def detect_artifact(GSR,th,Fs): ts, filtered, onsets, peaks, amplitudes = beda.eda(GSR.ravel(),Fs,False) first_detect = first_layer_artifact(GSR,th,Fs) detect = second_layer_artifact_detect(GSR,filtered,first_detect,Fs,5) return detect
def artifact_percentage_Simple(user_id,data_no): total_epoch = 0 artifact_epoch = 0 data,q=load_data(user_id,data_no) ts, filtered, onsets, peaks, amplitudes = beda.eda(data.ravel(),128,False) label = first_layer_artifact(filtered,10,128) total_epoch = len(label) for k in range(len(label)): if label[k] == -1 or label[k] == 0: artifact_epoch += 1 return artifact_epoch/total_epoch
def fig_proposed(GSR,sampling_rate):
ts, filtered, onsets, peaks, amplitudes = beda.eda(GSR.ravel(),sampling_rate,False)
SR = filtered
predict = detect_artifact(SR,10,sampling_rate)
predict_1 = detect_artifact(GSR,10,sampling_rate)
predict_2 = second_layer_artifact_detect(GSR,SR,predict_1,sampling_rate,5)
plot_GSR_and_label(GSR,predict_1,sampling_rate)
plt.savefig("CHEN DATA")
plt.close()
def extract_scrs(self, feature_path):
data = {}
for k, v in self.file_dict.items():
if k == "par1_palm":
rate = 1024.0
else:
rate = 128.0
eda_features = eda.eda(v["GSR_Skin_Conductance(uS)"].values,
sampling_rate=128.0)
print(type(eda_features))
data[k] = dict(eda_features)
pickle.dump(data, open(feature_path, 'wb'))
return data
def eda_extract(signal,
sampling_rate=1000.0,
min_amplitude=0.1,
inner_draw=False):
"""
Args:
signal: narray, EDA data.
sampling_rate: float, Sampling rate of EDA data.
min_amplitude: float, Minimum treshold by which to exclude SCRs.
Returns:
A dictionary representation of the information of EDA.
Notes:
*Authors*
- the bioSSPy dev team (https://github.com/PIA-Group/BioSPPy)
*Dependencies*
- biosppy
*See Also*
- BioSPPY: https://github.com/PIA-Group/BioSPPy
"""
output = eda.eda(signal=signal,
sampling_rate=1000.0,
show=inner_draw,
min_amplitude=0.1)
eda_per_minute_list = _count_eda_per_minute(output['filtered'],
interval_second=1 /
sampling_rate)
scl_per_minute_info = _get_scl_per_minute_info(eda_per_minute_list)
scr_per_minute_info = _get_scr_per_minute_info(output['onsets'],
output['amplitudes'])
eda_info = {
'signal_time': output['ts'],
'filtered': output['filtered'],
'onsets': output['onsets'],
'peaks': output['peaks'],
'amplitudes': output['amplitudes'],
'scl_per_minute_info': scl_per_minute_info,
'scr_per_minute_info': scr_per_minute_info
}
return eda_info
def getFiltered_Min(task,index,output,samp_rate):
vals = []
# making sure we are able to get values whether or not they are in a
# two-dimensional array
for i in range(len(task)):
try:
vals.append(task[i][index])
except:
vals.append(task[i])
vals = filter(lambda x:x !="", vals) # remove empty strings
# extract eda features using biosppy
# vals is raw eda data
out = eda.eda(signal=vals, sampling_rate=samp_rate, show=False)
# getting filtered EDA signal
out_resp_filtered = out[1].tolist() # using numpy, convert ndarry into a list
minimum = str(min(out_resp_filtered))
output.write(minimum + ', ')
def getFiltered_Min(task,index,output,samp_rate):
vals = []
# making sure we are able to get values whether or not they are in a
# two-dimensional array
for i in range(len(task)):
try:
vals.append(task[i][index])
except:
vals.append(task[i])
vals = filter(lambda x:x !="", vals) # remove empty strings
# extract eda features using biosppy
# vals is raw eda data
out = eda.eda(signal=vals, sampling_rate=samp_rate, show=False)
# getting filtered EDA signal
out_resp_filtered = out[1].tolist() # using numpy, convert ndarry into a list
minimum = str(min(out_resp_filtered))
output.write(minimum + ', ')
def eda_extract(signal, sampling_rate=1000.0, min_amplitude=0.1):
"""
Args:
signal: narray, EDA data.
sampling_rate: float, Sampling rate of EDA data.
min_amplitude: float, Minimum treshold by which to exclude SCRs.
Returns:
A dictionary representation of the information of EDA.
Notes:
*Authors*
- the bioSSPy dev team (https://github.com/PIA-Group/BioSPPy)
*Dependencies*
- biosppy
*See Also*
- BioSPPY: https://github.com/PIA-Group/BioSPPy
"""
output = eda.eda(signal=signal,
sampling_rate=1000.0,
show=False,
min_amplitude=0.1)
eda_info = {
'signal_time': output['ts'],
'filtered': output['filtered'],
'onsets': output['onsets'],
'peaks': output['peaks'],
'amplitudes': output['amplitudes'],
'EDA_ptp': np.ptp(signal),
'EDA_diff': signal[-1] - signal[0],
'SCL': np.mean(signal),
# 'SCL_normalized': np.mean(normalize(signal)),
'SCR_times': output['onsets'].size
}
return eda_info
def getSCRAvg(task, index, output, samp_rate):
vals = []
# making sure we are able to get values whether or not they are in a
# two-dimensional array
for i in range(len(task)):
try:
vals.append(task[i][index])
except:
vals.append(task[i])
vals = filter(lambda x: x != "", vals) # remove empty strings
out = eda.eda(signal=vals, sampling_rate=samp_rate, show=False)
# getting pulse amplitudes
out_scr = out[4].tolist() # using numpy, convert ndarry into a list
if (len(out_scr)) == 0: # no pulse amplitudes found
output.write('0' + ', ')
else:
average = str(int(sum(out_scr)) / len(out_scr))
output.write(average + ', ')
def getSCRAvg(task,index,output,samp_rate):
vals = []
# making sure we are able to get values whether or not they are in a
# two-dimensional array
for i in range(len(task)):
try:
vals.append(task[i][index])
except:
vals.append(task[i])
vals = filter(lambda x:x !="", vals) # remove empty strings
out = eda.eda(signal=vals, sampling_rate=samp_rate, show=False)
# getting pulse amplitudes
out_scr = out[4].tolist() # using numpy, convert ndarry into a list
if (len(out_scr)) == 0: # no pulse amplitudes found
output.write('0' + ', ')
else:
average = str(int(sum(out_scr)) / len(out_scr))
output.write(average + ', ')
#!/user/bin/env python3
# coding=utf-8
import numpy as np
from biosppy.signals import eda
# load raw ECG signal
signal = np.loadtxt('./data/test/extracted/Iris_kangxi_peyin_EDA.txt')
# process it and plot
out = eda.eda(signal=signal, sampling_rate=1000.0, show=True, min_amplitude=0.1)
continue
regex = re.search(r'(\d+)-answer-(\d+).json', f)
user = regex.group(1)
answer = regex.group(2)
f = open('./output/cut-normalized/{}-answer-{}.json'.format(
user, answer)).read()
x = json.loads(f)
if len(x['answerArousal']) == 0:
continue
try:
y = eda.eda(signal=x['gsr'], sampling_rate=1000, show=False)
except Exception as e:
failed += 1
continue
onsets = list(y['onsets'])
if len(onsets) == 0:
zero_onsets += 1
continue
onset = 0
while len(onsets) > 0 and onset < 1000:
onset = onsets.pop(0)
duration of SCR ocurrences
number of ocurrences
"""
#OJO Detected SCRs with an amplitude smaller that 10% of the maximum SCR
#amplitude in this segment were excluded.
#I DON'T KNOW IF THIS IS IMPLEMENTED IN BIOSPPY, CHECK => Checked, it's ok
#load eda data
eda_raw = np.load('eda.npy')
from biosppy.signals import eda as eda_biosppy
fs = 100
#get filtered eda
eda_obj = eda_biosppy.eda(eda_raw, sampling_rate=fs, show=False)
#get
print(eda_obj.keys())
"""
#get amplitudes and peaks using basic_scr
eda_scr = eda_biosppy.basic_scr(eda_obj['filtered'],sampling_rate = fs)
#discard amplitudes samller than 10% maximum amplitude
max_amp = np.max(eda_scr['amplitudes'])
thr = 0.1
amp = []
onsets =[]
peaks = []
for i,a in enumerate(eda_scr['amplitudes']):
import bioread
a = bioread.read(
'/media/Data/PTSD_KPE/physio_data/raw/kpe1223/scan_1/kpe1223.1_scripts_2017-01-30T08_17_08.acq'
)
# choose scripts channel
b = a.named_channels["GSR100C"].raw_data
a_resample = signal.decimate(b, 40)
plt.plot(b)
plt.plot(a_resample)
plt.show()
c = a_resample[int(7000 / 40):int(130000 / 40)]
out = eda.eda(signal=b, sampling_rate=1000., show=True)
len(out['filtered'])
plt.plot(out['ts'])
d = b[130000:252799]
out = eda.eda(signal=b, sampling_rate=1000., show=True)
#%% second scan
events_file2 = '/media/Data/PTSD_KPE/condition_files/sub-1223_ses-2.csv'
events = pd.read_csv(events_file2, sep=r'\s+')
a = bioread.read(
'/media/Data/PTSD_KPE/physio_data/raw/kpe1223/scan_2/kpe1223.2_scripts_2017-02-06T08_39_32.acq'
)
# choose scripts channel
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument("csv_file", type=str, help="File constaining the raw data")
parser.add_argument('-s',
'--sampling-rate',
type=int,
default=1000,
help="The sample rate")
parser.add_argument('-m',
'--min-amplitude',
type=float,
default=0.1,
help="Min amplitude (for EDA)")
args = parser.parse_args()
signals = np.loadtxt(args.csv_file, delimiter=',')
t = signals[:, 0]
bvp_raw = signals[:, 1]
eda_raw = signals[:, 2]
bvp_signal = bvp.bvp(bvp_raw, sampling_rate=args.sampling_rate)
eda_signal = eda.eda(eda_raw,
sampling_rate=args.sampling_rate,
min_amplitude=args.min_amplitude)
print(bvp_signal)
print(eda_signal)
#
# with open(csv_file_name, 'w') as csv_file:
# csv_reader = csv.reader(csv_file, delimiter=',')
# for row in csv_reader:
