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 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: