Add option to calculate features within windows and store it in CSV (all sensors).
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parent
74cf4ada1c
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3c058e4463
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config.yaml
14
config.yaml
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@ -481,7 +481,7 @@ EMPATICA_ACCELEROMETER:
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FEATURES: ["maxmagnitude", "minmagnitude", "avgmagnitude", "medianmagnitude", "stdmagnitude"]
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SRC_SCRIPT: src/features/empatica_accelerometer/dbdp/main.py
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CR:
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COMPUTE: True
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COMPUTE: False
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FEATURES: ["fqHighestPeakFreqs", "fqHighestPeaks", "fqEnergyFeat", "fqEntropyFeat", "fqHistogramBins","fqAbsMean", "fqSkewness", "fqKurtosis", "fqInterquart", # Freq features
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"meanLow", "areaLow", "totalAbsoluteAreaBand", "totalMagnitudeBand", "entropyBand", "skewnessBand", "kurtosisBand",
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"postureDistanceLow", "absoluteMeanBand", "absoluteAreaBand", "quartilesBand", "interQuartileRangeBand", "varianceBand",
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@ -510,7 +510,7 @@ EMPATICA_TEMPERATURE:
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CONTAINER: TEMP
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PROVIDERS:
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DBDP:
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COMPUTE: False
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COMPUTE: True
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FEATURES: ["maxtemp", "mintemp", "avgtemp", "mediantemp", "modetemp", "stdtemp", "diffmaxmodetemp", "diffminmodetemp", "entropytemp"]
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SRC_SCRIPT: src/features/empatica_temperature/dbdp/main.py
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CR:
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@ -521,7 +521,7 @@ EMPATICA_TEMPERATURE:
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"calcMeanCrossingRateAutocorr", "countAboveMeanAutocorr", "sumPer", "sumSquared", "squareSumOfComponent",
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"sumOfSquareComponents"]
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WINDOWS:
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COMPUTE: False
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COMPUTE: True
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WINDOW_LENGTH: 90 # specify window length in seconds
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SRC_SCRIPT: src/features/empatica_temperature/cr/main.py
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@ -530,7 +530,7 @@ EMPATICA_ELECTRODERMAL_ACTIVITY:
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CONTAINER: EDA
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PROVIDERS:
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DBDP:
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COMPUTE: False
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COMPUTE: True
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FEATURES: ["maxeda", "mineda", "avgeda", "medianeda", "modeeda", "stdeda", "diffmaxmodeeda", "diffminmodeeda", "entropyeda"]
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SRC_SCRIPT: src/features/empatica_electrodermal_activity/dbdp/main.py
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CR:
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@ -541,7 +541,7 @@ EMPATICA_ELECTRODERMAL_ACTIVITY:
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'avgPeakIncreaseTime', 'avgPeakDecreaseTime', 'avgPeakDuration', 'maxPeakResponseSlopeBefore', 'maxPeakResponseSlopeAfter',
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'signalOverallChange', 'changeDuration', 'changeRate', 'significantIncrease', 'significantDecrease']
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WINDOWS:
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COMPUTE: False
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COMPUTE: True
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WINDOW_LENGTH: 80 # specify window length in seconds
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SRC_SCRIPT: src/features/empatica_electrodermal_activity/cr/main.py
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@ -550,7 +550,7 @@ EMPATICA_BLOOD_VOLUME_PULSE:
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CONTAINER: BVP
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PROVIDERS:
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DBDP:
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COMPUTE: False
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COMPUTE: True
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FEATURES: ["fqHighestPeakFreqs", "fqHighestPeaks", "fqEnergyFeat", "fqEntropyFeat", "fqHistogramBins","fqAbsMean", "fqSkewness", "fqKurtosis", "fqInterquart", # Freq features
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"maxbvp", "minbvp", "avgbvp", "medianbvp", "modebvp", "stdbvp", "diffmaxmodebvp", "diffminmodebvp", "entropybvp"] # HRV features
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SRC_SCRIPT: src/features/empatica_blood_volume_pulse/dbdp/main.py
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@ -558,7 +558,7 @@ EMPATICA_BLOOD_VOLUME_PULSE:
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COMPUTE: True
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FEATURES: ['meanHr', 'ibi', 'sdnn', 'sdsd', 'rmssd', 'pnn20', 'pnn50', 'sd', 'sd2', 'sd1/sd2', 'numRR']
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WINDOWS:
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COMPUTE: False
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COMPUTE: True
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WINDOW_LENGTH: 4 # specify window length in seconds
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SRC_SCRIPT: src/features/empatica_blood_volume_pulse/cr/main.py
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@ -770,7 +770,8 @@ rule empatica_accelerometer_python_features:
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provider_key = "{provider_key}",
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sensor_key = "empatica_accelerometer"
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output:
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"data/interim/{pid}/empatica_accelerometer_features/empatica_accelerometer_python_{provider_key}.csv"
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"data/interim/{pid}/empatica_accelerometer_features/empatica_accelerometer_python_{provider_key}.csv",
