix + '_' + 'percentile_50'] = np.percentile(x, 50)
feature_dict[prefix + '_' + 'percentile_60'] = np.percentile(x, 60)
feature_dict[prefix + '_' + 'percentile_70'] = np.percentile(x, 70)
feature_dict[prefix + '_' + 'percentile_80'] = np.percentile(x, 80)
feature_dict[prefix + '_' + 'percentile_90'] = np.percentile(x, 90)
# scipy
feature_dict[prefix + '_' + 'skew'] = sp.stats.skew(x)
feature_dict[prefix + '_' + 'kurtosis'] = sp.stats.kurtosis(x)
feature_dict[prefix + '_' + 'kstat_1'] = sp.stats.kstat(x, 1)
feature_dict[prefix + '_' + 'kstat_2'] = sp.stats.kstat(x, 2)
feature_dict[prefix + '_' + 'kstat_3'] = sp.stats.kstat(x, 3)
feature_dict[prefix + '_' + 'kstat_4'] = sp.stats.kstat(x, 4)
feature_dict[prefix + '_' + 'moment_1'] = sp.stats.moment(x, 1)
feature_dict[prefix + '_' + 'moment_2'] = sp.stats.moment(x, 2)
feature_dict[prefix + '_' + 'moment_3'] = sp.stats.moment(x, 3)
feature_dict[prefix + '_' + 'moment_4'] = sp.stats.moment(x, 4)
# tsfresh
feature_dict[prefix + '_' +
'abs_energy'] = feature_calculators.abs_energy(x)
feature_dict[
prefix + '_' +
'abs_sum_of_changes'] = feature_calculators.absolute_sum_of_changes(
x)
feature_dict[
prefix + '_' +
'count_above_mean'] = feature_calculators.count_above_mean(x)
feature_dict[
prefix + '_' +
'count_below_mean'] = feature_calculators.count_below_mean(x)
feature_dict[prefix + '_' +
'mean_abs_change'] = feature_calculators.mean_abs_change(
x)
feature_dict[prefix + '_' +
'mean_change'] = feature_calculators.mean_change(x)
feature_dict[
prefix + '_' +
'var_larger_than_std_dev'] = feature_calculators.variance_larger_than_standard_deviation(
x)
feature_dict[prefix + '_' +
'range_minf_m4000'] = feature_calculators.range_count(
x, -np.inf, -4000)
feature_dict[prefix + '_' +
'range_m4000_m3000'] = feature_calculators.range_count(
x, -4000, -3000)
feature_dict[prefix + '_' +
'range_m3000_m2000'] = feature_calculators.range_count(
x, -3000, -2000)
feature_dict[prefix + '_' +
'range_m2000_m1000'] = feature_calculators.range_count(
x, -2000, -1000)
feature_dict[prefix + '_' +
'range_m1000_0'] = feature_calculators.range_count(
x, -1000, 0)
feature_dict[prefix + '_' +
'range_0_p1000'] = feature_calculators.range_count(
x, 0, 1000)
feature_dict[prefix + '_' +
'range_p1000_p2000'] = feature_calculators.range_count(
x, 1000, 2000)
feature_dict[prefix + '_' +
'range_p2000_p3000'] = feature_calculators.range_count(
x, 2000, 3000)
feature_dict[prefix + '_' +
'range_p3000_p4000'] = feature_calculators.range_count(
x, 3000, 4000)
feature_dict[prefix + '_' +
'range_p4000_pinf'] = feature_calculators.range_count(
x, 4000, np.inf)
feature_dict[
prefix + '_' +
'ratio_unique_values'] = feature_calculators.ratio_value_number_to_time_series_length(
x)
feature_dict[
prefix + '_' +
'first_loc_min'] = feature_calculators.first_location_of_minimum(x)
feature_dict[
prefix + '_' +
'first_loc_max'] = feature_calculators.first_location_of_maximum(x)
feature_dict[
prefix + '_' +
'last_loc_min'] = feature_calculators.last_location_of_minimum(x)
feature_dict[
prefix + '_' +
'last_loc_max'] = feature_calculators.last_location_of_maximum(x)
feature_dict[
prefix + '_' +
'time_rev_asym_stat_10'] = feature_calculators.time_reversal_asymmetry_statistic(
x, 10)
feature_dict[
prefix + '_' +
'time_rev_asym_stat_100'] = feature_calculators.time_reversal_asymmetry_statistic(
x, 100)
feature_dict[
prefix + '_' +
'time_rev_asym_stat_1000'] = feature_calculators.time_reversal_asymmetry_statistic(
x, 1000)
feature_dict[
prefix + '_' +
'autocorrelation_1'] = feature_calculators.autocorrelation(x, 1)
feature_dict[
prefix + '_' +
'autocorrelation_2'] = feature_calculators.autocorrelation(x, 2)
feature_dict[
prefix + '_' +
'autocorrelation_3'] = feature_calculators.autocorrelation(x, 3)
feature_dict[
prefix + '_' +
'autocorrelation_4'] = feature_calculators.autocorrelation(x, 4)
feature_dict[
prefix + '_' +
'autocorrelation_5'] = feature_calculators.autocorrelation(x, 5)
feature_dict[
prefix + '_' +
'autocorrelation_6'] = feature_calculators.autocorrelation(x, 6)
feature_dict[
prefix + '_' +
'autocorrelation_7'] = feature_calculators.autocorrelation(x, 7)
feature_dict[
prefix + '_' +
'autocorrelation_8'] = feature_calculators.autocorrelation(x, 8)
feature_dict[
prefix + '_' +
'autocorrelation_9'] = feature_calculators.autocorrelation(x, 9)
feature_dict[
prefix + '_' +
'autocorrelation_10'] = feature_calculators.autocorrelation(x, 10)
feature_dict[
prefix + '_' +
'autocorrelation_50'] = feature_calculators.autocorrelation(x, 50)
feature_dict[
prefix + '_' +
'autocorrelation_100'] = feature_calculators.autocorrelation(
x, 100)
feature_dict[
prefix + '_' +
'autocorrelation_1000'] = feature_calculators.autocorrelation(
x, 1000)
feature_dict[prefix + '_' + 'c3_1'] = feature_calculators.c3(x, 1)
feature_dict[prefix + '_' + 'c3_2'] = feature_calculators.c3(x, 2)
feature_dict[prefix + '_' + 'c3_3'] = feature_calculators.c3(x, 3)
feature_dict[prefix + '_' + 'c3_4'] = feature_calculators.c3(x, 4)
feature_dict[prefix + '_' + 'c3_5'] = feature_calculators.c3(x, 5)
feature_dict[prefix + '_' + 'c3_10'] = feature_calculators.c3(x, 10)
feature_dict[prefix + '_' + 'c3_100'] = feature_calculators.c3(x, 100)
for c in range(1, 34):
feature_dict[prefix + '_' + 'fft_{0}_real'.format(c)] = list(
feature_calculators.fft_coefficient(x, [{
'coeff': c,
'attr': 'real'
}]))[0][1]
feature_dict[prefix + '_' + 'fft_{0}_imag'.format(c)] = list(
feature_calculators.fft_coefficient(x, [{
'coeff': c,
'attr': 'imag'
}]))[0][1]
feature_dict[prefix + '_' + 'fft_{0}_ang'.format(c)] = list(
feature_calculators.fft_coefficient(x, [{
'coeff': c,
'attr': 'angle'
}]))[0][1]
feature_dict[
prefix + '_' +
'long_strk_above_mean'] = feature_calculators.longest_strike_above_mean(
x)
feature_dict[
prefix + '_' +
'long_strk_below_mean'] = feature_calculators.longest_strike_below_mean(
x)
feature_dict[prefix + '_' + 'cid_ce_0'] = feature_calculators.cid_ce(
x, 0)
feature_dict[prefix + '_' + 'cid_ce_1'] = feature_calculators.cid_ce(
x, 1)
feature_dict[prefix + '_' +
'binned_entropy_5'] = feature_calculators.binned_entropy(
x, 5)
feature_dict[prefix + '_' +
'binned_entropy_10'] = feature_calculators.binned_entropy(
x, 10)
feature_dict[prefix + '_' +
'binned_entropy_20'] = feature_calculators.binned_entropy(
x, 20)
feature_dict[prefix + '_' +
'binned_entropy_50'] = feature_calculators.binned_entropy(
x, 50)
feature_dict[prefix + '_' +
'binned_entropy_80'] = feature_calculators.binned_entropy(
x, 80)
feature_dict[
prefix + '_' +
'binned_entropy_100'] = feature_calculators.binned_entropy(x, 100)
feature_dict[prefix + '_' +
'num_crossing_0'] = feature_calculators.number_crossing_m(
x, 0)
feature_dict[prefix + '_' +
'num_peaks_1'] = feature_calculators.number_peaks(x, 1)
feature_dict[prefix + '_' +
'num_peaks_3'] = feature_calculators.number_peaks(x, 3)
feature_dict[prefix + '_' +
'num_peaks_5'] = feature_calculators.number_peaks(x, 5)
feature_dict[prefix + '_' +
'num_peaks_10'] = feature_calculators.number_peaks(x, 10)
feature_dict[prefix + '_' +
'num_peaks_50'] = feature_calculators.number_peaks(x, 50)
feature_dict[prefix + '_' +
'num_peaks_100'] = feature_calculators.number_peaks(
x, 100)
feature_dict[prefix + '_' +
'num_peaks_500'] = feature_calculators.number_peaks(
x, 500)
feature_dict[prefix + '_' + 'spkt_welch_density_1'] = list(
feature_calculators.spkt_welch_density(x, [{
'coeff': 1
}]))[0][1]
feature_dict[prefix + '_' + 'spkt_welch_density_2'] = list(
feature_calculators.spkt_welch_density(x, [{
'coeff': 2
}]))[0][1]
feature_dict[prefix + '_' + 'spkt_welch_density_5'] = list(
feature_calculators.spkt_welch_density(x, [{
'coeff': 5
}]))[0][1]
feature_dict[prefix + '_' + 'spkt_welch_density_8'] = list(
feature_calculators.spkt_welch_density(x, [{
'coeff': 8
}]))[0][1]
feature_dict[prefix + '_' + 'spkt_welch_density_10'] = list(
feature_calculators.spkt_welch_density(x, [{
'coeff': 10
}]))[0][1]
feature_dict[prefix + '_' + 'spkt_welch_density_50'] = list(
feature_calculators.spkt_welch_density(x, [{
'coeff': 50
}]))[0][1]
feature_dict[prefix + '_' + 'spkt_welch_density_100'] = list(
feature_calculators.spkt_welch_density(x, [{
'coeff': 100
}]))[0][1]
feature_dict[
prefix + '_' +
'time_rev_asym_stat_1'] = feature_calculators.time_reversal_asymmetry_statistic(
x, 1)
feature_dict[
prefix + '_' +
'time_rev_asym_stat_2'] = feature_calculators.time_reversal_asymmetry_statistic(
x, 2)
feature_dict[
prefix + '_' +
'time_rev_asym_stat_3'] = feature_calculators.time_reversal_asymmetry_statistic(
x, 3)
feature_dict[
prefix + '_' +
'time_rev_asym_stat_4'] = feature_calculators.time_reversal_asymmetry_statistic(
x, 4)
feature_dict[
prefix + '_' +
'time_rev_asym_stat_10'] = feature_calculators.time_reversal_asymmetry_statistic(
x, 10)
feature_dict[
prefix + '_' +
'time_rev_asym_stat_100'] = feature_calculators.time_reversal_asymmetry_statistic(
x, 100)
for r in range(20):
feature_dict[prefix + '_' + 'symmetry_looking_' +
str(r)] = feature_calculators.symmetry_looking(
x, [{
'r': r * 0.05
}])[0][1]
