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Update participant files structure and fitbit download rule

pull/103/head
JulioV 2020-10-20 19:12:01 -04:00
parent c835987d52
commit c266f6dd10
10 changed files with 356 additions and 220 deletions
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51
Snakefile
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@ -36,9 +36,9 @@ for provider in config["PHONE_MESSAGES"]["PROVIDERS"].keys():
for provider in config["PHONE_CALLS"]["PROVIDERS"].keys(): for provider in config["PHONE_CALLS"]["PROVIDERS"].keys():
if config["PHONE_CALLS"]["PROVIDERS"][provider]["COMPUTE"]: if config["PHONE_CALLS"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_calls_raw.csv", pid=config["PIDS"], sensor=config["PHONE_CALLS"]["DB_TABLE"])) files_to_compute.extend(expand("data/raw/{pid}/phone_calls_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_calls_with_datetime.csv", pid=config["PIDS"], sensor=config["PHONE_CALLS"]["DB_TABLE"])) files_to_compute.extend(expand("data/raw/{pid}/phone_calls_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_calls_with_datetime_unified.csv", pid=config["PIDS"], sensor=config["PHONE_CALLS"]["DB_TABLE"])) files_to_compute.extend(expand("data/raw/{pid}/phone_calls_with_datetime_unified.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_calls_features/phone_calls_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_CALLS"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower())) files_to_compute.extend(expand("data/interim/{pid}/phone_calls_features/phone_calls_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_CALLS"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_calls.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/processed/features/{pid}/phone_calls.csv", pid=config["PIDS"]))
@ -122,23 +122,6 @@ for provider in config["PHONE_WIFI_CONNECTED"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/interim/{pid}/phone_wifi_connected_features/phone_wifi_connected_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_WIFI_CONNECTED"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower())) files_to_compute.extend(expand("data/interim/{pid}/phone_wifi_connected_features/phone_wifi_connected_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_WIFI_CONNECTED"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_wifi_connected.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/processed/features/{pid}/phone_wifi_connected.csv", pid=config["PIDS"]))
if config["HEARTRATE"]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["HEARTRATE"]["DB_TABLE"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_{fitbit_data_type}_with_datetime.csv", pid=config["PIDS"], fitbit_data_type=["summary", "intraday"]))
files_to_compute.extend(expand("data/processed/{pid}/fitbit_heartrate_{day_segment}.csv", pid = config["PIDS"], day_segment = config["HEARTRATE"]["DAY_SEGMENTS"]))
if config["STEP"]["COMPUTE"]:
if config["STEP"]["EXCLUDE_SLEEP"]["EXCLUDE"] == True and config["STEP"]["EXCLUDE_SLEEP"]["TYPE"] == "FITBIT_BASED":
files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_{fitbit_data_type}_with_datetime.csv", pid=config["PIDS"], fitbit_data_type=["summary"]))
files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["STEP"]["DB_TABLE"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_step_{fitbit_data_type}_with_datetime.csv", pid=config["PIDS"], fitbit_data_type=["intraday"]))
files_to_compute.extend(expand("data/processed/{pid}/fitbit_step_{day_segment}.csv", pid = config["PIDS"], day_segment = config["STEP"]["DAY_SEGMENTS"]))
if config["SLEEP"]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["SLEEP"]["DB_TABLE"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_{fitbit_data_type}_with_datetime.csv", pid=config["PIDS"], fitbit_data_type=["intraday", "summary"]))
files_to_compute.extend(expand("data/processed/{pid}/fitbit_sleep_{day_segment}.csv", pid = config["PIDS"], day_segment = config["SLEEP"]["DAY_SEGMENTS"]))
for provider in config["PHONE_CONVERSATION"]["PROVIDERS"].keys(): for provider in config["PHONE_CONVERSATION"]["PROVIDERS"].keys():
if config["PHONE_CONVERSATION"]["PROVIDERS"][provider]["COMPUTE"]: if config["PHONE_CONVERSATION"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/phone_conversation_raw.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/raw/{pid}/phone_conversation_raw.csv", pid=config["PIDS"]))
@ -150,10 +133,10 @@ for provider in config["PHONE_CONVERSATION"]["PROVIDERS"].keys():
for provider in config["PHONE_LOCATIONS"]["PROVIDERS"].keys(): for provider in config["PHONE_LOCATIONS"]["PROVIDERS"].keys():
if config["PHONE_LOCATIONS"]["PROVIDERS"][provider]["COMPUTE"]: if config["PHONE_LOCATIONS"]["PROVIDERS"][provider]["COMPUTE"]:
if config["PHONE_LOCATIONS"]["LOCATIONS_TO_USE"] == "RESAMPLE_FUSED": if config["PHONE_LOCATIONS"]["LOCATIONS_TO_USE"] == "RESAMPLE_FUSED":
if config["PHONE_LOCATIONS"]["DB_TABLE"] in config["PHONE_VALID_SENSED_BINS"]["DB_TABLES"]: if "PHONE_LOCATIONS" in config["PHONE_VALID_SENSED_BINS"]["PHONE_SENSORS"]:
files_to_compute.extend(expand("data/interim/{pid}/phone_sensed_bins.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/interim/{pid}/phone_sensed_bins.csv", pid=config["PIDS"]))
else: else:
raise ValueError("Error: Add your locations table (and as many sensor tables as you have) to [PHONE_VALID_SENSED_BINS][DB_TABLES] in config.yaml. This is necessary to compute phone_sensed_bins (bins of time when the smartphone was sensing data) which is used to resample fused location data (RESAMPLED_FUSED)") raise ValueError("Error: Add PHONE_LOCATIONS (and as many PHONE_SENSORS as you have) to [PHONE_VALID_SENSED_BINS][PHONE_SENSORS] in config.yaml. This is necessary to compute phone_sensed_bins (bins of time when the smartphone was sensing data) which is used to resample fused location data (RESAMPLED_FUSED)")
files_to_compute.extend(expand("data/raw/{pid}/phone_locations_raw.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/raw/{pid}/phone_locations_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_locations_processed.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/interim/{pid}/phone_locations_processed.csv", pid=config["PIDS"]))
@ -161,6 +144,30 @@ for provider in config["PHONE_LOCATIONS"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/interim/{pid}/phone_locations_features/phone_locations_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_LOCATIONS"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower())) files_to_compute.extend(expand("data/interim/{pid}/phone_locations_features/phone_locations_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_LOCATIONS"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_locations.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/processed/features/{pid}/phone_locations.csv", pid=config["PIDS"]))
for provider in config["FITBIT_HEARTRATE"]["PROVIDERS"].keys():
if config["FITBIT_HEARTRATE"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_raw.csv", pid=config["PIDS"]))
# files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_{fitbit_data_type}_with_datetime.csv", pid=config["PIDS"], fitbit_data_type=["summary", "intraday"]))
# files_to_compute.extend(expand("data/processed/{pid}/fitbit_heartrate_{day_segment}.csv", pid = config["PIDS"], day_segment = config["HEARTRATE"]["DAY_SEGMENTS"]))
for provider in config["FITBIT_STEPS"]["PROVIDERS"].keys():
if config["FITBIT_STEPS"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/fitbit_steps_raw.csv", pid=config["PIDS"]))
# if config["STEP"]["COMPUTE"]:
# if config["STEP"]["EXCLUDE_SLEEP"]["EXCLUDE"] == True and config["STEP"]["EXCLUDE_SLEEP"]["TYPE"] == "FITBIT_BASED":
# files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_{fitbit_data_type}_with_datetime.csv", pid=config["PIDS"], fitbit_data_type=["summary"]))
# files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["STEP"]["TABLE"]))
# files_to_compute.extend(expand("data/raw/{pid}/fitbit_step_{fitbit_data_type}_with_datetime.csv", pid=config["PIDS"], fitbit_data_type=["intraday"]))
# files_to_compute.extend(expand("data/processed/{pid}/fitbit_step_{day_segment}.csv", pid = config["PIDS"], day_segment = config["STEP"]["DAY_SEGMENTS"]))
for provider in config["FITBIT_SLEEP"]["PROVIDERS"].keys():
if config["FITBIT_SLEEP"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_raw.csv", pid=config["PIDS"]))
# files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_{fitbit_data_type}_with_datetime.csv", pid=config["PIDS"], fitbit_data_type=["intraday", "summary"]))
# files_to_compute.extend(expand("data/processed/{pid}/fitbit_sleep_{day_segment}.csv", pid = config["PIDS"], day_segment = config["SLEEP"]["DAY_SEGMENTS"]))
# visualization for data exploration # visualization for data exploration
if config["HEATMAP_FEATURES_CORRELATIONS"]["PLOT"]: if config["HEATMAP_FEATURES_CORRELATIONS"]["PLOT"]:
files_to_compute.extend(expand("reports/data_exploration/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/heatmap_features_correlations.html", min_valid_hours_per_day=config["HEATMAP_FEATURES_CORRELATIONS"]["MIN_VALID_HOURS_PER_DAY"], min_valid_bins_per_hour=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_BINS_PER_HOUR"])) files_to_compute.extend(expand("reports/data_exploration/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/heatmap_features_correlations.html", min_valid_hours_per_day=config["HEATMAP_FEATURES_CORRELATIONS"]["MIN_VALID_HOURS_PER_DAY"], min_valid_bins_per_hour=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_BINS_PER_HOUR"]))

107
config.yaml
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@ -8,33 +8,46 @@ DAY_SEGMENTS: &day_segments
FILE: "data/external/daysegments_periodic.csv" FILE: "data/external/daysegments_periodic.csv"
INCLUDE_PAST_PERIODIC_SEGMENTS: FALSE # Only relevant if TYPE=PERIODIC, if set to TRUE we consider day segments back enough in the past as to include the first day of data INCLUDE_PAST_PERIODIC_SEGMENTS: FALSE # Only relevant if TYPE=PERIODIC, if set to TRUE we consider day segments back enough in the past as to include the first day of data
# Global timezone # Use tz codes from https://en.wikipedia.org/wiki/List_of_tz_database_time_zones. Double check your code, for example EST is not US Eastern Time.
# Use codes from https://en.wikipedia.org/wiki/List_of_tz_database_time_zones
# Double check your code, for example EST is not US Eastern Time.
TIMEZONE: &timezone TIMEZONE: &timezone
America/New_York America/New_York
DATABASE_GROUP: &database_group DATABASE_GROUP: &database_group
MY_GROUP MY_GROUP
DOWNLOAD_PARTICIPANTS: PARTICIPANT_FILES: # run snakemake -j1 -R parse_participant_files
IGNORED_DEVICE_IDS: [] # for example "5a1dd68c-6cd1-48fe-ae1e-14344ac5215f" PHONE_SECTION:
GROUP: *database_group INCLUDE: TRUE
PARSED_FROM: AWARE_DEVICE_TABLE #AWARE_DEVICE_TABLE or CSV_FILE
PARSED_SOURCE: *database_group # DB credentials group or CSV file path. If CSV file, it should have: device_id, pid (optional), label (optional), start_date (optional), end_date (optional)
IGNORED_DEVICE_IDS: []
FITBIT_SECTION:
INCLUDE: FALSE
SAME_AS_PHONE: FALSE # If TRUE, all config below is ignored
PARSED_FROM: CSV_FILE
PARSED_SOURCE: "external/my_fitbit_participants.csv" # CSV file should have: device_id, pid (optional), label (optional), start_date (optional), end_date (optional)
# Download data config SENSOR_DATA:
DOWNLOAD_DATASET: PHONE:
GROUP: *database_group SOURCE:
TYPE: DATABASE
# Readable datetime config DATABASE_GROUP: *database_group
READABLE_DATETIME: DEVICE_ID_COLUMN: device_id # column name
FIXED_TIMEZONE: *timezone TIMEZONE:
TYPE: SINGLE # SINGLE or MULTIPLE
VALUE: *timezone # IF TYPE=SINGLE, timezone code (e.g. America/New_York, see attribute TIMEZONE above). If TYPE=MULTIPLE, a table in your database with two columns (timestamp, timezone) where timestamp is a unix timestamp and timezone is one of https://en.wikipedia.org/wiki/List_of_tz_database_time_zones
FITBIT:
SOURCE:
TYPE: DATABASE # DATABASE or CSV_FILES (set each FITBIT_SENSOR TABLE attribute accordingly)
DATABASE_GROUP: *database_group
DEVICE_ID_COLUMN: device_id # column name
PHONE_VALID_SENSED_BINS: PHONE_VALID_SENSED_BINS:
COMPUTE: False # This flag is automatically ignored (set to True) if you are extracting PHONE_VALID_SENSED_DAYS or screen or Barnett's location features COMPUTE: False # This flag is automatically ignored (set to True) if you are extracting PHONE_VALID_SENSED_DAYS or screen or Barnett's location features
BIN_SIZE: &bin_size 5 # (in minutes) BIN_SIZE: &bin_size 5 # (in minutes)
# Add as many PHONE sensors as you have, they all improve the computation of PHONE_VALID_SENSED_BINS and PHONE_VALID_SENSED_DAYS. # Add as many PHONE sensors as you have, they all improve the computation of PHONE_VALID_SENSED_BINS and PHONE_VALID_SENSED_DAYS.
# If you are extracting screen or Barnett/Doryab location features, PHONE_SCREEN and PHONE_LOCATIONS tables are mandatory. # If you are extracting screen or Barnett/Doryab location features, PHONE_SCREEN and PHONE_LOCATIONS tables are mandatory.
# You can choose any of the keys shown below, just make sure its DB_TABLE exists in your database! # You can choose any of the keys shown below, just make sure its TABLE exists in your database!
# PHONE_MESSAGES, PHONE_CALLS, PHONE_LOCATIONS, PHONE_BLUETOOTH, PHONE_ACTIVITY_RECOGNITION, PHONE_BATTERY, PHONE_SCREEN, PHONE_LIGHT, # PHONE_MESSAGES, PHONE_CALLS, PHONE_LOCATIONS, PHONE_BLUETOOTH, PHONE_ACTIVITY_RECOGNITION, PHONE_BATTERY, PHONE_SCREEN, PHONE_LIGHT,
# PHONE_ACCELEROMETER, PHONE_APPLICATIONS_FOREGROUND, PHONE_WIFI_VISIBLE, PHONE_WIFI_CONNECTED, PHONE_CONVERSATION # PHONE_ACCELEROMETER, PHONE_APPLICATIONS_FOREGROUND, PHONE_WIFI_VISIBLE, PHONE_WIFI_CONNECTED, PHONE_CONVERSATION
PHONE_SENSORS: [] PHONE_SENSORS: []
@ -46,7 +59,7 @@ PHONE_VALID_SENSED_DAYS:
# Communication SMS features config, TYPES and FEATURES keys need to match # Communication SMS features config, TYPES and FEATURES keys need to match
PHONE_MESSAGES: PHONE_MESSAGES:
DB_TABLE: messages TABLE: messages
PROVIDERS: PROVIDERS:
RAPIDS: RAPIDS:
COMPUTE: False COMPUTE: False
@ -59,10 +72,10 @@ PHONE_MESSAGES:
# Communication call features config, TYPES and FEATURES keys need to match # Communication call features config, TYPES and FEATURES keys need to match
PHONE_CALLS: PHONE_CALLS:
DB_TABLE: calls TABLE: calls
PROVIDERS: PROVIDERS:
RAPIDS: RAPIDS:
COMPUTE: False COMPUTE: True
CALL_TYPES: [missed, incoming, outgoing] CALL_TYPES: [missed, incoming, outgoing]
FEATURES: FEATURES:
missed: [count, distinctcontacts, timefirstcall, timelastcall, countmostfrequentcontact] missed: [count, distinctcontacts, timefirstcall, timelastcall, countmostfrequentcontact]
@ -72,7 +85,7 @@ PHONE_CALLS:
SRC_FOLDER: "rapids" # inside src/features/phone_calls SRC_FOLDER: "rapids" # inside src/features/phone_calls
PHONE_LOCATIONS: PHONE_LOCATIONS:
DB_TABLE: locations TABLE: locations
LOCATIONS_TO_USE: FUSED_RESAMPLED # ALL, GPS OR FUSED_RESAMPLED LOCATIONS_TO_USE: FUSED_RESAMPLED # ALL, GPS OR FUSED_RESAMPLED
FUSED_RESAMPLED_CONSECUTIVE_THRESHOLD: 30 # minutes, only replicate location samples to the next sensed bin if the phone did not stop collecting data for more than this threshold FUSED_RESAMPLED_CONSECUTIVE_THRESHOLD: 30 # minutes, only replicate location samples to the next sensed bin if the phone did not stop collecting data for more than this threshold
FUSED_RESAMPLED_TIME_SINCE_VALID_LOCATION: 720 # minutes, only replicate location samples to consecutive sensed bins if they were logged within this threshold after a valid location row FUSED_RESAMPLED_TIME_SINCE_VALID_LOCATION: 720 # minutes, only replicate location samples to consecutive sensed bins if they were logged within this threshold after a valid location row
@ -99,7 +112,7 @@ PHONE_LOCATIONS:
SRC_LANGUAGE: "r" SRC_LANGUAGE: "r"
PHONE_BLUETOOTH: PHONE_BLUETOOTH:
DB_TABLE: bluetooth TABLE: bluetooth
PROVIDERS: PROVIDERS:
RAPIDS: RAPIDS:
COMPUTE: False COMPUTE: False
@ -109,12 +122,12 @@ PHONE_BLUETOOTH:
PHONE_ACTIVITY_RECOGNITION: PHONE_ACTIVITY_RECOGNITION:
DB_TABLE: TABLE:
ANDROID: plugin_google_activity_recognition ANDROID: plugin_google_activity_recognition
IOS: plugin_ios_activity_recognition IOS: plugin_ios_activity_recognition
PROVIDERS: PROVIDERS:
RAPIDS: RAPIDS:
COMPUTE: False COMPUTE: True
FEATURES: ["count", "mostcommonactivity", "countuniqueactivities", "durationstationary", "durationmobile", "durationvehicle"] FEATURES: ["count", "mostcommonactivity", "countuniqueactivities", "durationstationary", "durationmobile", "durationvehicle"]
ACTIVITY_CLASSES: ACTIVITY_CLASSES:
STATIONARY: ["still", "tilting"] STATIONARY: ["still", "tilting"]
@ -124,7 +137,7 @@ PHONE_ACTIVITY_RECOGNITION:
SRC_LANGUAGE: "python" SRC_LANGUAGE: "python"
PHONE_BATTERY: PHONE_BATTERY:
DB_TABLE: battery TABLE: battery
PROVIDERS: PROVIDERS:
RAPIDS: RAPIDS:
COMPUTE: False COMPUTE: False
@ -133,7 +146,7 @@ PHONE_BATTERY:
SRC_LANGUAGE: "python" SRC_LANGUAGE: "python"
PHONE_SCREEN: PHONE_SCREEN:
DB_TABLE: screen TABLE: screen
PROVIDERS: PROVIDERS:
RAPIDS: RAPIDS:
COMPUTE: False COMPUTE: False
@ -146,7 +159,7 @@ PHONE_SCREEN:
SRC_LANGUAGE: "python" SRC_LANGUAGE: "python"
PHONE_LIGHT: PHONE_LIGHT:
DB_TABLE: light TABLE: light
PROVIDERS: PROVIDERS:
RAPIDS: RAPIDS:
COMPUTE: False COMPUTE: False
@ -155,7 +168,7 @@ PHONE_LIGHT:
SRC_LANGUAGE: "python" SRC_LANGUAGE: "python"
PHONE_ACCELEROMETER: PHONE_ACCELEROMETER:
DB_TABLE: accelerometer TABLE: accelerometer
PROVIDERS: PROVIDERS:
RAPIDS: RAPIDS:
COMPUTE: False COMPUTE: False
@ -173,7 +186,7 @@ PHONE_ACCELEROMETER:
SRC_LANGUAGE: "python" SRC_LANGUAGE: "python"
PHONE_APPLICATIONS_FOREGROUND: PHONE_APPLICATIONS_FOREGROUND:
DB_TABLE: applications_foreground TABLE: applications_foreground
APPLICATION_CATEGORIES: APPLICATION_CATEGORIES:
CATALOGUE_SOURCE: FILE # FILE (genres are read from CATALOGUE_FILE) or GOOGLE (genres are scrapped from the Play Store) 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" CATALOGUE_FILE: "data/external/stachl_application_genre_catalogue.csv"
@ -194,7 +207,7 @@ PHONE_APPLICATIONS_FOREGROUND:
SRC_LANGUAGE: "python" SRC_LANGUAGE: "python"
PHONE_WIFI_VISIBLE: PHONE_WIFI_VISIBLE:
DB_TABLE: "wifi" TABLE: "wifi"
PROVIDERS: PROVIDERS:
RAPIDS: RAPIDS:
COMPUTE: False COMPUTE: False
@ -203,7 +216,7 @@ PHONE_WIFI_VISIBLE:
SRC_LANGUAGE: "r" SRC_LANGUAGE: "r"
PHONE_WIFI_CONNECTED: PHONE_WIFI_CONNECTED:
DB_TABLE: "sensor_wifi" TABLE: "sensor_wifi"
PROVIDERS: PROVIDERS:
RAPIDS: RAPIDS:
COMPUTE: False COMPUTE: False
@ -212,12 +225,12 @@ PHONE_WIFI_CONNECTED:
SRC_LANGUAGE: "r" SRC_LANGUAGE: "r"
PHONE_CONVERSATION: PHONE_CONVERSATION:
DB_TABLE: TABLE:
ANDROID: plugin_studentlife_audio_android ANDROID: plugin_studentlife_audio_android
IOS: plugin_studentlife_audio IOS: plugin_studentlife_audio
PROVIDERS: PROVIDERS:
RAPIDS: RAPIDS:
COMPUTE: False COMPUTE: True
FEATURES: ["minutessilence", "minutesnoise", "minutesvoice", "minutesunknown","sumconversationduration","avgconversationduration", FEATURES: ["minutessilence", "minutesnoise", "minutesvoice", "minutesunknown","sumconversationduration","avgconversationduration",
