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Removed all standardizaton rules and configurations.

notes
Primoz 2022-09-19 06:16:26 +00:00
parent 62982866cd
commit 18b63127de
4 changed files with 4 additions and 318 deletions
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122
Snakefile
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@ -33,12 +33,6 @@ for provider in config["PHONE_DATA_YIELD"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/processed/features/{pid}/phone_data_yield.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if provider in config["STANDARDIZATION"]["PROVIDERS"]["OTHER"]["LIST"] and config["STANDARDIZATION"]["PROVIDERS"]["OTHER"]["COMPUTE"] \
and config["PHONE_DATA_YIELD"]["PROVIDERS"][provider]["STANDARDIZE_FEATURES"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_phone_data_yield.csv", pid=config["PIDS"]))
if config["STANDARDIZATION"]["MERGE_ALL"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/z_all_sensor_features.csv")
for provider in config["PHONE_MESSAGES"]["PROVIDERS"].keys():
if config["PHONE_MESSAGES"]["PROVIDERS"][provider]["COMPUTE"]:
@ -48,12 +42,6 @@ for provider in config["PHONE_MESSAGES"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/processed/features/{pid}/phone_messages.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if provider in config["STANDARDIZATION"]["PROVIDERS"]["OTHER"]["LIST"] and config["STANDARDIZATION"]["PROVIDERS"]["OTHER"]["COMPUTE"] \
and config["PHONE_MESSAGES"]["PROVIDERS"][provider]["STANDARDIZE_FEATURES"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_phone_messages.csv", pid=config["PIDS"]))
if config["STANDARDIZATION"]["MERGE_ALL"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/z_all_sensor_features.csv")
for provider in config["PHONE_CALLS"]["PROVIDERS"].keys():
if config["PHONE_CALLS"]["PROVIDERS"][provider]["COMPUTE"]:
@ -68,12 +56,6 @@ for provider in config["PHONE_CALLS"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/processed/features/{pid}/phone_calls.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if provider in config["STANDARDIZATION"]["PROVIDERS"]["OTHER"]["LIST"] and config["STANDARDIZATION"]["PROVIDERS"]["OTHER"]["COMPUTE"] \
and config["PHONE_CALLS"]["PROVIDERS"][provider]["STANDARDIZE_FEATURES"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_phone_calls.csv", pid=config["PIDS"]))
if config["STANDARDIZATION"]["MERGE_ALL"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/z_all_sensor_features.csv")
for provider in config["PHONE_BLUETOOTH"]["PROVIDERS"].keys():
if config["PHONE_BLUETOOTH"]["PROVIDERS"][provider]["COMPUTE"]:
@ -83,12 +65,6 @@ for provider in config["PHONE_BLUETOOTH"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/processed/features/{pid}/phone_bluetooth.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if provider in config["STANDARDIZATION"]["PROVIDERS"]["OTHER"]["LIST"] and config["STANDARDIZATION"]["PROVIDERS"]["OTHER"]["COMPUTE"] \
and config["PHONE_BLUETOOTH"]["PROVIDERS"][provider]["STANDARDIZE_FEATURES"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_phone_bluetooth.csv", pid=config["PIDS"]))
if config["STANDARDIZATION"]["MERGE_ALL"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/z_all_sensor_features.csv")
for provider in config["PHONE_ACTIVITY_RECOGNITION"]["PROVIDERS"].keys():
if config["PHONE_ACTIVITY_RECOGNITION"]["PROVIDERS"][provider]["COMPUTE"]:
@ -101,12 +77,6 @@ for provider in config["PHONE_ACTIVITY_RECOGNITION"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/processed/features/{pid}/phone_activity_recognition.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if provider in config["STANDARDIZATION"]["PROVIDERS"]["OTHER"]["LIST"] and config["STANDARDIZATION"]["PROVIDERS"]["OTHER"]["COMPUTE"] \
and config["PHONE_ACTIVITY_RECOGNITION"]["PROVIDERS"][provider]["STANDARDIZE_FEATURES"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_phone_activity_recognition.csv", pid=config["PIDS"]))
if config["STANDARDIZATION"]["MERGE_ALL"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/z_all_sensor_features.csv")
for provider in config["PHONE_BATTERY"]["PROVIDERS"].keys():
if config["PHONE_BATTERY"]["PROVIDERS"][provider]["COMPUTE"]:
@ -118,12 +88,6 @@ for provider in config["PHONE_BATTERY"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/processed/features/{pid}/phone_battery.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if provider in config["STANDARDIZATION"]["PROVIDERS"]["OTHER"]["LIST"] and config["STANDARDIZATION"]["PROVIDERS"]["OTHER"]["COMPUTE"] \
and config["PHONE_BATTERY"]["PROVIDERS"][provider]["STANDARDIZE_FEATURES"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_phone_battery.csv", pid=config["PIDS"]))
if config["STANDARDIZATION"]["MERGE_ALL"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/z_all_sensor_features.csv")
for provider in config["PHONE_SCREEN"]["PROVIDERS"].keys():
