diff --git a/calculatingfeatures b/calculatingfeatures deleted file mode 160000 index 98e6207e..00000000 --- a/calculatingfeatures +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 98e6207ecc23a23b1f621a11f28eb87cbfb7f9da diff --git a/config.yaml b/config.yaml index 5833db60..0ab0bcba 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: [p031] #p01, p02, p03] # See https://www.rapids.science/latest/setup/configuration/#automatic-creation-of-participant-files CREATE_PARTICIPANT_FILES: @@ -51,7 +51,7 @@ PHONE_DATA_STREAMS: aware_postgresql: DATABASE_GROUP: PSQL_STRAW - + aware_csv: FOLDER: data/external/aware_csv @@ -80,12 +80,12 @@ PHONE_ACCELEROMETER: # See https://www.rapids.science/latest/features/phone-activity-recognition/ PHONE_ACTIVITY_RECOGNITION: CONTAINER: - ANDROID: plugin_google_activity_recognition + ANDROID: google_ar IOS: plugin_ios_activity_recognition EPISODE_THRESHOLD_BETWEEN_ROWS: 5 # minutes. Max time difference for two consecutive rows to be considered within the same AR episode. PROVIDERS: RAPIDS: - COMPUTE: False + COMPUTE: True FEATURES: ["count", "mostcommonactivity", "countuniqueactivities", "durationstationary", "durationmobile", "durationvehicle"] ACTIVITY_CLASSES: STATIONARY: ["still", "tilting"] @@ -105,16 +105,17 @@ PHONE_APPLICATIONS_CRASHES: # See https://www.rapids.science/latest/features/phone-applications-foreground/ PHONE_APPLICATIONS_FOREGROUND: - CONTAINER: applications_foreground + CONTAINER: applications APPLICATION_CATEGORIES: CATALOGUE_SOURCE: FILE # FILE (genres are read from CATALOGUE_FILE) or GOOGLE (genres are scrapped from the Play Store) CATALOGUE_FILE: "data/external/stachl_application_genre_catalogue.csv" + PACKAGE_NAMES_HASHED: True UPDATE_CATALOGUE_FILE: False # if CATALOGUE_SOURCE is equal to FILE, whether or not to update CATALOGUE_FILE, if CATALOGUE_SOURCE is equal to GOOGLE all scraped genres will be saved to CATALOGUE_FILE SCRAPE_MISSING_CATEGORIES: False # whether or not to scrape missing genres, only effective if CATALOGUE_SOURCE is equal to FILE. If CATALOGUE_SOURCE is equal to GOOGLE, all genres are scraped anyway PROVIDERS: RAPIDS: - COMPUTE: False - INCLUDE_EPISODE_FEATURES: False + COMPUTE: True + INCLUDE_EPISODE_FEATURES: True SINGLE_CATEGORIES: ["all", "email"] MULTIPLE_CATEGORIES: social: ["socialnetworks", "socialmediatools"] @@ -124,7 +125,7 @@ PHONE_APPLICATIONS_FOREGROUND: dating: ["com.tinder", "com.relance.happycouple", "com.kiwi.joyride"] SINGLE_APPS: ["top1global", "com.facebook.moments", "com.google.android.youtube", "com.twitter.android"] # There's no entropy for single apps EXCLUDED_CATEGORIES: [] - EXCLUDED_APPS: ["com.fitbit.FitbitMobile", "com.aware.plugin.upmc.cancer"] + EXCLUDED_APPS: ["com.fitbit.FitbitMobile", "com.aware.plugin.upmc.cancer"] # TODO list system apps? FEATURES: APP_EVENTS: ["countevent", "timeoffirstuse", "timeoflastuse", "frequencyentropy"] APP_EPISODES: ["countepisode", "minduration", "maxduration", "meanduration", "sumduration"] @@ -134,7 +135,7 @@ PHONE_APPLICATIONS_FOREGROUND: # See https://www.rapids.science/latest/features/phone-applications-notifications/ PHONE_APPLICATIONS_NOTIFICATIONS: - CONTAINER: applications_notifications + CONTAINER: notifications APPLICATION_CATEGORIES: CATALOGUE_SOURCE: FILE # FILE (genres are read from CATALOGUE_FILE) or GOOGLE (genres are scrapped from the Play Store) CATALOGUE_FILE: "data/external/stachl_application_genre_catalogue.csv" @@ -148,7 +149,7 @@ PHONE_BATTERY: EPISODE_THRESHOLD_BETWEEN_ROWS: 30 # minutes. Max time difference for two consecutive rows to be considered within the same battery episode. PROVIDERS: RAPIDS: - COMPUTE: False + COMPUTE: True FEATURES: ["countdischarge", "sumdurationdischarge", "countcharge", "sumdurationcharge", "avgconsumptionrate", "maxconsumptionrate"] SRC_SCRIPT: src/features/phone_battery/rapids/main.py @@ -157,12 +158,12 @@ PHONE_BLUETOOTH: CONTAINER: bluetooth PROVIDERS: RAPIDS: - COMPUTE: False + COMPUTE: True FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"] SRC_SCRIPT: src/features/phone_bluetooth/rapids/main.R DORYAB: - COMPUTE: False + COMPUTE: True FEATURES: ALL: DEVICES: ["countscans", "uniquedevices", "meanscans", "stdscans"] @@ -183,7 +184,7 @@ PHONE_CALLS: CONTAINER: call PROVIDERS: RAPIDS: - COMPUTE: False + COMPUTE: True FEATURES_TYPE: EPISODES # EVENTS or EPISODES CALL_TYPES: [missed, incoming, outgoing] FEATURES: @@ -193,7 +194,7 @@ PHONE_CALLS: SRC_SCRIPT: src/features/phone_calls/rapids/main.R # See https://www.rapids.science/latest/features/phone-conversation/ -PHONE_CONVERSATION: +PHONE_CONVERSATION: # TODO Adapt for speech CONTAINER: ANDROID: plugin_studentlife_audio_android IOS: plugin_studentlife_audio @@ -212,14 +213,34 @@ PHONE_CONVERSATION: # See https://www.rapids.science/latest/features/phone-data-yield/ PHONE_DATA_YIELD: - SENSORS: [] + SENSORS: [#PHONE_ACCELEROMETER, + PHONE_ACTIVITY_RECOGNITION, + PHONE_APPLICATIONS_FOREGROUND, + PHONE_APPLICATIONS_NOTIFICATIONS, + PHONE_BATTERY, + PHONE_BLUETOOTH, + PHONE_CALLS, + PHONE_LIGHT, + PHONE_LOCATIONS, + PHONE_MESSAGES, + PHONE_SCREEN, + PHONE_WIFI_VISIBLE] PROVIDERS: RAPIDS: - COMPUTE: False + 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. SRC_SCRIPT: src/features/phone_data_yield/rapids/main.R +PHONE_ESM: + CONTAINER: esm + PROVIDERS: + STRAW: + COMPUTE: False + SCALES: ["PANAS_positive_affect", "PANAS_negative_affect", "JCQ_job_demand", "JCQ_job_control", "JCQ_supervisor_support", "JCQ_coworker_support"] + FEATURES: [mean] + SRC_SCRIPT: src/features/phone_esm/straw/main.py + # See https://www.rapids.science/latest/features/phone-keyboard/ PHONE_KEYBOARD: CONTAINER: keyboard @@ -231,10 +252,10 @@ PHONE_KEYBOARD: # See https://www.rapids.science/latest/features/phone-light/ PHONE_LIGHT: - CONTAINER: light + CONTAINER: light_sensor PROVIDERS: RAPIDS: - COMPUTE: False + COMPUTE: True FEATURES: ["count", "maxlux", "minlux", "avglux", "medianlux", "stdlux"] SRC_SCRIPT: src/features/phone_light/rapids/main.py @@ -248,7 +269,7 @@ PHONE_LOCATIONS: PROVIDERS: DORYAB: - COMPUTE: False + COMPUTE: True FEATURES: ["locationvariance","loglocationvariance","totaldistance","avgspeed","varspeed", "numberofsignificantplaces","numberlocationtransitions","radiusgyration","timeattop1location","timeattop2location","timeattop3location","movingtostaticratio","outlierstimepercent","maxlengthstayatclusters","minlengthstayatclusters","avglengthstayatclusters","stdlengthstayatclusters","locationentropy","normalizedlocationentropy","timeathome", "homelabel"] DBSCAN_EPS: 100 # meters DBSCAN_MINSAMPLES: 5 @@ -263,7 +284,7 @@ PHONE_LOCATIONS: SRC_SCRIPT: src/features/phone_locations/doryab/main.py BARNETT: - COMPUTE: False + COMPUTE: True 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 @@ -278,10 +299,10 @@ PHONE_LOG: # See https://www.rapids.science/latest/features/phone-messages/ PHONE_MESSAGES: - CONTAINER: messages + CONTAINER: sms PROVIDERS: RAPIDS: - COMPUTE: False + COMPUTE: True MESSAGES_TYPES : [received, sent] FEATURES: received: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact] @@ -293,7 +314,7 @@ PHONE_SCREEN: CONTAINER: screen PROVIDERS: RAPIDS: - COMPUTE: False + COMPUTE: True REFERENCE_HOUR_FIRST_USE: 0 IGNORE_EPISODES_SHORTER_THAN: 0 # in minutes, set to 0 to disable IGNORE_EPISODES_LONGER_THAN: 360 # in minutes, set to 0 to disable @@ -315,12 +336,13 @@ PHONE_WIFI_VISIBLE: CONTAINER: wifi PROVIDERS: RAPIDS: - COMPUTE: False + COMPUTE: True FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"] SRC_SCRIPT: src/features/phone_wifi_visible/rapids/main.R + ######################################################################################################################## # FITBIT # ######################################################################################################################## @@ -484,13 +506,13 @@ EMPATICA_ACCELEROMETER: FEATURES: ["maxmagnitude", "minmagnitude", "avgmagnitude", "medianmagnitude", "stdmagnitude"] SRC_SCRIPT: src/features/empatica_accelerometer/dbdp/main.py CR: - COMPUTE: False + COMPUTE: True FEATURES: ["totalMagnitudeBand", "absoluteMeanBand", "varianceBand"] # Acc features WINDOWS: COMPUTE: True WINDOW_LENGTH: 15 # specify window length in seconds SECOND_ORDER_FEATURES: ['mean', 'median', 'sd', 'nlargest', 'nsmallest', 'count_windows'] - STANDARDIZE_FEATURES: False + STANDARDIZE_FEATURES: True SRC_SCRIPT: src/features/empatica_accelerometer/cr/main.py @@ -512,14 +534,14 @@ EMPATICA_TEMPERATURE: FEATURES: ["maxtemp", "mintemp", "avgtemp", "mediantemp", "modetemp", "stdtemp", "diffmaxmodetemp", "diffminmodetemp", "entropytemp"] SRC_SCRIPT: src/features/empatica_temperature/dbdp/main.py CR: - COMPUTE: False + COMPUTE: True FEATURES: ["maximum", "minimum", "meanAbsChange", "longestStrikeAboveMean", "longestStrikeBelowMean", "stdDev", "median", "meanChange", "sumSquared", "squareSumOfComponent", "sumOfSquareComponents"] WINDOWS: COMPUTE: True WINDOW_LENGTH: 300 # specify window length in seconds SECOND_ORDER_FEATURES: ['mean', 'median', 'sd', 'nlargest', 'nsmallest', 'count_windows'] - STANDARDIZE_FEATURES: False + STANDARDIZE_FEATURES: True SRC_SCRIPT: src/features/empatica_temperature/cr/main.py # See https://www.rapids.science/latest/features/empatica-electrodermal-activity/ @@ -541,7 +563,7 @@ 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: False + STANDARDIZE_FEATURES: True IMPUTE_NANS: False SRC_SCRIPT: src/features/empatica_electrodermal_activity/cr/main.py @@ -554,14 +576,14 @@ EMPATICA_BLOOD_VOLUME_PULSE: FEATURES: ["maxbvp", "minbvp", "avgbvp", "medianbvp", "modebvp", "stdbvp", "diffmaxmodebvp", "diffminmodebvp", "entropybvp"] SRC_SCRIPT: src/features/empatica_blood_volume_pulse/dbdp/main.py CR: - COMPUTE: False + COMPUTE: True FEATURES: ['meanHr', 'ibi', 'sdnn', 'sdsd', 'rmssd', 'pnn20', 'pnn50', 'sd', 'sd2', 'sd1/sd2', 'numRR', # Time features 'VLF', 'LF', 'LFnorm', 'HF', 'HFnorm', 'LF/HF', 'fullIntegral'] # Freq features WINDOWS: 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: False + 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/ @@ -573,7 +595,7 @@ EMPATICA_INTER_BEAT_INTERVAL: FEATURES: ["maxibi", "minibi", "avgibi", "medianibi", "modeibi", "stdibi", "diffmaxmodeibi", "diffminmodeibi", "entropyibi"] SRC_SCRIPT: src/features/empatica_inter_beat_interval/dbdp/main.py CR: - COMPUTE: False + COMPUTE: True FEATURES: ['meanHr', 'ibi', 'sdnn', 'sdsd', 'rmssd', 'pnn20', 'pnn50', 'sd', 'sd2', 'sd1/sd2', 'numRR', # Time features 'VLF', 'LF', 'LFnorm', 'HF', 'HFnorm', 'LF/HF', 'fullIntegral'] # Freq features PATCH_WITH_BVP: True @@ -581,7 +603,7 @@ 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: False + STANDARDIZE_FEATURES: True SRC_SCRIPT: src/features/empatica_inter_beat_interval/cr/main.py # See https://www.rapids.science/latest/features/empatica-tags/ diff --git a/data/external/empatica/empatica1/E4 Data.zip b/data/external/empatica/empatica1/E4 Data.zip index ad07905e..aa26b26f 100644 Binary files a/data/external/empatica/empatica1/E4 Data.zip and b/data/external/empatica/empatica1/E4 Data.zip differ