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"data/interim/{pid}/empatica_accelerometer_features/empatica_accelerometer_python_{provider_key}_windows.csv"
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script:
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"../src/features/entry.py"
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@ -796,7 +797,8 @@ rule empatica_heartrate_python_features:
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provider_key = "{provider_key}",
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sensor_key = "empatica_heartrate"
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output:
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"data/interim/{pid}/empatica_heartrate_features/empatica_heartrate_python_{provider_key}.csv"
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"data/interim/{pid}/empatica_heartrate_features/empatica_heartrate_python_{provider_key}.csv",
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"data/interim/{pid}/empatica_heartrate_features/empatica_heartrate_python_{provider_key}_windows.csv"
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script:
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"../src/features/entry.py"
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@ -822,7 +824,8 @@ rule empatica_temperature_python_features:
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provider_key = "{provider_key}",
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sensor_key = "empatica_temperature"
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output:
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"data/interim/{pid}/empatica_temperature_features/empatica_temperature_python_{provider_key}.csv"
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"data/interim/{pid}/empatica_temperature_features/empatica_temperature_python_{provider_key}.csv",
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"data/interim/{pid}/empatica_temperature_features/empatica_temperature_python_{provider_key}_windows.csv"
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script:
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"../src/features/entry.py"
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@ -848,7 +851,8 @@ rule empatica_electrodermal_activity_python_features:
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provider_key = "{provider_key}",
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sensor_key = "empatica_electrodermal_activity"
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output:
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"data/interim/{pid}/empatica_electrodermal_activity_features/empatica_electrodermal_activity_python_{provider_key}.csv"
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"data/interim/{pid}/empatica_electrodermal_activity_features/empatica_electrodermal_activity_python_{provider_key}.csv",
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"data/interim/{pid}/empatica_electrodermal_activity_features/empatica_electrodermal_activity_python_{provider_key}_windows.csv"
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script:
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"../src/features/entry.py"
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@ -874,7 +878,8 @@ rule empatica_blood_volume_pulse_python_features:
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provider_key = "{provider_key}",
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sensor_key = "empatica_blood_volume_pulse"
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output:
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"data/interim/{pid}/empatica_blood_volume_pulse_features/empatica_blood_volume_pulse_python_{provider_key}.csv"
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"data/interim/{pid}/empatica_blood_volume_pulse_features/empatica_blood_volume_pulse_python_{provider_key}.csv",
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"data/interim/{pid}/empatica_blood_volume_pulse_features/empatica_blood_volume_pulse_python_{provider_key}_windows.csv"
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script:
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"../src/features/entry.py"
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@ -900,7 +905,8 @@ rule empatica_inter_beat_interval_python_features:
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provider_key = "{provider_key}",
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sensor_key = "empatica_inter_beat_interval"
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output:
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"data/interim/{pid}/empatica_inter_beat_interval_features/empatica_inter_beat_interval_python_{provider_key}.csv"
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"data/interim/{pid}/empatica_inter_beat_interval_features/empatica_inter_beat_interval_python_{provider_key}.csv",
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"data/interim/{pid}/empatica_inter_beat_interval_features/empatica_inter_beat_interval_python_{provider_key}_windows.csv"
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script:
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"../src/features/entry.py"
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@ -53,7 +53,9 @@ def cr_features(sensor_data_files, time_segment, provider, filter_data_by_segmen
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requested_intraday_features = provider["FEATURES"]
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if provider["WINDOWS"]["COMPUTE"]:
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calc_windows = kwargs.get('calc_windows', False)
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if provider["WINDOWS"]["COMPUTE"] and calc_windows:
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requested_window_length = provider["WINDOWS"]["WINDOW_LENGTH"]
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else:
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requested_window_length = None
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@ -47,7 +47,9 @@ def cr_features(sensor_data_files, time_segment, provider, filter_data_by_segmen
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requested_intraday_features = provider["FEATURES"]
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if provider["WINDOWS"]["COMPUTE"]:
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calc_windows = kwargs.get('calc_windows', False)
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if provider["WINDOWS"]["COMPUTE"] and calc_windows:
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requested_window_length = provider["WINDOWS"]["WINDOW_LENGTH"]
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else:
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requested_window_length = None