if config["PHONE_SCREEN"]["PROVIDERS"][provider]["COMPUTE"]:
@ -140,12 +104,6 @@ for provider in config["PHONE_SCREEN"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/processed/features/{pid}/phone_screen.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if provider in config["STANDARDIZATION"]["PROVIDERS"]["OTHER"]["LIST"] and config["STANDARDIZATION"]["PROVIDERS"]["OTHER"]["COMPUTE"] \
and config["PHONE_SCREEN"]["PROVIDERS"][provider]["STANDARDIZE_FEATURES"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_phone_screen.csv", pid=config["PIDS"]))
if config["STANDARDIZATION"]["MERGE_ALL"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/z_all_sensor_features.csv")
for provider in config["PHONE_LIGHT"]["PROVIDERS"].keys():
if config["PHONE_LIGHT"]["PROVIDERS"][provider]["COMPUTE"]:
@ -155,12 +113,6 @@ for provider in config["PHONE_LIGHT"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/processed/features/{pid}/phone_light.csv", pid=config["PIDS"],))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if provider in config["STANDARDIZATION"]["PROVIDERS"]["OTHER"]["LIST"] and config["STANDARDIZATION"]["PROVIDERS"]["OTHER"]["COMPUTE"] \
and config["PHONE_LIGHT"]["PROVIDERS"][provider]["STANDARDIZE_FEATURES"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_phone_light.csv", pid=config["PIDS"]))
if config["STANDARDIZATION"]["MERGE_ALL"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/z_all_sensor_features.csv")
for provider in config["PHONE_ACCELEROMETER"]["PROVIDERS"].keys():
if config["PHONE_ACCELEROMETER"]["PROVIDERS"][provider]["COMPUTE"]:
@ -184,12 +136,6 @@ for provider in config["PHONE_APPLICATIONS_FOREGROUND"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/processed/features/{pid}/phone_applications_foreground.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if provider in config["STANDARDIZATION"]["PROVIDERS"]["OTHER"]["LIST"] and config["STANDARDIZATION"]["PROVIDERS"]["OTHER"]["COMPUTE"] \
and config["PHONE_APPLICATIONS_FOREGROUND"]["PROVIDERS"][provider]["STANDARDIZE_FEATURES"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_phone_applications_foreground.csv", pid=config["PIDS"]))
if config["STANDARDIZATION"]["MERGE_ALL"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/z_all_sensor_features.csv")
for provider in config["PHONE_WIFI_VISIBLE"]["PROVIDERS"].keys():
if config["PHONE_WIFI_VISIBLE"]["PROVIDERS"][provider]["COMPUTE"]:
@ -199,12 +145,6 @@ for provider in config["PHONE_WIFI_VISIBLE"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/processed/features/{pid}/phone_wifi_visible.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if provider in config["STANDARDIZATION"]["PROVIDERS"]["OTHER"]["LIST"] and config["STANDARDIZATION"]["PROVIDERS"]["OTHER"]["COMPUTE"] \
and config["PHONE_WIFI_VISIBLE"]["PROVIDERS"][provider]["STANDARDIZE_FEATURES"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_phone_wifi_visible.csv", pid=config["PIDS"]))
if config["STANDARDIZATION"]["MERGE_ALL"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/z_all_sensor_features.csv")
for provider in config["PHONE_WIFI_CONNECTED"]["PROVIDERS"].keys():
if config["PHONE_WIFI_CONNECTED"]["PROVIDERS"][provider]["COMPUTE"]:
@ -233,12 +173,6 @@ for provider in config["PHONE_ESM"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/processed/features/{pid}/phone_esm.csv", pid=config["PIDS"]))
# files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv",pid=config["PIDS"]))
# files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if provider in config["STANDARDIZATION"]["PROVIDERS"]["OTHER"]["LIST"] and config["STANDARDIZATION"]["PROVIDERS"]["OTHER"]["COMPUTE"] \
and config["PHONE_ESM"]["PROVIDERS"][provider]["STANDARDIZE_FEATURES"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_phone_esm.csv", pid=config["PIDS"]))
if config["STANDARDIZATION"]["MERGE_ALL"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/z_all_sensor_features.csv")
# We can delete these if's as soon as we add feature PROVIDERS to any of these sensors
if isinstance(config["PHONE_APPLICATIONS_CRASHES"]["PROVIDERS"], dict):
@ -304,12 +238,6 @@ for provider in config["PHONE_LOCATIONS"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/processed/features/{pid}/phone_locations.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if provider in config["STANDARDIZATION"]["PROVIDERS"]["OTHER"]["LIST"] and config["STANDARDIZATION"]["PROVIDERS"]["OTHER"]["COMPUTE"] \
and config["PHONE_LOCATIONS"]["PROVIDERS"][provider]["STANDARDIZE_FEATURES"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_phone_locations.csv", pid=config["PIDS"]))
if config["STANDARDIZATION"]["MERGE_ALL"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/z_all_sensor_features.csv")
for provider in config["FITBIT_CALORIES_INTRADAY"]["PROVIDERS"].keys():
if config["FITBIT_CALORIES_INTRADAY"]["PROVIDERS"][provider]["COMPUTE"]:
