import pandas as pd from sklearn.preprocessing import StandardScaler from cr_features.helper_functions import convert_to2d, hrv_features from cr_features.hrv import extract_hrv_features_2d_wrapper from cr_features_helper_methods import extract_second_order_features import sys # pd.set_option('display.max_rows', 1000) pd.set_option('display.max_columns', None) def extract_bvp_features_from_intraday_data(bvp_intraday_data, features, window_length, time_segment, filter_data_by_segment): bvp_intraday_features = pd.DataFrame(columns=["local_segment"] + features) if not bvp_intraday_data.empty: sample_rate = 64 bvp_intraday_data = filter_data_by_segment(bvp_intraday_data, time_segment) if not bvp_intraday_data.empty: bvp_intraday_features = pd.DataFrame() # apply methods from calculate features module if window_length is None: bvp_intraday_features = \ bvp_intraday_data.groupby('local_segment').apply(\ lambda x: extract_hrv_features_2d_wrapper( convert_to2d(x['blood_volume_pulse'], x.shape[0]), sampling=sample_rate, hampel_fiter=False, median_filter=False, mod_z_score_filter=True, feature_names=features)) else: bvp_intraday_features = \ bvp_intraday_data.groupby('local_segment').apply(\ lambda x: extract_hrv_features_2d_wrapper( convert_to2d(x['blood_volume_pulse'], window_length*sample_rate), sampling=sample_rate, hampel_fiter=False, median_filter=False, mod_z_score_filter=True, feature_names=features)) bvp_intraday_features.reset_index(inplace=True) return bvp_intraday_features def cr_features(sensor_data_files, time_segment, provider, filter_data_by_segment, *args, **kwargs): bvp_intraday_data = pd.read_csv(sensor_data_files["sensor_data"]) requested_intraday_features = provider["FEATURES"] calc_windows = kwargs.get('calc_windows', False) if provider["WINDOWS"]["COMPUTE"] and calc_windows: requested_window_length = provider["WINDOWS"]["WINDOW_LENGTH"] else: requested_window_length = None # name of the features this function can compute base_intraday_features_names = hrv_features # the subset of requested features this function can compute intraday_features_to_compute = list(set(requested_intraday_features) & set(base_intraday_features_names)) # extract features from intraday data bvp_intraday_features = extract_bvp_features_from_intraday_data(bvp_intraday_data, intraday_features_to_compute, requested_window_length, time_segment, filter_data_by_segment) if calc_windows: if provider["WINDOWS"].get("STANDARDIZE_SO_FEATURES", False): fo_columns = bvp_intraday_features.columns.values[2:] fo_columns_z_score = [col + "_zscore" for col in fo_columns] bvp_intraday_features[fo_columns_z_score] = StandardScaler().fit_transform(bvp_intraday_features[fo_columns]) so_features_names = provider["WINDOWS"]["SECOND_ORDER_FEATURES"] bvp_second_order_features = extract_second_order_features(bvp_intraday_features, so_features_names) return bvp_intraday_features, bvp_second_order_features return bvp_intraday_features