"sdconversationduration","minconversationduration","maxconversationduration","timefirstconversation","timelastconversation","sumenergy", "sdconversationduration","minconversationduration","maxconversationduration","timefirstconversation","timelastconversation","sumenergy",
"avgenergy","sdenergy","minenergy","maxenergy","silencesensedfraction","noisesensedfraction", "avgenergy","sdenergy","minenergy","maxenergy","silencesensedfraction","noisesensedfraction",
@ -229,23 +242,27 @@ PHONE_CONVERSATION:
SRC_LANGUAGE: "python" SRC_LANGUAGE: "python"
HEARTRATE: FITBIT_HEARTRATE:
COMPUTE: False TABLE: "fitbit_data"
DB_TABLE: fitbit_data PARSE_JSON: TRUE
DAY_SEGMENTS: *day_segments PROVIDERS:
SUMMARY_FEATURES: ["restinghr"] # calories features' accuracy depend on the accuracy of the participants fitbit profile (e.g. heigh, weight) use with care: ["caloriesoutofrange", "caloriesfatburn", "caloriescardio", "caloriespeak"] RAPIDS:
COMPUTE: True
SUMMARY_FEATURES: ["restinghr"] # calories features' accuracy depend on the accuracy of the participants fitbit profile (e.g. height, weight) use these with care: ["caloriesoutofrange", "caloriesfatburn", "caloriescardio", "caloriespeak"]
INTRADAY_FEATURES: ["maxhr", "minhr", "avghr", "medianhr", "modehr", "stdhr", "diffmaxmodehr", "diffminmodehr", "entropyhr", "minutesonoutofrangezone", "minutesonfatburnzone", "minutesoncardiozone", "minutesonpeakzone"] INTRADAY_FEATURES: ["maxhr", "minhr", "avghr", "medianhr", "modehr", "stdhr", "diffmaxmodehr", "diffminmodehr", "entropyhr", "minutesonoutofrangezone", "minutesonfatburnzone", "minutesoncardiozone", "minutesonpeakzone"]
STEP: FITBIT_STEPS:
COMPUTE: False TABLE: fitbit_data
DB_TABLE: fitbit_data PARSE_JSON: TRUE
DAY_SEGMENTS: *day_segments
EXCLUDE_SLEEP: EXCLUDE_SLEEP:
EXCLUDE: False EXCLUDE: False
TYPE: FIXED # FIXED OR FITBIT_BASED (CONFIGURE FITBIT's SLEEP DB_TABLE) TYPE: FIXED # FIXED OR FITBIT_BASED (configure FITBIT_SLEEP section)
FIXED: FIXED:
START: "23:00" START: "23:00"
END: "07:00" END: "07:00"
PROVIDERS:
RAPIDS:
COMPUTE: TRUE
FEATURES: FEATURES:
ALL_STEPS: ["sumallsteps", "maxallsteps", "minallsteps", "avgallsteps", "stdallsteps"] ALL_STEPS: ["sumallsteps", "maxallsteps", "minallsteps", "avgallsteps", "stdallsteps"]
SEDENTARY_BOUT: ["countepisode", "sumduration", "maxduration", "minduration", "avgduration", "stdduration"] SEDENTARY_BOUT: ["countepisode", "sumduration", "maxduration", "minduration", "avgduration", "stdduration"]
@ -253,10 +270,12 @@ STEP:
THRESHOLD_ACTIVE_BOUT: 10 # steps THRESHOLD_ACTIVE_BOUT: 10 # steps
INCLUDE_ZERO_STEP_ROWS: False INCLUDE_ZERO_STEP_ROWS: False
SLEEP: FITBIT_SLEEP:
COMPUTE: False TABLE: fitbit_data
DB_TABLE: fitbit_data PARSE_JSON: TRUE
DAY_SEGMENTS: *day_segments PROVIDERS:
RAPIDS:
COMPUTE: TRUE
SLEEP_TYPES: ["main", "nap", "all"] SLEEP_TYPES: ["main", "nap", "all"]
SUMMARY_FEATURES: ["sumdurationafterwakeup", "sumdurationasleep", "sumdurationawake", "sumdurationtofallasleep", "sumdurationinbed", "avgefficiency", "countepisode"] SUMMARY_FEATURES: ["sumdurationafterwakeup", "sumdurationasleep", "sumdurationawake", "sumdurationtofallasleep", "sumdurationinbed", "avgefficiency", "countepisode"]

108
rules/features.smk
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@ -6,28 +6,6 @@ rule join_features_from_providers:
script: script:
"../src/features/join_features_from_providers.R" "../src/features/join_features_from_providers.R"
rule resample_episodes:
input:
"data/interim/{pid}/{sensor}_episodes.csv"
output:
"data/interim/{pid}/{sensor}_episodes_resampled.csv"
script:
"../src/features/utils/resample_episodes.R"
rule resample_episodes_with_datetime:
input:
sensor_input = "data/interim/{pid}/{sensor}_episodes_resampled.csv",
day_segments = "data/interim/day_segments/{pid}_day_segments.csv"
params:
timezones = None,
fixed_timezone = config["READABLE_DATETIME"]["FIXED_TIMEZONE"],
day_segments_type = config["DAY_SEGMENTS"]["TYPE"],
include_past_periodic_segments = config["DAY_SEGMENTS"]["INCLUDE_PAST_PERIODIC_SEGMENTS"]
output:
"data/interim/{pid}/{sensor}_episodes_resampled_with_datetime.csv"
script:
"../src/data/readable_datetime.R"
rule phone_accelerometer_python_features: rule phone_accelerometer_python_features:
input: input:
sensor_data = "data/raw/{pid}/phone_accelerometer_with_datetime.csv", sensor_data = "data/raw/{pid}/phone_accelerometer_with_datetime.csv",
@ -234,48 +212,48 @@ rule phone_wifi_visible_r_features:
script: script:
"../src/features/entry.R" "../src/features/entry.R"
rule fitbit_heartrate_features: # rule fitbit_heartrate_features:
input: # input:
heartrate_summary_data = "data/raw/{pid}/fitbit_heartrate_summary_with_datetime.csv", # heartrate_summary_data = "data/raw/{pid}/fitbit_heartrate_summary_with_datetime.csv",
heartrate_intraday_data = "data/raw/{pid}/fitbit_heartrate_intraday_with_datetime.csv" # heartrate_intraday_data = "data/raw/{pid}/fitbit_heartrate_intraday_with_datetime.csv"
params: # params:
day_segment = "{day_segment}", # day_segment = "{day_segment}",
summary_features = config["HEARTRATE"]["SUMMARY_FEATURES"], # summary_features = config["HEARTRATE"]["SUMMARY_FEATURES"],
intraday_features = config["HEARTRATE"]["INTRADAY_FEATURES"] # intraday_features = config["HEARTRATE"]["INTRADAY_FEATURES"]
output: # output:
"data/processed/{pid}/fitbit_heartrate_{day_segment}.csv" # "data/processed/{pid}/fitbit_heartrate_{day_segment}.csv"
script: # script:
"../src/features/fitbit_heartrate_features.py" # "../src/features/fitbit_heartrate_features.py"
rule fitbit_step_features: # rule fitbit_step_features:
input: # input:
step_data = "data/raw/{pid}/fitbit_step_intraday_with_datetime.csv", # step_data = "data/raw/{pid}/fitbit_step_intraday_with_datetime.csv",
sleep_data = optional_steps_sleep_input # sleep_data = optional_steps_sleep_input
params: # params:
day_segment = "{day_segment}", # day_segment = "{day_segment}",
features_all_steps = config["STEP"]["FEATURES"]["ALL_STEPS"], # features_all_steps = config["STEP"]["FEATURES"]["ALL_STEPS"],
features_sedentary_bout = config["STEP"]["FEATURES"]["SEDENTARY_BOUT"], # features_sedentary_bout = config["STEP"]["FEATURES"]["SEDENTARY_BOUT"],
features_active_bout = config["STEP"]["FEATURES"]["ACTIVE_BOUT"], # features_active_bout = config["STEP"]["FEATURES"]["ACTIVE_BOUT"],
threshold_active_bout = config["STEP"]["THRESHOLD_ACTIVE_BOUT"], # threshold_active_bout = config["STEP"]["THRESHOLD_ACTIVE_BOUT"],
include_zero_step_rows = config["STEP"]["INCLUDE_ZERO_STEP_ROWS"], # include_zero_step_rows = config["STEP"]["INCLUDE_ZERO_STEP_ROWS"],
exclude_sleep = config["STEP"]["EXCLUDE_SLEEP"]["EXCLUDE"], # exclude_sleep = config["STEP"]["EXCLUDE_SLEEP"]["EXCLUDE"],
exclude_sleep_type = config["STEP"]["EXCLUDE_SLEEP"]["TYPE"], # exclude_sleep_type = config["STEP"]["EXCLUDE_SLEEP"]["TYPE"],
exclude_sleep_fixed_start = config["STEP"]["EXCLUDE_SLEEP"]["FIXED"]["START"], # exclude_sleep_fixed_start = config["STEP"]["EXCLUDE_SLEEP"]["FIXED"]["START"],
exclude_sleep_fixed_end = config["STEP"]["EXCLUDE_SLEEP"]["FIXED"]["END"], # exclude_sleep_fixed_end = config["STEP"]["EXCLUDE_SLEEP"]["FIXED"]["END"],
output: # output:
"data/processed/{pid}/fitbit_step_{day_segment}.csv" # "data/processed/{pid}/fitbit_step_{day_segment}.csv"
script: # script:
"../src/features/fitbit_step_features.py" # "../src/features/fitbit_step_features.py"
rule fitbit_sleep_features: # rule fitbit_sleep_features:
input: # input:
sleep_summary_data = "data/raw/{pid}/fitbit_sleep_summary_with_datetime.csv", # sleep_summary_data = "data/raw/{pid}/fitbit_sleep_summary_with_datetime.csv",
sleep_intraday_data = "data/raw/{pid}/fitbit_sleep_intraday_with_datetime.csv" # sleep_intraday_data = "data/raw/{pid}/fitbit_sleep_intraday_with_datetime.csv"
params: # params:
day_segment = "{day_segment}", # day_segment = "{day_segment}",
summary_features = config["SLEEP"]["SUMMARY_FEATURES"], # summary_features = config["SLEEP"]["SUMMARY_FEATURES"],
sleep_types = config["SLEEP"]["SLEEP_TYPES"] # sleep_types = config["SLEEP"]["SLEEP_TYPES"]
output: # output:
"data/processed/{pid}/fitbit_sleep_{day_segment}.csv" # "data/processed/{pid}/fitbit_sleep_{day_segment}.csv"
script: # script:
"../src/features/fitbit_sleep_features.py" # "../src/features/fitbit_sleep_features.py"

146
rules/preprocessing.smk
View File

@ -3,7 +3,7 @@ rule restore_sql_file:
sql_file = "data/external/rapids_example.sql", sql_file = "data/external/rapids_example.sql",
db_credentials = ".env" db_credentials = ".env"
params: params:
group = config["DOWNLOAD_PARTICIPANTS"]["GROUP"] group = config["DATABASE_GROUP"]
output: output:
touch("data/interim/restore_sql_file.done") touch("data/interim/restore_sql_file.done")
script: script:
@ -15,28 +15,40 @@ rule create_example_participant_files:
shell: shell:
"echo 'a748ee1a-1d0b-4ae9-9074-279a2b6ba524\nandroid\ntest01\n2020/04/23,2020/05/04\n' >> ./data/external/example01 && echo '13dbc8a3-dae3-4834-823a-4bc96a7d459d\nios\ntest02\n2020/04/23,2020/05/04\n' >> ./data/external/example02" "echo 'a748ee1a-1d0b-4ae9-9074-279a2b6ba524\nandroid\ntest01\n2020/04/23,2020/05/04\n' >> ./data/external/example01 && echo '13dbc8a3-dae3-4834-823a-4bc96a7d459d\nios\ntest02\n2020/04/23,2020/05/04\n' >> ./data/external/example02"