@ -400,13 +328,6 @@ for provider in config["EMPATICA_ACCELEROMETER"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/processed/features/{pid}/empatica_accelerometer.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if provider in config["STANDARDIZATION"]["PROVIDERS"] and config["STANDARDIZATION"]["PROVIDERS"][provider]["COMPUTE"] \
and config["EMPATICA_ACCELEROMETER"]["PROVIDERS"][provider]["WINDOWS"]["STANDARDIZE_FEATURES"]:
files_to_compute.extend(expand("data/interim/{pid}/empatica_accelerometer_features/z_empatica_accelerometer_{language}_{provider_key}_windows.csv", pid=config["PIDS"], language=get_script_language(config["STANDARDIZATION"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/z_empatica_accelerometer.csv", pid=config["PIDS"]))
if config["STANDARDIZATION"]["MERGE_ALL"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/z_all_sensor_features.csv")
for provider in config["EMPATICA_HEARTRATE"]["PROVIDERS"].keys():
if config["EMPATICA_HEARTRATE"]["PROVIDERS"][provider]["COMPUTE"]:
@ -426,13 +347,6 @@ for provider in config["EMPATICA_TEMPERATURE"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/processed/features/{pid}/empatica_temperature.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if provider in config["STANDARDIZATION"]["PROVIDERS"] and config["STANDARDIZATION"]["PROVIDERS"][provider]["COMPUTE"] \
and config["EMPATICA_TEMPERATURE"]["PROVIDERS"][provider]["WINDOWS"]["STANDARDIZE_FEATURES"]:
files_to_compute.extend(expand("data/interim/{pid}/empatica_temperature_features/z_empatica_temperature_{language}_{provider_key}_windows.csv", pid=config["PIDS"], language=get_script_language(config["STANDARDIZATION"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/z_empatica_temperature.csv", pid=config["PIDS"]))
if config["STANDARDIZATION"]["MERGE_ALL"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/z_all_sensor_features.csv")
for provider in config["EMPATICA_ELECTRODERMAL_ACTIVITY"]["PROVIDERS"].keys():
if config["EMPATICA_ELECTRODERMAL_ACTIVITY"]["PROVIDERS"][provider]["COMPUTE"]:
@ -442,13 +356,6 @@ for provider in config["EMPATICA_ELECTRODERMAL_ACTIVITY"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/processed/features/{pid}/empatica_electrodermal_activity.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if provider in config["STANDARDIZATION"]["PROVIDERS"] and config["STANDARDIZATION"]["PROVIDERS"][provider]["COMPUTE"] \
and config["EMPATICA_ELECTRODERMAL_ACTIVITY"]["PROVIDERS"][provider]["WINDOWS"]["STANDARDIZE_FEATURES"]:
files_to_compute.extend(expand("data/interim/{pid}/empatica_electrodermal_activity_features/z_empatica_electrodermal_activity_{language}_{provider_key}_windows.csv", pid=config["PIDS"], language=get_script_language(config["STANDARDIZATION"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/z_empatica_electrodermal_activity.csv", pid=config["PIDS"]))
if config["STANDARDIZATION"]["MERGE_ALL"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/z_all_sensor_features.csv")
for provider in config["EMPATICA_BLOOD_VOLUME_PULSE"]["PROVIDERS"].keys():
if config["EMPATICA_BLOOD_VOLUME_PULSE"]["PROVIDERS"][provider]["COMPUTE"]:
@ -458,13 +365,6 @@ for provider in config["EMPATICA_BLOOD_VOLUME_PULSE"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/processed/features/{pid}/empatica_blood_volume_pulse.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if provider in config["STANDARDIZATION"]["PROVIDERS"] and config["STANDARDIZATION"]["PROVIDERS"][provider]["COMPUTE"] \
and config["EMPATICA_BLOOD_VOLUME_PULSE"]["PROVIDERS"][provider]["WINDOWS"]["STANDARDIZE_FEATURES"]:
files_to_compute.extend(expand("data/interim/{pid}/empatica_blood_volume_pulse_features/z_empatica_blood_volume_pulse_{language}_{provider_key}_windows.csv", pid=config["PIDS"], language=get_script_language(config["STANDARDIZATION"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/z_empatica_blood_volume_pulse.csv", pid=config["PIDS"]))
if config["STANDARDIZATION"]["MERGE_ALL"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/z_all_sensor_features.csv")
for provider in config["EMPATICA_INTER_BEAT_INTERVAL"]["PROVIDERS"].keys():
if config["EMPATICA_INTER_BEAT_INTERVAL"]["PROVIDERS"][provider]["COMPUTE"]:
@ -474,13 +374,6 @@ for provider in config["EMPATICA_INTER_BEAT_INTERVAL"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/processed/features/{pid}/empatica_inter_beat_interval.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if provider in config["STANDARDIZATION"]["PROVIDERS"] and config["STANDARDIZATION"]["PROVIDERS"][provider]["COMPUTE"] \
and config["EMPATICA_INTER_BEAT_INTERVAL"]["PROVIDERS"][provider]["WINDOWS"]["STANDARDIZE_FEATURES"]:
files_to_compute.extend(expand("data/interim/{pid}/empatica_inter_beat_interval_features/z_empatica_inter_beat_interval_{language}_{provider_key}_windows.csv", pid=config["PIDS"], language=get_script_language(config["STANDARDIZATION"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/z_empatica_inter_beat_interval.csv", pid=config["PIDS"]))
if config["STANDARDIZATION"]["MERGE_ALL"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/z_all_sensor_features.csv")
if isinstance(config["EMPATICA_TAGS"]["PROVIDERS"], dict):
for provider in config["EMPATICA_TAGS"]["PROVIDERS"].keys():
@ -517,24 +410,15 @@ for provider in config["ALL_CLEANING_INDIVIDUAL"]["PROVIDERS"].keys():
if config["ALL_CLEANING_INDIVIDUAL"]["PROVIDERS"][provider]["COMPUTE"]:
if provider == "STRAW":
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features_cleaned_" + provider.lower() + "_py.csv", pid=config["PIDS"]))
if config["ALL_CLEANING_INDIVIDUAL"]["CLEAN_STANDARDIZED"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_all_sensor_features_cleaned_" + provider.lower() + "_py.csv", pid=config["PIDS"]))
else:
else:
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features_cleaned_" + provider.lower() + "_R.csv", pid=config["PIDS"]))
if config["ALL_CLEANING_INDIVIDUAL"]["CLEAN_STANDARDIZED"]:
files_to_compute.extend(expand("data/processed/features/{pid}/z_all_sensor_features_cleaned_" + provider.lower() + "_R.csv", pid=config["PIDS"]))
for provider in config["ALL_CLEANING_OVERALL"]["PROVIDERS"].keys():
if config["ALL_CLEANING_OVERALL"]["PROVIDERS"][provider]["COMPUTE"]:
if provider == "STRAW":
files_to_compute.extend(expand("data/processed/features/all_participants/all_sensor_features_cleaned_" + provider.lower() +"_py.csv"))
if config["ALL_CLEANING_OVERALL"]["CLEAN_STANDARDIZED"]:
files_to_compute.extend(expand("data/processed/features/all_participants/z_all_sensor_features_cleaned_" + provider.lower() +"_py.csv"))
else:
files_to_compute.extend(expand("data/processed/features/all_participants/all_sensor_features_cleaned_" + provider.lower() +"_R.csv"))
if config["ALL_CLEANING_OVERALL"]["CLEAN_STANDARDIZED"]:
files_to_compute.extend(expand("data/processed/features/all_participants/z_all_sensor_features_cleaned_" + provider.lower() +"_R.csv"))
else:
files_to_compute.extend(expand("data/processed/features/all_participants/all_sensor_features_cleaned_" + provider.lower() +"_R.csv"))
# Baseline features
if config["PARAMS_FOR_ANALYSIS"]["BASELINE"]["COMPUTE"]:

38
config.yaml
View File

@ -93,7 +93,6 @@ PHONE_ACTIVITY_RECOGNITION:
STATIONARY: ["still", "tilting"]
MOBILE: ["on_foot", "walking", "running", "on_bicycle"]
VEHICLE: ["in_vehicle"]
STANDARDIZE_FEATURES: True
SRC_SCRIPT: src/features/phone_activity_recognition/rapids/main.py
# See https://www.rapids.science/latest/features/phone-applications-crashes/
@ -134,7 +133,6 @@ PHONE_APPLICATIONS_FOREGROUND:
APP_EPISODES: ["countepisode", "minduration", "maxduration", "meanduration", "sumduration"]
IGNORE_EPISODES_SHORTER_THAN: 0 # in minutes, set to 0 to disable
IGNORE_EPISODES_LONGER_THAN: 300 # in minutes, set to 0 to disable
STANDARDIZE_FEATURES: True
SRC_SCRIPT: src/features/phone_applications_foreground/rapids/main.py
# See https://www.rapids.science/latest/features/phone-applications-notifications/
@ -155,7 +153,6 @@ PHONE_BATTERY:
RAPIDS:
COMPUTE: True
FEATURES: ["countdischarge", "sumdurationdischarge", "countcharge", "sumdurationcharge", "avgconsumptionrate", "maxconsumptionrate"]
STANDARDIZE_FEATURES: True
SRC_SCRIPT: src/features/phone_battery/rapids/main.py
# See https://www.rapids.science/latest/features/phone-bluetooth/
@ -165,7 +162,6 @@ PHONE_BLUETOOTH:
RAPIDS:
COMPUTE: True
FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
STANDARDIZE_FEATURES: True
SRC_SCRIPT: src/features/phone_bluetooth/rapids/main.R
DORYAB:
@ -183,7 +179,6 @@ PHONE_BLUETOOTH:
DEVICES: ["countscans", "uniquedevices", "meanscans", "stdscans"]
SCANS_MOST_FREQUENT_DEVICE: ["withinsegments", "acrosssegments", "acrossdataset"]
SCANS_LEAST_FREQUENT_DEVICE: ["withinsegments", "acrosssegments", "acrossdataset"]
STANDARDIZE_FEATURES: True
SRC_SCRIPT: src/features/phone_bluetooth/doryab/main.py
# See https://www.rapids.science/latest/features/phone-calls/
@ -198,7 +193,6 @@ PHONE_CALLS:
missed: [count, distinctcontacts, timefirstcall, timelastcall, countmostfrequentcontact]
incoming: [count, distinctcontacts, meanduration, sumduration, minduration, maxduration, stdduration, modeduration, entropyduration, timefirstcall, timelastcall, countmostfrequentcontact]
outgoing: [count, distinctcontacts, meanduration, sumduration, minduration, maxduration, stdduration, modeduration, entropyduration, timefirstcall, timelastcall, countmostfrequentcontact]
STANDARDIZE_FEATURES: True
SRC_SCRIPT: src/features/phone_calls/rapids/main.R
# See https://www.rapids.science/latest/features/phone-conversation/
@ -238,7 +232,6 @@ PHONE_DATA_YIELD:
COMPUTE: True
FEATURES: [ratiovalidyieldedminutes, ratiovalidyieldedhours]
MINUTE_RATIO_THRESHOLD_FOR_VALID_YIELDED_HOURS: 0.5 # 0 to 1, minimum percentage of valid minutes in an hour to be considered valid.
STANDARDIZE_FEATURES: True
SRC_SCRIPT: src/features/phone_data_yield/rapids/main.R
PHONE_ESM:
@ -248,7 +241,6 @@ PHONE_ESM:
COMPUTE: True
SCALES: ["PANAS_positive_affect", "PANAS_negative_affect", "JCQ_job_demand", "JCQ_job_control", "JCQ_supervisor_support", "JCQ_coworker_support"]
FEATURES: [mean]
STANDARDIZE_FEATURES: True
SRC_SCRIPT: src/features/phone_esm/straw/main.py
# See https://www.rapids.science/latest/features/phone-keyboard/
@ -267,7 +259,6 @@ PHONE_LIGHT:
RAPIDS:
COMPUTE: True
FEATURES: ["count", "maxlux", "minlux", "avglux", "medianlux", "stdlux"]
STANDARDIZE_FEATURES: True
SRC_SCRIPT: src/features/phone_light/rapids/main.py
# See https://www.rapids.science/latest/features/phone-locations/
@ -292,7 +283,6 @@ PHONE_LOCATIONS:
MINIMUM_DAYS_TO_DETECT_HOME_CHANGES: 3
CLUSTERING_ALGORITHM: DBSCAN # DBSCAN, OPTICS
RADIUS_FOR_HOME: 100
STANDARDIZE_FEATURES: True
SRC_SCRIPT: src/features/phone_locations/doryab/main.py
BARNETT:
@ -300,7 +290,6 @@ PHONE_LOCATIONS:
FEATURES: ["hometime","disttravelled","rog","maxdiam","maxhomedist","siglocsvisited","avgflightlen","stdflightlen","avgflightdur","stdflightdur","probpause","siglocentropy","circdnrtn","wkenddayrtn"]
IF_MULTIPLE_TIMEZONES: USE_MOST_COMMON
MINUTES_DATA_USED: False # Use this for quality control purposes, how many minutes of data (location coordinates gruped by minute) were used to compute features
STANDARDIZE_FEATURES: True
SRC_SCRIPT: src/features/phone_locations/barnett/main.R
# See https://www.rapids.science/latest/features/phone-log/
@ -320,7 +309,6 @@ PHONE_MESSAGES:
FEATURES:
received: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
sent: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
STANDARDIZE_FEATURES: True
SRC_SCRIPT: src/features/phone_messages/rapids/main.R
# See https://www.rapids.science/latest/features/phone-screen/
@ -334,7 +322,6 @@ PHONE_SCREEN:
IGNORE_EPISODES_LONGER_THAN: 360 # in minutes, set to 0 to disable
FEATURES: ["countepisode", "sumduration", "maxduration", "minduration", "avgduration", "stdduration", "firstuseafter"] # "episodepersensedminutes" needs to be added later
EPISODE_TYPES: ["unlock"]
STANDARDIZE_FEATURES: True
SRC_SCRIPT: src/features/phone_screen/rapids/main.py
# See https://www.rapids.science/latest/features/phone-wifi-connected/
@ -353,7 +340,6 @@ PHONE_WIFI_VISIBLE:
RAPIDS:
COMPUTE: True
FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
STANDARDIZE_FEATURES: True
SRC_SCRIPT: src/features/phone_wifi_visible/rapids/main.R
@ -455,7 +441,6 @@ FITBIT_SLEEP_INTRADAY:
UNIFIED: [awake, asleep]
SLEEP_TYPES: [main, nap, all]
SRC_SCRIPT: src/features/fitbit_sleep_intraday/rapids/main.py
PRICE:
COMPUTE: False
FEATURES: [avgduration, avgratioduration, avgstarttimeofepisodemain, avgendtimeofepisodemain, avgmidpointofepisodemain, stdstarttimeofepisodemain, stdendtimeofepisodemain, stdmidpointofepisodemain, socialjetlag, rmssdmeanstarttimeofepisodemain, rmssdmeanendtimeofepisodemain, rmssdmeanmidpointofepisodemain, rmssdmedianstarttimeofepisodemain, rmssdmedianendtimeofepisodemain, rmssdmedianmidpointofepisodemain]
@ -528,7 +513,6 @@ EMPATICA_ACCELEROMETER:
COMPUTE: True
WINDOW_LENGTH: 15 # specify window length in seconds
SECOND_ORDER_FEATURES: ['mean', 'median', 'sd', 'nlargest', 'nsmallest', 'count_windows']
STANDARDIZE_FEATURES: True
SRC_SCRIPT: src/features/empatica_accelerometer/cr/main.py
@ -557,7 +541,6 @@ EMPATICA_TEMPERATURE:
COMPUTE: True
WINDOW_LENGTH: 300 # specify window length in seconds
SECOND_ORDER_FEATURES: ['mean', 'median', 'sd', 'nlargest', 'nsmallest', 'count_windows']
STANDARDIZE_FEATURES: True
SRC_SCRIPT: src/features/empatica_temperature/cr/main.py
# See https://www.rapids.science/latest/features/empatica-electrodermal-activity/
@ -579,7 +562,6 @@ EMPATICA_ELECTRODERMAL_ACTIVITY:
COMPUTE: True
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: True
IMPUTE_NANS: True
SRC_SCRIPT: src/features/empatica_electrodermal_activity/cr/main.py
@ -599,7 +581,6 @@ EMPATICA_BLOOD_VOLUME_PULSE:
COMPUTE: True
WINDOW_LENGTH: 300 # specify window length in seconds
SECOND_ORDER_FEATURES: ['mean', 'median', 'sd', 'nlargest', 'nsmallest', 'count_windows', 'hrv_num_windows_non_nan']
STANDARDIZE_FEATURES: True
SRC_SCRIPT: src/features/empatica_blood_volume_pulse/cr/main.py
# See https://www.rapids.science/latest/features/empatica-inter-beat-interval/
@ -619,7 +600,6 @@ EMPATICA_INTER_BEAT_INTERVAL:
COMPUTE: True
WINDOW_LENGTH: 300 # specify window length in seconds
SECOND_ORDER_FEATURES: ['mean', 'median', 'sd', 'nlargest', 'nsmallest', 'count_windows', 'hrv_num_windows_non_nan']
STANDARDIZE_FEATURES: True
SRC_SCRIPT: src/features/empatica_inter_beat_interval/cr/main.py
# See https://www.rapids.science/latest/features/empatica-tags/
@ -667,7 +647,6 @@ HEATMAP_FEATURE_CORRELATION_MATRIX:
########################################################################################################################
ALL_CLEANING_INDIVIDUAL:
CLEAN_STANDARDIZED: True
PROVIDERS:
RAPIDS:
COMPUTE: True
@ -702,7 +681,6 @@ ALL_CLEANING_INDIVIDUAL:
SRC_SCRIPT: src/features/all_cleaning_individual/straw/main.py
ALL_CLEANING_OVERALL:
CLEAN_STANDARDIZED: True
PROVIDERS:
RAPIDS:
COMPUTE: True
@ -737,22 +715,6 @@ ALL_CLEANING_OVERALL:
SRC_SCRIPT: src/features/all_cleaning_overall/straw/main.py
########################################################################################################################
# Z-score standardization #
########################################################################################################################
STANDARDIZATION: # Standardization for both providers is executed if only one of two providers is marked COMPUTE: TRUE
MERGE_ALL: True # Creates the joint standardized file for each participant and all participants. Similar to merge_sensor_features_for_all_participants rule
PROVIDERS:
CR:
COMPUTE: True
SRC_SCRIPT: src/features/standardization/main.py
OTHER:
COMPUTE: True
LIST: [RAPIDS, DORYAB, BARNETT, STRAW]
SRC_SCRIPT: src/features/standardization/main.py
########################################################################################################################
# Baseline #
########################################################################################################################

21
rules/common.smk
View File

@ -40,15 +40,6 @@ def find_features_files(wildcards):
feature_files.extend(expand("data/interim/{{pid}}/{sensor_key}_features/{sensor_key}_{language}_{provider_key}.csv", sensor_key=wildcards.sensor_key.lower(), language=get_script_language(provider["SRC_SCRIPT"]), provider_key=provider_key.lower()))
return(feature_files)
def find_empaticas_standardized_features_files(wildcards):
feature_files = []
if "empatica" in wildcards.sensor_key:
for provider_key, provider in config[(wildcards.sensor_key).upper()]["PROVIDERS"].items():
if provider["COMPUTE"] and provider.get("WINDOWS", False) and provider["WINDOWS"]["COMPUTE"]:
if "empatica" in wildcards.sensor_key:
feature_files.extend(expand("data/interim/{{pid}}/{sensor_key}_features/z_{sensor_key}_{language}_{provider_key}.csv", sensor_key=wildcards.sensor_key.lower(), language=get_script_language(provider["SRC_SCRIPT"]), provider_key=provider_key.lower()))
return(feature_files)
def find_joint_non_empatica_sensor_files(wildcards):
joined_files = []
for config_key in config.keys():
@ -82,18 +73,6 @@ def input_merge_sensor_features_for_individual_participants(wildcards):
break
return feature_files
def input_merge_standardized_sensor_features_for_individual_participants(wildcards):
feature_files = []
for config_key in config.keys():
if config_key.startswith(("PHONE", "FITBIT", "EMPATICA")) and "PROVIDERS" in config[config_key] and isinstance(config[config_key]["PROVIDERS"], dict):
for provider_key, provider in config[config_key]["PROVIDERS"].items():
if "COMPUTE" in provider.keys() and provider["COMPUTE"] and ("STANDARDIZE_FEATURES" in provider.keys() and provider["STANDARDIZE_FEATURES"] or
"WINDOWS" in provider.keys() and "STANDARDIZE_FEATURES" in provider["WINDOWS"].keys() and provider["WINDOWS"]["STANDARDIZE_FEATURES"]):
feature_files.append("data/processed/features/{pid}/z_" + config_key.lower() + ".csv")
break
return feature_files
def get_phone_sensor_names():
phone_sensor_names = []
for config_key in config.keys():

141
rules/features.smk
View File

@ -796,20 +796,6 @@ rule empatica_accelerometer_python_features:
script:
"../src/features/entry.py"
