diff --git a/calculatingfeatures b/calculatingfeatures new file mode 160000 index 00000000..98e6207e --- /dev/null +++ b/calculatingfeatures @@ -0,0 +1 @@ +Subproject commit 98e6207ecc23a23b1f621a11f28eb87cbfb7f9da diff --git a/config.yaml b/config.yaml index 9ff1e19b..16c1ed9e 100644 --- a/config.yaml +++ b/config.yaml @@ -3,7 +3,7 @@ ######################################################################################################################## # See https://www.rapids.science/latest/setup/configuration/#participant-files -PIDS: [p02] #p01, p02, p03] +PIDS: [p01] #p01, p02, p03] # See https://www.rapids.science/latest/setup/configuration/#automatic-creation-of-participant-files CREATE_PARTICIPANT_FILES: @@ -542,6 +542,7 @@ EMPATICA_ELECTRODERMAL_ACTIVITY: WINDOW_LENGTH: 60 # specify window length in seconds SECOND_ORDER_FEATURES: ['mean', 'median', 'sd', 'nlargest', 'nsmallest', count_windows, eda_num_peaks_non_zero] STANDARDIZE_FEATURES: False + IMPUTE_NANS: False SRC_SCRIPT: src/features/empatica_electrodermal_activity/cr/main.py # See https://www.rapids.science/latest/features/empatica-blood-volume-pulse/ diff --git a/eda_windows_p01_window_60_thresh_default.png b/eda_windows_p01_window_60_thresh_default.png deleted file mode 100644 index b8a8e548..00000000 Binary files a/eda_windows_p01_window_60_thresh_default.png and /dev/null differ diff --git a/eda_windows_p02_window_60_thresh_default.png b/eda_windows_p02_window_60_thresh_default.png deleted file mode 100644 index d9f7d61b..00000000 Binary files a/eda_windows_p02_window_60_thresh_default.png and /dev/null differ diff --git a/src/features/empatica_electrodermal_activity/cr/main.py b/src/features/empatica_electrodermal_activity/cr/main.py index 1d56839d..6b9e6fac 100644 --- a/src/features/empatica_electrodermal_activity/cr/main.py +++ b/src/features/empatica_electrodermal_activity/cr/main.py @@ -63,6 +63,11 @@ def cr_features(sensor_data_files, time_segment, provider, filter_data_by_segmen requested_window_length, time_segment, filter_data_by_segment) if calc_windows: + if provider["WINDOWS"]["IMPUTE_NANS"]: + eda_intraday_features[eda_intraday_features["numPeaks"] == 0] = \ + eda_intraday_features[eda_intraday_features["numPeaks"] == 0].fillna(0) + pd.set_option('display.max_columns', None) + so_features_names = provider["WINDOWS"]["SECOND_ORDER_FEATURES"] eda_second_order_features = extract_second_order_features(eda_intraday_features, so_features_names) diff --git a/src/features/entry.py b/src/features/entry.py index dea1e1df..288ba168 100644 --- a/src/features/entry.py +++ b/src/features/entry.py @@ -28,7 +28,8 @@ else: elif "empatica" in sensor_key: pd.DataFrame().to_csv(snakemake.output[1], index=False) - sensor_features = fetch_provider_features(provider, provider_key, sensor_key, sensor_data_files, time_segments_file, calc_windows=False) + if not calc_windows: + sensor_features = fetch_provider_features(provider, provider_key, sensor_key, sensor_data_files, time_segments_file, calc_windows=False) if not calc_windows: sensor_features.to_csv(snakemake.output[0], index=False) diff --git a/tests/scripts/missing_values_heatmap.py b/tests/scripts/missing_values_heatmap.py index 3826e371..20e7d33f 100644 --- a/tests/scripts/missing_values_heatmap.py +++ b/tests/scripts/missing_values_heatmap.py @@ -5,7 +5,7 @@ import matplotlib.pyplot as plt # path = "/rapids/data/processed/features/all_participants/all_sensor_features.csv" # all features all participants # path = "/rapids/data/interim/p03/empatica_accelerometer_features/empatica_accelerometer_python_cr_windows.csv" -path = "/rapids/data/interim/p02/empatica_electrodermal_activity_features/empatica_electrodermal_activity_python_cr_windows.csv" +path = "/rapids/data/interim/p01/empatica_electrodermal_activity_features/empatica_electrodermal_activity_python_cr_windows.csv" # path = "/rapids/data/interim/p02/empatica_inter_beat_interval_features/empatica_inter_beat_interval_python_cr_windows.csv" # path = "/rapids/data/interim/p02/empatica_blood_volume_pulse_features/empatica_blood_volume_pulse_python_cr_windows.csv" # path = "/rapids/data/interim/p02/empatica_temperature_features/empatica_temperature_python_cr_windows.csv"