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 TS_feature3(signal):
max_ts = ts.maximum(signal)
mean_rs = ts.mean(signal)
mean_abs_change = ts.mean_abs_change(signal)
mean_change = ts.mean_change(signal)
median_ts = ts.median(signal)
minimum_ts = ts.minimum(signal)
return max_ts, mean_rs, mean_abs_change, mean_change, median_ts, minimum_ts
def time_series_median(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.median(x)
def scalar_feature_extraction(column):
retval = np.zeros([1, 10], dtype=float)
retval[0][0] = tffe.count_above_mean(column.values)
retval[0][1] = tffe.mean(column.values)
retval[0][2] = tffe.maximum(column.values)
retval[0][3] = tffe.median(column.values)
retval[0][4] = tffe.minimum(column.values)
retval[0][5] = tffe.sample_entropy(column.values)
if (isNaN(retval[0][5])):
retval[0][5] = 0
retval[0][6] = tffe.skewness(column.values)
retval[0][7] = tffe.variance(column.values)
retval[0][8] = tffe.longest_strike_above_mean(column.values)
retval[0][9] = tffe.longest_strike_below_mean(column.values)
return retval
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 MedianDeviation(fragment):
return fc.median([val-fc.median(fragment) for val in fragment])
def MedianDifference(fragment):
return fc.median(np.diff(fragment))
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 get_median(arr):
res = np.array([median(arr)])
res = np.nan_to_num(res)
return res
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