rule empatica_accelerometer_python_features_standardization:
input:
windows_features_data = "data/interim/{pid}/empatica_accelerometer_features/empatica_accelerometer_python_{provider_key}_windows.csv"
params:
provider = config["STANDARDIZATION"]["PROVIDERS"]["CR"],
provider_key = "{provider_key}",
sensor_key = "empatica_accelerometer",
provider_main = config["EMPATICA_ACCELEROMETER"]["PROVIDERS"]["CR"]
output:
"data/interim/{pid}/empatica_accelerometer_features/z_empatica_accelerometer_python_{provider_key}.csv",
"data/interim/{pid}/empatica_accelerometer_features/z_empatica_accelerometer_python_{provider_key}_windows.csv"
script:
"../src/features/standardization/main.py"
rule empatica_accelerometer_r_features:
input:
sensor_data = "data/raw/{pid}/empatica_accelerometer_with_datetime.csv",
@ -864,20 +850,6 @@ rule empatica_temperature_python_features:
script:
"../src/features/entry.py"
rule empatica_temperature_python_features_standardization:
input:
windows_features_data = "data/interim/{pid}/empatica_temperature_features/empatica_temperature_python_{provider_key}_windows.csv"
params:
provider = config["STANDARDIZATION"]["PROVIDERS"]["CR"],
provider_key = "{provider_key}",
sensor_key = "empatica_temperature",
provider_main = config["EMPATICA_TEMPERATURE"]["PROVIDERS"]["CR"]
output:
"data/interim/{pid}/empatica_temperature_features/z_empatica_temperature_python_{provider_key}.csv",
"data/interim/{pid}/empatica_temperature_features/z_empatica_temperature_python_{provider_key}_windows.csv"
script:
"../src/features/standardization/main.py"
rule empatica_temperature_r_features:
input:
sensor_data = "data/raw/{pid}/empatica_temperature_with_datetime.csv",
@ -905,20 +877,6 @@ rule empatica_electrodermal_activity_python_features:
script:
"../src/features/entry.py"
rule empatica_electrodermal_activity_python_features_standardization:
input:
windows_features_data = "data/interim/{pid}/empatica_electrodermal_activity_features/empatica_electrodermal_activity_python_{provider_key}_windows.csv"
params:
provider = config["STANDARDIZATION"]["PROVIDERS"]["CR"],
provider_key = "{provider_key}",
sensor_key = "empatica_electrodermal_activity",
provider_main = config["EMPATICA_ELECTRODERMAL_ACTIVITY"]["PROVIDERS"]["CR"]
output:
"data/interim/{pid}/empatica_electrodermal_activity_features/z_empatica_electrodermal_activity_python_{provider_key}.csv",
"data/interim/{pid}/empatica_electrodermal_activity_features/z_empatica_electrodermal_activity_python_{provider_key}_windows.csv"
script:
"../src/features/standardization/main.py"
rule empatica_electrodermal_activity_r_features:
input:
sensor_data = "data/raw/{pid}/empatica_electrodermal_activity_with_datetime.csv",
@ -946,20 +904,6 @@ rule empatica_blood_volume_pulse_python_features:
script:
"../src/features/entry.py"
rule empatica_blood_volume_pulse_python_cr_features_standardization:
input:
windows_features_data = "data/interim/{pid}/empatica_blood_volume_pulse_features/empatica_blood_volume_pulse_python_{provider_key}_windows.csv"
params:
provider = config["STANDARDIZATION"]["PROVIDERS"]["CR"],
provider_key = "{provider_key}",
sensor_key = "empatica_blood_volume_pulse",
provider_main = config["EMPATICA_BLOOD_VOLUME_PULSE"]["PROVIDERS"]["CR"]
output:
"data/interim/{pid}/empatica_blood_volume_pulse_features/z_empatica_blood_volume_pulse_python_{provider_key}.csv",
"data/interim/{pid}/empatica_blood_volume_pulse_features/z_empatica_blood_volume_pulse_python_{provider_key}_windows.csv"
script:
"../src/features/standardization/main.py"
rule empatica_blood_volume_pulse_r_features:
input:
sensor_data = "data/raw/{pid}/empatica_blood_volume_pulse_with_datetime.csv",
@ -987,20 +931,6 @@ rule empatica_inter_beat_interval_python_features:
script:
"../src/features/entry.py"
rule empatica_inter_beat_interval_python_features_standardization:
input:
windows_features_data = "data/interim/{pid}/empatica_inter_beat_interval_features/empatica_inter_beat_interval_python_{provider_key}_windows.csv"
params:
provider = config["STANDARDIZATION"]["PROVIDERS"]["CR"],
provider_key = "{provider_key}",
sensor_key = "empatica_inter_beat_interval",
provider_main = config["EMPATICA_INTER_BEAT_INTERVAL"]["PROVIDERS"]["CR"]
output:
"data/interim/{pid}/empatica_inter_beat_interval_features/z_empatica_inter_beat_interval_python_{provider_key}.csv",
"data/interim/{pid}/empatica_inter_beat_interval_features/z_empatica_inter_beat_interval_python_{provider_key}_windows.csv"
script:
"../src/features/standardization/main.py"
rule empatica_inter_beat_interval_r_features:
input:
sensor_data = "data/raw/{pid}/empatica_inter_beat_interval_with_datetime.csv",
@ -1048,38 +978,6 @@ rule merge_sensor_features_for_individual_participants:
script:
"../src/features/utils/merge_sensor_features_for_individual_participants.R"
rule join_standardized_features_from_empatica:
input:
sensor_features = find_empaticas_standardized_features_files
wildcard_constraints:
sensor_key = '(empatica).*'
output:
"data/processed/features/{pid}/z_{sensor_key}.csv"
script:
"../src/features/utils/join_features_from_providers.R"
rule standardize_features_from_providers_no_empatica:
input:
sensor_features = find_joint_non_empatica_sensor_files
wildcard_constraints:
sensor_key = '(phone|fitbit).*'
params:
provider = config["STANDARDIZATION"]["PROVIDERS"]["OTHER"],
provider_key = "OTHER",
sensor_key = "{sensor_key}"
output:
"data/processed/features/{pid}/z_{sensor_key}.csv"
script:
"../src/features/standardization/main.py"
rule merge_standardized_sensor_features_for_individual_participants:
input:
feature_files = input_merge_standardized_sensor_features_for_individual_participants
output:
"data/processed/features/{pid}/z_all_sensor_features.csv"
script:
"../src/features/utils/merge_sensor_features_for_individual_participants.R"
rule merge_sensor_features_for_all_participants:
input:
feature_files = expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"])
@ -1088,14 +986,6 @@ rule merge_sensor_features_for_all_participants:
script:
"../src/features/utils/merge_sensor_features_for_all_participants.R"
rule merge_standardized_sensor_features_for_all_participants:
input:
feature_files = expand("data/processed/features/{pid}/z_all_sensor_features.csv", pid=config["PIDS"])
output:
"data/processed/features/all_participants/z_all_sensor_features.csv"
script:
"../src/features/utils/merge_standardized_sensor_features_for_all_participants.R"
rule clean_sensor_features_for_individual_participants:
input:
sensor_data = rules.merge_sensor_features_for_individual_participants.output
@ -1107,7 +997,7 @@ rule clean_sensor_features_for_individual_participants:
script_extension = "{script_extension}",
sensor_key = "all_cleaning_individual"
output:
"data/processed/features/{pid}/all_sensor_features_cleaned_{provider_key}_{script_extension}.csv" # bo predstavljalo probleme za naprej (kako iskati datoteke + standardizacija itd.)
"data/processed/features/{pid}/all_sensor_features_cleaned_{provider_key}_{script_extension}.csv"
script:
"../src/features/entry.{params.script_extension}"
@ -1123,32 +1013,3 @@ rule clean_sensor_features_for_all_participants:
"data/processed/features/all_participants/all_sensor_features_cleaned_{provider_key}_{script_extension}.csv"
script:
"../src/features/entry.{params.script_extension}"
rule clean_standardized_sensor_features_for_individual_participants:
input:
sensor_data = rules.merge_standardized_sensor_features_for_individual_participants.output
wildcard_constraints:
pid = "("+"|".join(config["PIDS"])+")"
params:
provider = lambda wildcards: config["ALL_CLEANING_INDIVIDUAL"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
script_extension = "{script_extension}",
sensor_key = "all_cleaning_individual"
output:
"data/processed/features/{pid}/z_all_sensor_features_cleaned_{provider_key}_{script_extension}.csv"
script:
"../src/features/entry.{params.script_extension}"
rule clean_standardized_sensor_features_for_all_participants:
input:
sensor_data = rules.merge_standardized_sensor_features_for_all_participants.output
params:
provider = lambda wildcards: config["ALL_CLEANING_OVERALL"]["PROVIDERS"][wildcards.provider_key.upper()],
provider_key = "{provider_key}",
script_extension = "{script_extension}",
sensor_key = "all_cleaning_overall"
output:
"data/processed/features/all_participants/z_all_sensor_features_cleaned_{provider_key}_{script_extension}.csv"
script:
"../src/features/entry.{params.script_extension}"