for r in range(1, 20):
feature_dict[
prefix + '_' + 'large_standard_deviation_' +
str(r)] = feature_calculators.large_standard_deviation(
x, r * 0.05)
for r in range(1, 10):
feature_dict[prefix + '_' + 'quantile_' +
str(r)] = feature_calculators.quantile(x, r * 0.1)
for r in ['mean', 'median', 'var']:
feature_dict[prefix + '_' + 'agg_autocorr_' +
r] = feature_calculators.agg_autocorrelation(
x, [{
'f_agg': r,
'maxlag': 40
}])[0][-1]
#for r in range(1, 6):
# feature_dict[prefix+'_'+'number_cwt_peaks_'+str(r)] = feature_calculators.number_cwt_peaks(x, r)
for r in range(1, 10):
feature_dict[prefix + '_' + 'index_mass_quantile_' +
str(r)] = feature_calculators.index_mass_quantile(
x, [{
'q': r
}])[0][1]
#for ql in [0., .2, .4, .6, .8]:
# for qh in [.2, .4, .6, .8, 1.]:
# if ql < qh:
# for b in [False, True]:
# for f in ["mean", "var"]:
# feature_dict[prefix+'_'+'change_quantiles_'+str(ql)+'_'+str(qh)+'_'+str(b)+'_'+str(f)] = feature_calculators.change_quantiles(x, ql, qh, b, f)
#for r in [.1, .3, .5, .7, .9]:
# feature_dict[prefix+'_'+'approximate_entropy_'+str(r)] = feature_calculators.approximate_entropy(x, 2, r)
feature_dict[
prefix + '_' +
'max_langevin_fixed_point'] = feature_calculators.max_langevin_fixed_point(
x, 3, 30)
for r in ['pvalue', 'rvalue', 'intercept', 'slope', 'stderr']:
feature_dict[prefix + '_' + 'linear_trend_' +
str(r)] = feature_calculators.linear_trend(
x, [{
'attr': r
}])[0][1]
for r in ['pvalue', 'teststat', 'usedlag']:
feature_dict[prefix + '_' + 'augmented_dickey_fuller_' +
r] = feature_calculators.augmented_dickey_fuller(
x, [{
'attr': r
}])[0][1]
for r in [0.5, 1, 1.5, 2, 2.5, 3, 5, 6, 7, 10]:
feature_dict[prefix + '_' + 'ratio_beyond_r_sigma_' +
str(r)] = feature_calculators.ratio_beyond_r_sigma(
x, r)
#for attr in ["pvalue", "rvalue", "intercept", "slope", "stderr"]:
# feature_dict[prefix+'_'+'linear_trend_timewise_'+attr] = feature_calculators.linear_trend_timewise(x, [{'attr': attr}])[0][1]
#for attr in ["rvalue", "intercept", "slope", "stderr"]:
# for i in [5, 10, 50]:
# for f in ["max", "min", "mean", "var"]:
# feature_dict[prefix+'_'+'agg_linear_trend_'+attr+'_'+str(i)+'_'+f] = feature_calculators.agg_linear_trend(x, [{'attr': attr, 'chunk_len': i, 'f_agg': f}])[0][-1]
#for width in [2, 5, 10, 20]:
# for coeff in range(15):
# for w in [2, 5, 10, 20]:
# feature_dict[prefix+'_'+'cwt_coefficients_'+str(width)+'_'+str(coeff)+'_'+str(w)] = list(feature_calculators.cwt_coefficients(x, [{'widths': width, 'coeff': coeff, 'w': w}]))[0][1]
#for r in range(10):
# feature_dict[prefix+'_'+'partial_autocorr_'+str(r)] = feature_calculators.partial_autocorrelation(x, [{'lag': r}])[0][1]
# "ar_coefficient": [{"coeff": coeff, "k": k} for coeff in range(5) for k in [10]],
# "fft_coefficient": [{"coeff": k, "attr": a} for a, k in product(["real", "imag", "abs", "angle"], range(100))],
# "fft_aggregated": [{"aggtype": s} for s in ["centroid", "variance", "skew", "kurtosis"]],
# "value_count": [{"value": value} for value in [0, 1, -1]],
# "range_count": [{"min": -1, "max": 1}, {"min": 1e12, "max": 0}, {"min": 0, "max": 1e12}],
# "friedrich_coefficients": (lambda m: [{"coeff": coeff, "m": m, "r": 30} for coeff in range(m + 1)])(3),
# "energy_ratio_by_chunks": [{"num_segments": 10, "segment_focus": i} for i in range(10)],
return feature_dict
# percentile feats
feature_dict['percentile_10'] = np.percentile(x, 10)
feature_dict['percentile_60'] = np.percentile(x, 60)
feature_dict['percentile_90'] = np.percentile(x, 90)
# quantile feat
feature_dict['quantile_1'] = np.percentie(x, 25)
feature_dict['quantile_2'] = np.percentie(x, 50)
feature_dict['quantile_3'] = np.percentie(x, 75)
feature_dict['quantile_4'] = np.percentie(x, 99)
# ts fresh can be used for time series features when we have a list of features
# in a given period of time
from tsfresh.feature_extraction import feature_calculators as fc
feature_dict['abs_energey'] = fc.abs_energy(x)
feature_dict['count_above_mean'] = fc.count_above_mean(x)
feature_dict['count_below_mean'] = fc.count_below_mean(x)
feature_dict['mean_abs_change'] = fc.mean_abs_change(x)
feature_dict['mean_change'] = fc.mean_change(x)
# polynomial features
import pandas as pd
import numpy as np
from sklearn import preprocessing
df = pd.DataFrame(np.random.rand(100, 2), columns=['f1', 'f2'])
pf = preprocessing.PolynomialFeatures(degree=2,
interaction_only=False,
include_bias=False)
pf.fit(df)
def abs_energy(arr):
return feature_calculators.abs_energy(arr)
def transform_pack3(df):
