Alternating Second order and full segment features corresponding to config settings.
Primoz
parent
9cf9e1fe14
commit
31e36e7400
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@ -3,7 +3,7 @@
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########################################################################################################################
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# See https://www.rapids.science/latest/setup/configuration/#participant-files
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PIDS: [p02, p01]
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PIDS: [p01] #,p02]
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# See https://www.rapids.science/latest/setup/configuration/#automatic-creation-of-participant-files
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CREATE_PARTICIPANT_FILES:
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@ -477,11 +477,11 @@ EMPATICA_ACCELEROMETER:
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CONTAINER: ACC
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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: ["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: 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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"meanLow", "areaLow", "totalAbsoluteAreaBand", "totalMagnitudeBand", "entropyBand", "skewnessBand", "kurtosisBand",
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"postureDistanceLow", "absoluteMeanBand", "absoluteAreaBand", "quartilesBand", "interQuartileRangeBand", "varianceBand",
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@ -502,7 +502,7 @@ EMPATICA_HEARTRATE:
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CONTAINER: HR
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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: ["maxhr", "minhr", "avghr", "medianhr", "modehr", "stdhr", "diffmaxmodehr", "diffminmodehr", "entropyhr"]
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SRC_SCRIPT: src/features/empatica_heartrate/dbdp/main.py
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@ -771,8 +771,7 @@ rule empatica_accelerometer_python_features:
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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}_windows.csv",
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"data/interim/{pid}/empatica_accelerometer_features/empatica_accelerometer_python_{provider_key}_windows_SO_features.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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@ -799,8 +798,7 @@ rule empatica_heartrate_python_features:
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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}_windows.csv",
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"data/interim/{pid}/empatica_heartrate_features/empatica_heartrate_python_{provider_key}_windows_SO_features.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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@ -827,8 +825,7 @@ rule empatica_temperature_python_features:
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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}_windows.csv",
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"data/interim/{pid}/empatica_temperature_features/empatica_temperature_python_{provider_key}_windows_SO_features.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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@ -855,8 +852,7 @@ rule empatica_electrodermal_activity_python_features:
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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}_windows.csv",
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"data/interim/{pid}/empatica_electrodermal_activity_features/empatica_electrodermal_activity_python_{provider_key}_windows_SO_features.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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@ -883,8 +879,7 @@ rule empatica_blood_volume_pulse_python_features:
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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}_windows.csv",
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"data/interim/{pid}/empatica_blood_volume_pulse_features/empatica_blood_volume_pulse_python_{provider_key}_windows_SO_features.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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@ -911,8 +906,7 @@ rule empatica_inter_beat_interval_python_features:
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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}_windows.csv",
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"data/interim/{pid}/empatica_inter_beat_interval_features/empatica_inter_beat_interval_python_{provider_key}_windows_SO_features.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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@ -11,7 +11,7 @@ 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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print("WINDOWS COMPUTE 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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@ -23,16 +23,14 @@ else:
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time_segments_file = snakemake.input["time_segments_labels"]
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if calc_windows:
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first_order_features, second_order_features = fetch_provider_features(provider, provider_key, sensor_key, sensor_data_files, time_segments_file, calc_windows=calc_windows)
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first_order_features.to_csv(snakemake.output[1], index=False)
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second_order_features.to_csv(snakemake.output[2], index=False)
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calc_windows = False
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window_features, second_order_features = fetch_provider_features(provider, provider_key, sensor_key, sensor_data_files, time_segments_file, calc_windows=True)
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second_order_features.to_csv(snakemake.output[0], index=False)
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window_features.to_csv(snakemake.output[1], index=False)
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elif "empatica" in sensor_key:
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pd.DataFrame().to_csv(snakemake.output[1], index=False)
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pd.DataFrame().to_csv(snakemake.output[2], index=False)
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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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sensor_features = fetch_provider_features(provider, provider_key, sensor_key, sensor_data_files, time_segments_file, calc_windows=False)
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sensor_features.to_csv(snakemake.output[0], index=False)
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if not calc_windows:
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sensor_features.to_csv(snakemake.output[0], index=False)
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