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Alternating Second order and full segment features corresponding to config settings.

sociality-task
Primoz 2022-05-11 08:50:15 +00:00
parent 9cf9e1fe14
commit 31e36e7400
3 changed files with 17 additions and 25 deletions
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8
config.yaml
View File

@ -3,7 +3,7 @@
######################################################################################################################## ########################################################################################################################
# See https://www.rapids.science/latest/setup/configuration/#participant-files # See https://www.rapids.science/latest/setup/configuration/#participant-files
PIDS: [p02, p01] PIDS: [p01] #,p02]
# See https://www.rapids.science/latest/setup/configuration/#automatic-creation-of-participant-files # See https://www.rapids.science/latest/setup/configuration/#automatic-creation-of-participant-files
CREATE_PARTICIPANT_FILES: CREATE_PARTICIPANT_FILES:
@ -477,11 +477,11 @@ EMPATICA_ACCELEROMETER:
CONTAINER: ACC CONTAINER: ACC
PROVIDERS: PROVIDERS:
DBDP: DBDP:
COMPUTE: False COMPUTE: True
FEATURES: ["maxmagnitude", "minmagnitude", "avgmagnitude", "medianmagnitude", "stdmagnitude"] FEATURES: ["maxmagnitude", "minmagnitude", "avgmagnitude", "medianmagnitude", "stdmagnitude"]
SRC_SCRIPT: src/features/empatica_accelerometer/dbdp/main.py SRC_SCRIPT: src/features/empatica_accelerometer/dbdp/main.py
CR: CR:
COMPUTE: False COMPUTE: True
FEATURES: ["fqHighestPeakFreqs", "fqHighestPeaks", "fqEnergyFeat", "fqEntropyFeat", "fqHistogramBins","fqAbsMean", "fqSkewness", "fqKurtosis", "fqInterquart", # Freq features FEATURES: ["fqHighestPeakFreqs", "fqHighestPeaks", "fqEnergyFeat", "fqEntropyFeat", "fqHistogramBins","fqAbsMean", "fqSkewness", "fqKurtosis", "fqInterquart", # Freq features
"meanLow", "areaLow", "totalAbsoluteAreaBand", "totalMagnitudeBand", "entropyBand", "skewnessBand", "kurtosisBand", "meanLow", "areaLow", "totalAbsoluteAreaBand", "totalMagnitudeBand", "entropyBand", "skewnessBand", "kurtosisBand",
"postureDistanceLow", "absoluteMeanBand", "absoluteAreaBand", "quartilesBand", "interQuartileRangeBand", "varianceBand", "postureDistanceLow", "absoluteMeanBand", "absoluteAreaBand", "quartilesBand", "interQuartileRangeBand", "varianceBand",
@ -502,7 +502,7 @@ EMPATICA_HEARTRATE:
CONTAINER: HR CONTAINER: HR
PROVIDERS: PROVIDERS:
DBDP: DBDP:
COMPUTE: False COMPUTE: True
FEATURES: ["maxhr", "minhr", "avghr", "medianhr", "modehr", "stdhr", "diffmaxmodehr", "diffminmodehr", "entropyhr"] FEATURES: ["maxhr", "minhr", "avghr", "medianhr", "modehr", "stdhr", "diffmaxmodehr", "diffminmodehr", "entropyhr"]
SRC_SCRIPT: src/features/empatica_heartrate/dbdp/main.py SRC_SCRIPT: src/features/empatica_heartrate/dbdp/main.py