""" augment X from tsfresh features"""
x = df.values
output = {}
output['kstat_1'] = stats.kstat(x, 1)
output['kstat_2'] = stats.kstat(x, 2)
output['kstat_3'] = stats.kstat(x, 3)
output['kstat_4'] = stats.kstat(x, 4)
output['abs_energy'] = feature_calculators.abs_energy(x)
output['abs_sum_of_changes'] = feature_calculators.absolute_sum_of_changes(
x)
output['count_above_mean'] = feature_calculators.count_above_mean(x)
output['count_below_mean'] = feature_calculators.count_below_mean(x)
output['range_minf_m4000'] = feature_calculators.range_count(
x, -np.inf, -4000)
output['range_m4000_m3000'] = feature_calculators.range_count(
x, -4000, -3000)
output['range_m3000_m2000'] = feature_calculators.range_count(
x, -3000, -2000)
output['range_m2000_m1000'] = feature_calculators.range_count(
x, -2000, -1000)
output['range_m1000_0'] = feature_calculators.range_count(x, -1000, 0)
output['range_0_p1000'] = feature_calculators.range_count(x, 0, 1000)
output['range_p1000_p2000'] = feature_calculators.range_count(
x, 1000, 2000)
output['range_p2000_p3000'] = feature_calculators.range_count(
x, 2000, 3000)
output['range_p3000_p4000'] = feature_calculators.range_count(
x, 3000, 4000)
output['range_p4000_pinf'] = feature_calculators.range_count(
x, 4000, np.inf)
output[
'ratio_unique_values'] = feature_calculators.ratio_value_number_to_time_series_length(
x)
output['first_loc_min'] = feature_calculators.first_location_of_minimum(x)
output['first_loc_max'] = feature_calculators.first_location_of_maximum(x)
output['last_loc_min'] = feature_calculators.last_location_of_minimum(x)
output['last_loc_max'] = feature_calculators.last_location_of_maximum(x)
output[
'time_rev_asym_stat_10'] = feature_calculators.time_reversal_asymmetry_statistic(
x, 10)
output[
'time_rev_asym_stat_100'] = feature_calculators.time_reversal_asymmetry_statistic(
x, 100)
output[
'time_rev_asym_stat_1000'] = feature_calculators.time_reversal_asymmetry_statistic(
x, 1000)
output['autocorrelation_10'] = feature_calculators.autocorrelation(x, 10)
output['autocorrelation_100'] = feature_calculators.autocorrelation(x, 100)
output['autocorrelation_1000'] = feature_calculators.autocorrelation(
x, 1000)
output['autocorrelation_5000'] = feature_calculators.autocorrelation(
x, 5000)
output['c3_5'] = feature_calculators.c3(x, 5)
output['c3_10'] = feature_calculators.c3(x, 10)
output['c3_100'] = feature_calculators.c3(x, 100)
output[
'long_strk_above_mean'] = feature_calculators.longest_strike_above_mean(
x)
output[
'long_strk_below_mean'] = feature_calculators.longest_strike_below_mean(
x)
output['cid_ce_0'] = feature_calculators.cid_ce(x, 0)
output['cid_ce_1'] = feature_calculators.cid_ce(x, 1)
output['binned_entropy_10'] = feature_calculators.binned_entropy(x, 10)
output['binned_entropy_50'] = feature_calculators.binned_entropy(x, 50)
output['binned_entropy_80'] = feature_calculators.binned_entropy(x, 80)
output['binned_entropy_100'] = feature_calculators.binned_entropy(x, 100)
tmp = np.abs(x)
output['num_crossing_0'] = feature_calculators.number_crossing_m(tmp, 0)
output['num_crossing_10'] = feature_calculators.number_crossing_m(tmp, 10)
output['num_crossing_100'] = feature_calculators.number_crossing_m(
tmp, 100)
output['num_peaks_10'] = feature_calculators.number_peaks(tmp, 10)
output['num_peaks_50'] = feature_calculators.number_peaks(tmp, 50)
output['num_peaks_100'] = feature_calculators.number_peaks(tmp, 100)
output['num_peaks_500'] = feature_calculators.number_peaks(tmp, 500)
output['spkt_welch_density_1'] = list(
feature_calculators.spkt_welch_density(x, [{
'coeff': 1
}]))[0][1]
output['spkt_welch_density_10'] = list(
feature_calculators.spkt_welch_density(x, [{
'coeff': 10
}]))[0][1]
output['spkt_welch_density_50'] = list(
feature_calculators.spkt_welch_density(x, [{
'coeff': 50
}]))[0][1]
output['spkt_welch_density_100'] = list(
feature_calculators.spkt_welch_density(x, [{
'coeff': 100
}]))[0][1]
output[
'time_rev_asym_stat_1'] = feature_calculators.time_reversal_asymmetry_statistic(
x, 1)
output[
'time_rev_asym_stat_10'] = feature_calculators.time_reversal_asymmetry_statistic(
x, 10)
output[
'time_rev_asym_stat_100'] = feature_calculators.time_reversal_asymmetry_statistic(
x, 100)
return output
def features(self, x, y, seg_id, denoise=False):
if (denoise == True):
x_hp = high_pass_filter(x, low_cutoff=10000, sample_rate=4000000)
x = denoise_signal(x_hp, wavelet='haar', level=1)
feature_dict = dict()
feature_dict['target'] = y
feature_dict['seg_id'] = seg_id