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@ -46,7 +46,9 @@ def cr_features(sensor_data_files, time_segment, provider, filter_data_by_segmen
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requested_intraday_features = provider["FEATURES"]
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if provider["WINDOWS"]["COMPUTE"]:
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calc_windows = kwargs.get('calc_windows', False)
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if provider["WINDOWS"]["COMPUTE"] and calc_windows:
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requested_window_length = provider["WINDOWS"]["WINDOW_LENGTH"]
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else:
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requested_window_length = None
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@ -45,7 +45,10 @@ def cr_features(sensor_data_files, time_segment, provider, filter_data_by_segmen
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temperature_intraday_data = pd.read_csv(sensor_data_files["sensor_data"])
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requested_intraday_features = provider["FEATURES"]
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if provider["WINDOWS"]["COMPUTE"]:
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calc_windows = kwargs.get('calc_windows', False)
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if provider["WINDOWS"]["COMPUTE"] and calc_windows:
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requested_window_length = provider["WINDOWS"]["WINDOW_LENGTH"]
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else:
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requested_window_length = None
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@ -7,6 +7,13 @@ provider = snakemake.params["provider"]
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provider_key = snakemake.params["provider_key"]
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sensor_key = snakemake.params["sensor_key"]
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calc_windows = False
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try:
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calc_windows = provider["WINDOWS"]["COMPUTE"]
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except KeyError:
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print("Compute window key not found in config.yaml!")
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if sensor_key == "all_cleaning_individual" or sensor_key == "all_cleaning_overall":
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# Data cleaning
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sensor_features = run_provider_cleaning_script(provider, provider_key, sensor_key, sensor_data_files)
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@ -14,6 +21,14 @@ else:
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# Extract sensor features
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del sensor_data_files["time_segments_labels"]
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time_segments_file = snakemake.input["time_segments_labels"]
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sensor_features = fetch_provider_features(provider, provider_key, sensor_key, sensor_data_files, time_segments_file)
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sensor_features = fetch_provider_features(provider, provider_key, sensor_key, sensor_data_files, time_segments_file, calc_windows=calc_windows)
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# Calculation over multiple windows in case of Empatica's CR-features
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if calc_windows:
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sensor_features.to_csv(snakemake.output[1], index=False)
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sensor_features = fetch_provider_features(provider, provider_key, sensor_key, sensor_data_files, time_segments_file, calc_windows=False)
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elif "empatica" in sensor_key and provider_key == "dbdp":
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pd.DataFrame().to_csv(snakemake.output[1], index=False)
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sensor_features.to_csv(snakemake.output[0], index=False)
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@ -88,7 +88,7 @@ def chunk_episodes(sensor_episodes):
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return merged_sensor_episodes
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def fetch_provider_features(provider, provider_key, sensor_key, sensor_data_files, time_segments_file):
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def fetch_provider_features(provider, provider_key, sensor_key, sensor_data_files, time_segments_file, calc_windows=False):
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import pandas as pd
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from importlib import import_module, util
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@ -106,7 +106,7 @@ def fetch_provider_features(provider, provider_key, sensor_key, sensor_data_file
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time_segments_labels["label"] = [""]
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for time_segment in time_segments_labels["label"]:
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print("{} Processing {} {} {}".format(rapids_log_tag, sensor_key, provider_key, time_segment))
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features = feature_function(sensor_data_files, time_segment, provider, filter_data_by_segment=filter_data_by_segment, chunk_episodes=chunk_episodes)
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features = feature_function(sensor_data_files, time_segment, provider, filter_data_by_segment=filter_data_by_segment, chunk_episodes=chunk_episodes, calc_windows=calc_windows)
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if not "local_segment" in features.columns:
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raise ValueError("The dataframe returned by the " + sensor_key + " provider '" + provider_key + "' is missing the 'local_segment' column added by the 'filter_data_by_segment()' function. Check the provider script is using such function and is not removing 'local_segment' by accident (" + provider["SRC_SCRIPT"] + ")\n The 'local_segment' column is used to index a provider's features (each row corresponds to a different time segment instance (e.g. 2020-01-01, 2020-01-02, 2020-01-03, etc.)")
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features.columns = ["{}{}".format("" if col.startswith("local_segment") else (sensor_key + "_"+ provider_key + "_"), col) for col in features.columns]
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