rule download_participants: # rule download_participants:
params: # params:
group = config["DOWNLOAD_PARTICIPANTS"]["GROUP"], # group = config["DOWNLOAD_PARTICIPANTS"]["GROUP"],
ignored_device_ids = config["DOWNLOAD_PARTICIPANTS"]["IGNORED_DEVICE_IDS"], # ignored_device_ids = config["DOWNLOAD_PARTICIPANTS"]["IGNORED_DEVICE_IDS"],
timezone = config["TIMEZONE"] # timezone = config["TIMEZONE"]
priority: 1 # priority: 1
script: # script:
"../src/data/download_participants.R" # "../src/data/download_participants.R"
rule download_dataset: rule download_phone_data:
input: input:
"data/external/{pid}" "data/external/participant_files/{pid}.yaml"
params: params:
group = config["DOWNLOAD_DATASET"]["GROUP"], source = config["SENSOR_DATA"]["PHONE"]["SOURCE"],
sensor = "{sensor}", sensor = "phone_" + "{sensor}",
table = lambda wildcards: config[str(wildcards.sensor).upper()]["DB_TABLE"], table = lambda wildcards: config["PHONE_" + str(wildcards.sensor).upper()]["TABLE"],
timezone = config["TIMEZONE"], timezone = config["TIMEZONE"],
aware_multiplatform_tables = config["PHONE_ACTIVITY_RECOGNITION"]["DB_TABLE"]["ANDROID"] + "," + config["PHONE_ACTIVITY_RECOGNITION"]["DB_TABLE"]["IOS"] + "," + config["PHONE_CONVERSATION"]["DB_TABLE"]["ANDROID"] + "," + config["PHONE_CONVERSATION"]["DB_TABLE"]["IOS"], aware_multiplatform_tables = config["PHONE_ACTIVITY_RECOGNITION"]["TABLE"]["ANDROID"] + "," + config["PHONE_ACTIVITY_RECOGNITION"]["TABLE"]["IOS"] + "," + config["PHONE_CONVERSATION"]["TABLE"]["ANDROID"] + "," + config["PHONE_CONVERSATION"]["TABLE"]["IOS"],
output: output:
"data/raw/{pid}/{sensor}_raw.csv" "data/raw/{pid}/phone_{sensor}_raw.csv"
script: script:
"../src/data/download_dataset.R" "../src/data/download_phone_data.R"
rule download_fitbit_data:
input:
"data/external/participant_files/{pid}.yaml"
params:
source = config["SENSOR_DATA"]["FITBIT"]["SOURCE"],
sensor = "fitbit_" + "{sensor}",
table = lambda wildcards: config["FITBIT_" + str(wildcards.sensor).upper()]["TABLE"],
output:
"data/raw/{pid}/fitbit_{sensor}_raw.csv"
script:
"../src/data/download_fitbit_data.R"
rule compute_day_segments: rule compute_day_segments:
input: input:
@ -55,8 +67,8 @@ rule phone_readable_datetime:
sensor_input = "data/raw/{pid}/phone_{sensor}_raw.csv", sensor_input = "data/raw/{pid}/phone_{sensor}_raw.csv",
day_segments = "data/interim/day_segments/{pid}_day_segments.csv" day_segments = "data/interim/day_segments/{pid}_day_segments.csv"
params: params:
timezones = None, timezones = config["SENSOR_DATA"]["PHONE"]["TIMEZONE"]["TYPE"],
fixed_timezone = config["READABLE_DATETIME"]["FIXED_TIMEZONE"], fixed_timezone = config["SENSOR_DATA"]["PHONE"]["TIMEZONE"]["VALUE"],
day_segments_type = config["DAY_SEGMENTS"]["TYPE"], day_segments_type = config["DAY_SEGMENTS"]["TYPE"],
include_past_periodic_segments = config["DAY_SEGMENTS"]["INCLUDE_PAST_PERIODIC_SEGMENTS"] include_past_periodic_segments = config["DAY_SEGMENTS"]["INCLUDE_PAST_PERIODIC_SEGMENTS"]
output: output:
@ -97,7 +109,7 @@ rule phone_valid_sensed_days:
rule unify_ios_android: rule unify_ios_android:
input: input:
sensor_data = "data/raw/{pid}/{sensor}_with_datetime.csv", sensor_data = "data/raw/{pid}/{sensor}_with_datetime.csv",
participant_info = "data/external/{pid}" participant_info = "data/external/participant_files/{pid}.yaml"
params: params:
sensor = "{sensor}", sensor = "{sensor}",
output: output:
@ -105,7 +117,7 @@ rule unify_ios_android:
script: script:
"../src/data/unify_ios_android.R" "../src/data/unify_ios_android.R"
rule process_phone_location_types: rule process_phone_locations_types:
input: input:
locations = "data/raw/{pid}/phone_locations_raw.csv", locations = "data/raw/{pid}/phone_locations_raw.csv",
phone_sensed_timestamps = "data/interim/{pid}/phone_sensed_timestamps.csv", phone_sensed_timestamps = "data/interim/{pid}/phone_sensed_timestamps.csv",
@ -118,13 +130,13 @@ rule process_phone_location_types:
script: script:
"../src/data/process_location_types.R" "../src/data/process_location_types.R"
rule readable_datetime_location_processed: rule phone_locations_processed_with_datetime:
input: input:
sensor_input = "data/interim/{pid}/phone_locations_processed.csv", sensor_input = "data/interim/{pid}/phone_locations_processed.csv",