# create features here
# lists with parameters to iterate over them
percentiles = [
1, 5, 10, 20, 25, 30, 40, 50, 60, 70, 75, 80, 90, 95, 99
]
hann_windows = [50, 150, 1500, 15000]
spans = [300, 3000, 30000, 50000]
windows = [10, 50, 100, 500, 1000, 10000]
borders = list(range(-4000, 4001, 1000))
peaks = [10, 20, 50, 100]
coefs = [1, 5, 10, 50, 100]
lags = [10, 100, 1000, 10000]
autocorr_lags = [5, 10, 50, 100, 500, 1000, 5000, 10000]
# basic stats
feature_dict['mean'] = x.mean()
feature_dict['std'] = x.std()
feature_dict['max'] = x.max()
feature_dict['min'] = x.min()
# basic stats on absolute values
feature_dict['mean_change_abs'] = np.mean(np.diff(x))
feature_dict['abs_max'] = np.abs(x).max()
feature_dict['abs_mean'] = np.abs(x).mean()
feature_dict['abs_std'] = np.abs(x).std()
# geometric and harminic means
feature_dict['hmean'] = stats.hmean(np.abs(x[np.nonzero(x)[0]]))
feature_dict['gmean'] = stats.gmean(np.abs(x[np.nonzero(x)[0]]))
# k-statistic and moments
for i in range(1, 5):
feature_dict['kstat_{}'.format(i)] = stats.kstat(x, i)
feature_dict['moment_{}'.format(i)] = stats.moment(x, i)
for i in [1, 2]:
feature_dict['kstatvar_{}'.format(i)] = stats.kstatvar(x, i)
# aggregations on various slices of data
for agg_type, slice_length, direction in product(
['std', 'min', 'max', 'mean'], [1000, 10000, 50000],
['first', 'last']):
if direction == 'first':
feature_dict['{}_{}_{}'.format(
agg_type, direction,
slice_length)] = x[:slice_length].agg(agg_type)
elif direction == 'last':
feature_dict['{}_{}_{}'.format(
agg_type, direction,
slice_length)] = x[-slice_length:].agg(agg_type)
feature_dict['max_to_min'] = x.max() / np.abs(x.min())
feature_dict['max_to_min_diff'] = x.max() - np.abs(x.min())
feature_dict['count_big'] = len(x[np.abs(x) > 500])
feature_dict['sum'] = x.sum()
feature_dict['mean_change_rate'] = calc_change_rate(x)
# calc_change_rate on slices of data
for slice_length, direction in product([1000, 10000, 50000],
['first', 'last']):
if direction == 'first':
feature_dict['mean_change_rate_{}_{}'.format(
direction,
slice_length)] = calc_change_rate(x[:slice_length])
elif direction == 'last':
feature_dict['mean_change_rate_{}_{}'.format(
direction,
slice_length)] = calc_change_rate(x[-slice_length:])
# percentiles on original and absolute values
for p in percentiles:
feature_dict['percentile_{}'.format(p)] = np.percentile(x, p)
feature_dict['abs_percentile_{}'.format(p)] = np.percentile(
np.abs(x), p)
feature_dict['trend'] = add_trend_feature(x)
feature_dict['abs_trend'] = add_trend_feature(x, abs_values=True)
feature_dict['mad'] = x.mad()
feature_dict['kurt'] = x.kurtosis()
feature_dict['skew'] = x.skew()
feature_dict['med'] = x.median()
feature_dict['Hilbert_mean'] = np.abs(hilbert(x)).mean()
for hw in hann_windows:
feature_dict['Hann_window_mean_{}'.format(hw)] = (
convolve(x, hann(hw), mode='same') / sum(hann(hw))).mean()
feature_dict['classic_sta_lta1_mean'] = classic_sta_lta(x, 500,
10000).mean()
feature_dict['classic_sta_lta2_mean'] = classic_sta_lta(
x, 5000, 100000).mean()
feature_dict['classic_sta_lta3_mean'] = classic_sta_lta(x, 3333,
6666).mean()
feature_dict['classic_sta_lta4_mean'] = classic_sta_lta(
x, 10000, 25000).mean()
feature_dict['classic_sta_lta5_mean'] = classic_sta_lta(x, 50,
1000).mean()
feature_dict['classic_sta_lta6_mean'] = classic_sta_lta(x, 100,
5000).mean()
feature_dict['classic_sta_lta7_mean'] = classic_sta_lta(x, 333,
666).mean()
feature_dict['classic_sta_lta8_mean'] = classic_sta_lta(
x, 4000, 10000).mean()
# exponential rolling statistics
ewma = pd.Series.ewm
for s in spans:
feature_dict['exp_Moving_average_{}_mean'.format(s)] = (ewma(
x, span=s).mean(skipna=True)).mean(skipna=True)
feature_dict['exp_Moving_average_{}_std'.format(s)] = (ewma(
x, span=s).mean(skipna=True)).std(skipna=True)
feature_dict['exp_Moving_std_{}_mean'.format(s)] = (ewma(
x, span=s).std(skipna=True)).mean(skipna=True)
feature_dict['exp_Moving_std_{}_std'.format(s)] = (ewma(
x, span=s).std(skipna=True)).std(skipna=True)
feature_dict['iqr1'] = np.subtract(*np.percentile(x, [95, 5]))
feature_dict['ave10'] = stats.trim_mean(x, 0.1)
for slice_length, threshold in product([50000, 100000, 150000],
[5, 10, 20, 50, 100]):
feature_dict['count_big_{}_threshold_{}'.format(
slice_length,
threshold)] = (np.abs(x[-slice_length:]) > threshold).sum()
feature_dict['count_big_{}_less_threshold_{}'.format(
slice_length,
threshold)] = (np.abs(x[-slice_length:]) < threshold).sum()