18
rules/features.smk
View File

@ -771,8 +771,7 @@ rule empatica_accelerometer_python_features:
sensor_key = "empatica_accelerometer" sensor_key = "empatica_accelerometer"
output: output:
"data/interim/{pid}/empatica_accelerometer_features/empatica_accelerometer_python_{provider_key}.csv", "data/interim/{pid}/empatica_accelerometer_features/empatica_accelerometer_python_{provider_key}.csv",
"data/interim/{pid}/empatica_accelerometer_features/empatica_accelerometer_python_{provider_key}_windows.csv", "data/interim/{pid}/empatica_accelerometer_features/empatica_accelerometer_python_{provider_key}_windows.csv"
"data/interim/{pid}/empatica_accelerometer_features/empatica_accelerometer_python_{provider_key}_windows_SO_features.csv"
script: script:
"../src/features/entry.py" "../src/features/entry.py"
@ -799,8 +798,7 @@ rule empatica_heartrate_python_features:
sensor_key = "empatica_heartrate" sensor_key = "empatica_heartrate"
output: output:
"data/interim/{pid}/empatica_heartrate_features/empatica_heartrate_python_{provider_key}.csv", "data/interim/{pid}/empatica_heartrate_features/empatica_heartrate_python_{provider_key}.csv",
"data/interim/{pid}/empatica_heartrate_features/empatica_heartrate_python_{provider_key}_windows.csv", "data/interim/{pid}/empatica_heartrate_features/empatica_heartrate_python_{provider_key}_windows.csv"
"data/interim/{pid}/empatica_heartrate_features/empatica_heartrate_python_{provider_key}_windows_SO_features.csv"
script: script:
"../src/features/entry.py" "../src/features/entry.py"
@ -827,8 +825,7 @@ rule empatica_temperature_python_features:
sensor_key = "empatica_temperature" sensor_key = "empatica_temperature"
output: output:
"data/interim/{pid}/empatica_temperature_features/empatica_temperature_python_{provider_key}.csv", "data/interim/{pid}/empatica_temperature_features/empatica_temperature_python_{provider_key}.csv",
"data/interim/{pid}/empatica_temperature_features/empatica_temperature_python_{provider_key}_windows.csv", "data/interim/{pid}/empatica_temperature_features/empatica_temperature_python_{provider_key}_windows.csv"
"data/interim/{pid}/empatica_temperature_features/empatica_temperature_python_{provider_key}_windows_SO_features.csv"
script: script:
"../src/features/entry.py" "../src/features/entry.py"
@ -855,8 +852,7 @@ rule empatica_electrodermal_activity_python_features:
sensor_key = "empatica_electrodermal_activity" sensor_key = "empatica_electrodermal_activity"
output: output:
"data/interim/{pid}/empatica_electrodermal_activity_features/empatica_electrodermal_activity_python_{provider_key}.csv", "data/interim/{pid}/empatica_electrodermal_activity_features/empatica_electrodermal_activity_python_{provider_key}.csv",
"data/interim/{pid}/empatica_electrodermal_activity_features/empatica_electrodermal_activity_python_{provider_key}_windows.csv", "data/interim/{pid}/empatica_electrodermal_activity_features/empatica_electrodermal_activity_python_{provider_key}_windows.csv"
"data/interim/{pid}/empatica_electrodermal_activity_features/empatica_electrodermal_activity_python_{provider_key}_windows_SO_features.csv"
script: script:
"../src/features/entry.py" "../src/features/entry.py"
@ -883,8 +879,7 @@ rule empatica_blood_volume_pulse_python_features:
sensor_key = "empatica_blood_volume_pulse" sensor_key = "empatica_blood_volume_pulse"
output: output:
"data/interim/{pid}/empatica_blood_volume_pulse_features/empatica_blood_volume_pulse_python_{provider_key}.csv", "data/interim/{pid}/empatica_blood_volume_pulse_features/empatica_blood_volume_pulse_python_{provider_key}.csv",
"data/interim/{pid}/empatica_blood_volume_pulse_features/empatica_blood_volume_pulse_python_{provider_key}_windows.csv", "data/interim/{pid}/empatica_blood_volume_pulse_features/empatica_blood_volume_pulse_python_{provider_key}_windows.csv"
"data/interim/{pid}/empatica_blood_volume_pulse_features/empatica_blood_volume_pulse_python_{provider_key}_windows_SO_features.csv"
script: script:
"../src/features/entry.py" "../src/features/entry.py"
@ -911,8 +906,7 @@ rule empatica_inter_beat_interval_python_features:
sensor_key = "empatica_inter_beat_interval" sensor_key = "empatica_inter_beat_interval"
output: output:
"data/interim/{pid}/empatica_inter_beat_interval_features/empatica_inter_beat_interval_python_{provider_key}.csv", "data/interim/{pid}/empatica_inter_beat_interval_features/empatica_inter_beat_interval_python_{provider_key}.csv",
"data/interim/{pid}/empatica_inter_beat_interval_features/empatica_inter_beat_interval_python_{provider_key}_windows.csv", "data/interim/{pid}/empatica_inter_beat_interval_features/empatica_inter_beat_interval_python_{provider_key}_windows.csv"
"data/interim/{pid}/empatica_inter_beat_interval_features/empatica_inter_beat_interval_python_{provider_key}_windows_SO_features.csv"
script: script:
"../src/features/entry.py" "../src/features/entry.py"

16
src/features/entry.py
View File

@ -11,7 +11,7 @@ calc_windows = False
try: try:
calc_windows = provider["WINDOWS"]["COMPUTE"] calc_windows = provider["WINDOWS"]["COMPUTE"]
except KeyError: except KeyError:
print("Compute window key not found in config.yaml!") print("WINDOWS COMPUTE key not found in config.yaml!")
if sensor_key == "all_cleaning_individual" or sensor_key == "all_cleaning_overall": if sensor_key == "all_cleaning_individual" or sensor_key == "all_cleaning_overall":
@ -23,16 +23,14 @@ else:
time_segments_file = snakemake.input["time_segments_labels"] time_segments_file = snakemake.input["time_segments_labels"]
if calc_windows: if calc_windows:
first_order_features, second_order_features = fetch_provider_features(provider, provider_key, sensor_key, sensor_data_files, time_segments_file, calc_windows=calc_windows) window_features, second_order_features = fetch_provider_features(provider, provider_key, sensor_key, sensor_data_files, time_segments_file, calc_windows=True)
first_order_features.to_csv(snakemake.output[1], index=False) second_order_features.to_csv(snakemake.output[0], index=False)
second_order_features.to_csv(snakemake.output[2], index=False) window_features.to_csv(snakemake.output[1], index=False)
calc_windows = False
elif "empatica" in sensor_key: elif "empatica" in sensor_key:
pd.DataFrame().to_csv(snakemake.output[1], index=False) pd.DataFrame().to_csv(snakemake.output[1], index=False)
pd.DataFrame().to_csv(snakemake.output[2], index=False)
sensor_features = fetch_provider_features(provider, provider_key, sensor_key, sensor_data_files, time_segments_file, calc_windows=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) sensor_features.to_csv(snakemake.output[0], index=False)