# tfresh features take too long to calculate, so I comment them for now
feature_dict['abs_energy'] = feature_calculators.abs_energy(x)
feature_dict[
'abs_sum_of_changes'] = feature_calculators.absolute_sum_of_changes(
x)
feature_dict[
'count_above_mean'] = feature_calculators.count_above_mean(x)
feature_dict[
'count_below_mean'] = feature_calculators.count_below_mean(x)
feature_dict['mean_abs_change'] = feature_calculators.mean_abs_change(
x)
feature_dict['mean_change'] = feature_calculators.mean_change(x)
feature_dict[
'var_larger_than_std_dev'] = feature_calculators.variance_larger_than_standard_deviation(
x)
feature_dict['range_minf_m4000'] = feature_calculators.range_count(
x, -np.inf, -4000)
feature_dict['range_p4000_pinf'] = feature_calculators.range_count(
x, 4000, np.inf)
for i, j in zip(borders, borders[1:]):
feature_dict['range_{}_{}'.format(
i, j)] = feature_calculators.range_count(x, i, j)
feature_dict[
'ratio_unique_values'] = feature_calculators.ratio_value_number_to_time_series_length(
x)
feature_dict[
'first_loc_min'] = feature_calculators.first_location_of_minimum(x)
feature_dict[
'first_loc_max'] = feature_calculators.first_location_of_maximum(x)
feature_dict[
'last_loc_min'] = feature_calculators.last_location_of_minimum(x)
feature_dict[
'last_loc_max'] = feature_calculators.last_location_of_maximum(x)
for lag in lags:
feature_dict['time_rev_asym_stat_{}'.format(
lag)] = feature_calculators.time_reversal_asymmetry_statistic(
x, lag)
for autocorr_lag in autocorr_lags:
feature_dict['autocorrelation_{}'.format(
autocorr_lag)] = feature_calculators.autocorrelation(
x, autocorr_lag)
feature_dict['c3_{}'.format(
autocorr_lag)] = feature_calculators.c3(x, autocorr_lag)
for coeff, attr in product([1, 2, 3, 4, 5], ['real', 'imag', 'angle']):
feature_dict['fft_{}_{}'.format(coeff, attr)] = list(
feature_calculators.fft_coefficient(x, [{
'coeff': coeff,
'attr': attr
}]))[0][1]
feature_dict[
'long_strk_above_mean'] = feature_calculators.longest_strike_above_mean(
x)
feature_dict[
'long_strk_below_mean'] = feature_calculators.longest_strike_below_mean(
x)
feature_dict['cid_ce_0'] = feature_calculators.cid_ce(x, 0)
feature_dict['cid_ce_1'] = feature_calculators.cid_ce(x, 1)
for p in percentiles:
feature_dict['binned_entropy_{}'.format(
p)] = feature_calculators.binned_entropy(x, p)
feature_dict['num_crossing_0'] = feature_calculators.number_crossing_m(
x, 0)
for peak in peaks:
feature_dict['num_peaks_{}'.format(
peaks)] = feature_calculators.number_peaks(x, peak)
for c in coefs:
feature_dict['spkt_welch_density_{}'.format(c)] = list(
feature_calculators.spkt_welch_density(x, [{
'coeff': c
}]))[0][1]
feature_dict['time_rev_asym_stat_{}'.format(
c)] = feature_calculators.time_reversal_asymmetry_statistic(
x, c)
# statistics on rolling windows of various sizes
for w in windows:
x_roll_std = x.rolling(w).std().dropna().values
x_roll_mean = x.rolling(w).mean().dropna().values
feature_dict['ave_roll_std_{}'.format(w)] = x_roll_std.mean()
feature_dict['std_roll_std_{}'.format(w)] = x_roll_std.std()
feature_dict['max_roll_std_{}'.format(w)] = x_roll_std.max()
feature_dict['min_roll_std_{}'.format(w)] = x_roll_std.min()
for p in percentiles:
feature_dict['percentile_roll_std_{}_window_{}'.format(
p, w)] = np.percentile(x_roll_std, p)
feature_dict['av_change_abs_roll_std_{}'.format(w)] = np.mean(
np.diff(x_roll_std))
feature_dict['av_change_rate_roll_std_{}'.format(w)] = np.mean(
np.nonzero((np.diff(x_roll_std) / x_roll_std[:-1]))[0])
feature_dict['abs_max_roll_std_{}'.format(w)] = np.abs(
x_roll_std).max()
feature_dict['ave_roll_mean_{}'.format(w)] = x_roll_mean.mean()
feature_dict['std_roll_mean_{}'.format(w)] = x_roll_mean.std()
feature_dict['max_roll_mean_{}'.format(w)] = x_roll_mean.max()
feature_dict['min_roll_mean_{}'.format(w)] = x_roll_mean.min()
for p in percentiles:
feature_dict['percentile_roll_mean_{}_window_{}'.format(
p, w)] = np.percentile(x_roll_mean, p)
feature_dict['av_change_abs_roll_mean_{}'.format(w)] = np.mean(
np.diff(x_roll_mean))
feature_dict['av_change_rate_roll_mean_{}'.format(w)] = np.mean(
np.nonzero((np.diff(x_roll_mean) / x_roll_mean[:-1]))[0])
feature_dict['abs_max_roll_mean_{}'.format(w)] = np.abs(
x_roll_mean).max()
return feature_dict
def log_energy(x):
return np.log(fc.abs_energy(x))
def get_abs_energy(arr):
res = np.array([abs_energy(arr)])
res = np.nan_to_num(res)
return res
def features(self, x, y, seg_id):
feature_dict = dict()
feature_dict['target'] = y
feature_dict['seg_id'] = seg_id
# create features here
# numpy
feature_dict['mean'] = np.mean(x)
feature_dict['max'] = np.max(x)
feature_dict['min'] = np.min(x)
feature_dict['std'] = np.std(x)
feature_dict['var'] = np.var(x)
feature_dict['ptp'] = np.ptp(x)
feature_dict['percentile_10'] = np.percentile(x, 10)
feature_dict['percentile_20'] = np.percentile(x, 20)
feature_dict['percentile_30'] = np.percentile(x, 30)
feature_dict['percentile_40'] = np.percentile(x, 40)
feature_dict['percentile_50'] = np.percentile(x, 50)
feature_dict['percentile_60'] = np.percentile(x, 60)
feature_dict['percentile_70'] = np.percentile(x, 70)
feature_dict['percentile_80'] = np.percentile(x, 80)
feature_dict['percentile_90'] = np.percentile(x, 90)
# scipy
feature_dict['skew'] = sp.stats.skew(x)
feature_dict['kurtosis'] = sp.stats.kurtosis(x)
feature_dict['kstat_1'] = sp.stats.kstat(x, 1)
feature_dict['kstat_2'] = sp.stats.kstat(x, 2)
feature_dict['kstat_3'] = sp.stats.kstat(x, 3)
feature_dict['kstat_4'] = sp.stats.kstat(x, 4)
feature_dict['moment_1'] = sp.stats.moment(x, 1)
feature_dict['moment_2'] = sp.stats.moment(x, 2)
feature_dict['moment_3'] = sp.stats.moment(x, 3)
feature_dict['moment_4'] = sp.stats.moment(x, 4)
feature_dict['abs_energy'] = feature_calculators.abs_energy(x)
feature_dict['abs_sum_of_changes'] = feature_calculators.absolute_sum_of_changes(x)
feature_dict['count_above_mean'] = feature_calculators.count_above_mean(x)
feature_dict['count_below_mean'] = feature_calculators.count_below_mean(x)
feature_dict['mean_abs_change'] = feature_calculators.mean_abs_change(x)
feature_dict['mean_change'] = feature_calculators.mean_change(x)
feature_dict['var_larger_than_std_dev'] = feature_calculators.variance_larger_than_standard_deviation(x)
feature_dict['range_minf_m4000'] = feature_calculators.range_count(x, -np.inf, -4000)
feature_dict['range_m4000_m3000'] = feature_calculators.range_count(x, -4000, -3000)
feature_dict['range_m3000_m2000'] = feature_calculators.range_count(x, -3000, -2000)
feature_dict['range_m2000_m1000'] = feature_calculators.range_count(x, -2000, -1000)
feature_dict['range_m1000_0'] = feature_calculators.range_count(x, -1000, 0)
feature_dict['range_0_p1000'] = feature_calculators.range_count(x, 0, 1000)
feature_dict['range_p1000_p2000'] = feature_calculators.range_count(x, 1000, 2000)
feature_dict['range_p2000_p3000'] = feature_calculators.range_count(x, 2000, 3000)
feature_dict['range_p3000_p4000'] = feature_calculators.range_count(x, 3000, 4000)
feature_dict['range_p4000_pinf'] = feature_calculators.range_count(x, 4000, np.inf)
feature_dict['ratio_unique_values'] = feature_calculators.ratio_value_number_to_time_series_length(x)
feature_dict['first_loc_min'] = feature_calculators.first_location_of_minimum(x)
feature_dict['first_loc_max'] = feature_calculators.first_location_of_maximum(x)
feature_dict['last_loc_min'] = feature_calculators.last_location_of_minimum(x)
feature_dict['last_loc_max'] = feature_calculators.last_location_of_maximum(x)
feature_dict['time_rev_asym_stat_10'] = feature_calculators.time_reversal_asymmetry_statistic(x, 10)
feature_dict['time_rev_asym_stat_100'] = feature_calculators.time_reversal_asymmetry_statistic(x, 100)
feature_dict['time_rev_asym_stat_1000'] = feature_calculators.time_reversal_asymmetry_statistic(x, 1000)
feature_dict['autocorrelation_5'] = feature_calculators.autocorrelation(x, 5)
feature_dict['autocorrelation_10'] = feature_calculators.autocorrelation(x, 10)
feature_dict['autocorrelation_50'] = feature_calculators.autocorrelation(x, 50)
feature_dict['autocorrelation_100'] = feature_calculators.autocorrelation(x, 100)
feature_dict['autocorrelation_1000'] = feature_calculators.autocorrelation(x, 1000)
feature_dict['c3_5'] = feature_calculators.c3(x, 5)
feature_dict['c3_10'] = feature_calculators.c3(x, 10)
feature_dict['c3_100'] = feature_calculators.c3(x, 100)
feature_dict['fft_1_real'] = list(feature_calculators.fft_coefficient(x, [{'coeff': 1, 'attr': 'real'}]))[0][1]
feature_dict['fft_1_imag'] = list(feature_calculators.fft_coefficient(x, [{'coeff': 1, 'attr': 'imag'}]))[0][1]
feature_dict['fft_1_ang'] = list(feature_calculators.fft_coefficient(x, [{'coeff': 1, 'attr': 'angle'}]))[0][1]
feature_dict['fft_2_real'] = list(feature_calculators.fft_coefficient(x, [{'coeff': 2, 'attr': 'real'}]))[0][1]
feature_dict['fft_2_imag'] = list(feature_calculators.fft_coefficient(x, [{'coeff': 2, 'attr': 'imag'}]))[0][1]
feature_dict['fft_2_ang'] = list(feature_calculators.fft_coefficient(x, [{'coeff': 2, 'attr': 'angle'}]))[0][1]
feature_dict['fft_3_real'] = list(feature_calculators.fft_coefficient(x, [{'coeff': 3, 'attr': 'real'}]))[0][1]
feature_dict['fft_3_imag'] = list(feature_calculators.fft_coefficient(x, [{'coeff': 3, 'attr': 'imag'}]))[0][1]
feature_dict['fft_3_ang'] = list(feature_calculators.fft_coefficient(x, [{'coeff': 3, 'attr': 'angle'}]))[0][1]
feature_dict['long_strk_above_mean'] = feature_calculators.longest_strike_above_mean(x)
feature_dict['long_strk_below_mean'] = feature_calculators.longest_strike_below_mean(x)
feature_dict['cid_ce_0'] = feature_calculators.cid_ce(x, 0)
feature_dict['cid_ce_1'] = feature_calculators.cid_ce(x, 1)
feature_dict['binned_entropy_5'] = feature_calculators.binned_entropy(x, 5)
feature_dict['binned_entropy_10'] = feature_calculators.binned_entropy(x, 10)
feature_dict['binned_entropy_20'] = feature_calculators.binned_entropy(x, 20)
feature_dict['binned_entropy_50'] = feature_calculators.binned_entropy(x, 50)
feature_dict['binned_entropy_80'] = feature_calculators.binned_entropy(x, 80)
feature_dict['binned_entropy_100'] = feature_calculators.binned_entropy(x, 100)
feature_dict['num_crossing_0'] = feature_calculators.number_crossing_m(x, 0)
feature_dict['num_peaks_10'] = feature_calculators.number_peaks(x, 10)
feature_dict['num_peaks_50'] = feature_calculators.number_peaks(x, 50)
feature_dict['num_peaks_100'] = feature_calculators.number_peaks(x, 100)
feature_dict['num_peaks_500'] = feature_calculators.number_peaks(x, 500)
feature_dict['spkt_welch_density_1'] = list(feature_calculators.spkt_welch_density(x, [{'coeff': 1}]))[0][1]
feature_dict['spkt_welch_density_10'] = list(feature_calculators.spkt_welch_density(x, [{'coeff': 10}]))[0][1]
feature_dict['spkt_welch_density_50'] = list(feature_calculators.spkt_welch_density(x, [{'coeff': 50}]))[0][1]
feature_dict['spkt_welch_density_100'] = list(feature_calculators.spkt_welch_density(x, [{'coeff': 100}]))[0][1]
feature_dict['time_rev_asym_stat_1'] = feature_calculators.time_reversal_asymmetry_statistic(x, 1)
feature_dict['time_rev_asym_stat_10'] = feature_calculators.time_reversal_asymmetry_statistic(x, 10)
feature_dict['time_rev_asym_stat_100'] = feature_calculators.time_reversal_asymmetry_statistic(x, 100)
return feature_dict
def main():
dirname = os.path.realpath('.')
filename = dirname + '\\GaPt07_01.txt'
data = open(filename, 'r')
totalData = {}
time = []
totalForceL = []
totalForceR = []
id = []
for line in data:
tempForce = line.split()
id.append(1)
time.append(float(tempForce[0]))
totalForceL.append(float(tempForce[17]))
totalForceR.append(float(tempForce[18]))
totalData["id"] = id
totalData["time"] = time
totalData["totalForceL"] = totalForceL
totalData["totalForceR"] = totalForceR
dataPandas = pd.DataFrame.from_dict(totalData)
extracted_features = {}
#extract_featuresL = extract_features(dataPandas, column_id="id", column_kind=None, column_value=None)
extracted_features["absEnergyL"] = tf.abs_energy(totalData["totalForceL"])
extracted_features["absEnergyR"] = tf.abs_energy(totalData["totalForceR"])
extracted_features["kurtosisL"] = tf.kurtosis(totalData["totalForceL"])
extracted_features["kurtosisR"] = tf.kurtosis(totalData["totalForceR"])
extracted_features["skewnessL"] = tf.skewness(totalData["totalForceL"])
extracted_features["skewnessR"] = tf.skewness(totalData["totalForceR"])
extracted_features["medianL"] = tf.median(totalData["totalForceL"])
extracted_features["medianR"] = tf.median(totalData["totalForceR"])
extracted_features["meanL"] = tf.mean(totalData["totalForceL"])
extracted_features["meanR"] = tf.mean(totalData["totalForceR"])
extracted_features["varianceL"] = tf.variance(totalData["totalForceL"])
extracted_features["varianceR"] = tf.variance(totalData["totalForceR"])
temp = tf.fft_aggregated(totalData["totalForceL"], [{
"aggtype": "centroid"
}, {
"aggtype": "variance"
}, {
"aggtype": "skew"
}, {
"aggtype": "kurtosis"
}])
int = 0
for list in temp:
if int == 0:
extracted_features["fftCentroidL"] = list
if int == 1:
extracted_features["fftVarianceL"] = list
if int == 2:
extracted_features["fftSkewL"] = list
if int == 3:
extracted_features["fftKurtosisL"] = list
int += 1
temp2 = tf.fft_aggregated(totalData["totalForceR"], [{
"aggtype": "centroid"
}, {
"aggtype": "variance"
}, {
"aggtype": "skew"
}, {
"aggtype": "kurtosis"
}])
int = 0
for list in temp2:
if int == 0:
extracted_features["fftCentroidR"] = list
if int == 1:
extracted_features["fftVarianceR"] = list
if int == 2:
extracted_features["fftSkewR"] = list
if int == 3:
extracted_features["fftKurtosisR"] = list
int += 1