day_segments = "data/interim/day_segments/{pid}_day_segments.csv" day_segments = "data/interim/day_segments/{pid}_day_segments.csv"
params: params:
timezones = None, timezones = config["SENSOR_DATA"]["PHONE"]["TIMEZONE"]["TYPE"],
fixed_timezone = config["READABLE_DATETIME"]["FIXED_TIMEZONE"], fixed_timezone = config["SENSOR_DATA"]["PHONE"]["TIMEZONE"]["VALUE"],
day_segments_type = config["DAY_SEGMENTS"]["TYPE"], day_segments_type = config["DAY_SEGMENTS"]["TYPE"],
include_past_periodic_segments = config["DAY_SEGMENTS"]["INCLUDE_PAST_PERIODIC_SEGMENTS"] include_past_periodic_segments = config["DAY_SEGMENTS"]["INCLUDE_PAST_PERIODIC_SEGMENTS"]
output: output:
@ -132,6 +144,28 @@ rule readable_datetime_location_processed:
script: script:
"../src/data/readable_datetime.R" "../src/data/readable_datetime.R"
rule resample_episodes:
input:
"data/interim/{pid}/{sensor}_episodes.csv"
output:
"data/interim/{pid}/{sensor}_episodes_resampled.csv"
script:
"../src/features/utils/resample_episodes.R"
rule resample_episodes_with_datetime:
input:
sensor_input = "data/interim/{pid}/{sensor}_episodes_resampled.csv",
day_segments = "data/interim/day_segments/{pid}_day_segments.csv"
params:
timezones = config["SENSOR_DATA"]["PHONE"]["TIMEZONE"]["TYPE"],
fixed_timezone = config["SENSOR_DATA"]["PHONE"]["TIMEZONE"]["VALUE"],
day_segments_type = config["DAY_SEGMENTS"]["TYPE"],
include_past_periodic_segments = config["DAY_SEGMENTS"]["INCLUDE_PAST_PERIODIC_SEGMENTS"]
output:
"data/interim/{pid}/{sensor}_episodes_resampled_with_datetime.csv"
script:
"../src/data/readable_datetime.R"
rule phone_application_categories: rule phone_application_categories:
input: input:
"data/raw/{pid}/phone_applications_foreground_with_datetime.csv" "data/raw/{pid}/phone_applications_foreground_with_datetime.csv"
@ -145,37 +179,37 @@ rule phone_application_categories:
script: script:
"../src/data/application_categories.R" "../src/data/application_categories.R"
rule fitbit_heartrate_with_datetime: # rule fitbit_heartrate_with_datetime:
input: # input:
expand("data/raw/{{pid}}/{fitbit_table}_raw.csv", fitbit_table=config["HEARTRATE"]["DB_TABLE"]) # expand("data/raw/{{pid}}/{fitbit_table}_raw.csv", fitbit_table=config["HEARTRATE"]["TABLE"])
params: # params:
local_timezone = config["READABLE_DATETIME"]["FIXED_TIMEZONE"], # local_timezone = config["READABLE_DATETIME"]["FIXED_TIMEZONE"],
fitbit_sensor = "heartrate" # fitbit_sensor = "heartrate"
output: # output:
summary_data = "data/raw/{pid}/fitbit_heartrate_summary_with_datetime.csv", # summary_data = "data/raw/{pid}/fitbit_heartrate_summary_with_datetime.csv",
intraday_data = "data/raw/{pid}/fitbit_heartrate_intraday_with_datetime.csv" # intraday_data = "data/raw/{pid}/fitbit_heartrate_intraday_with_datetime.csv"
script: # script:
"../src/data/fitbit_readable_datetime.py" # "../src/data/fitbit_readable_datetime.py"
rule fitbit_step_with_datetime: # rule fitbit_step_with_datetime:
input: # input:
expand("data/raw/{{pid}}/{fitbit_table}_raw.csv", fitbit_table=config["STEP"]["DB_TABLE"]) # expand("data/raw/{{pid}}/{fitbit_table}_raw.csv", fitbit_table=config["STEP"]["TABLE"])
params: # params:
local_timezone = config["READABLE_DATETIME"]["FIXED_TIMEZONE"], # local_timezone = config["READABLE_DATETIME"]["FIXED_TIMEZONE"],
fitbit_sensor = "steps" # fitbit_sensor = "steps"
output: # output:
intraday_data = "data/raw/{pid}/fitbit_step_intraday_with_datetime.csv" # intraday_data = "data/raw/{pid}/fitbit_step_intraday_with_datetime.csv"
script: # script:
"../src/data/fitbit_readable_datetime.py" # "../src/data/fitbit_readable_datetime.py"
rule fitbit_sleep_with_datetime: # rule fitbit_sleep_with_datetime:
input: # input:
expand("data/raw/{{pid}}/{fitbit_table}_raw.csv", fitbit_table=config["SLEEP"]["DB_TABLE"]) # expand("data/raw/{{pid}}/{fitbit_table}_raw.csv", fitbit_table=config["SLEEP"]["TABLE"])
params: # params:
local_timezone = config["READABLE_DATETIME"]["FIXED_TIMEZONE"], # local_timezone = config["READABLE_DATETIME"]["FIXED_TIMEZONE"],
fitbit_sensor = "sleep" # fitbit_sensor = "sleep"
output: # output:
summary_data = "data/raw/{pid}/fitbit_sleep_summary_with_datetime.csv", # summary_data = "data/raw/{pid}/fitbit_sleep_summary_with_datetime.csv",
intraday_data = "data/raw/{pid}/fitbit_sleep_intraday_with_datetime.csv" # intraday_data = "data/raw/{pid}/fitbit_sleep_intraday_with_datetime.csv"
script: # script:
"../src/data/fitbit_readable_datetime.py" # "../src/data/fitbit_readable_datetime.py"

2
rules/reports.smk
View File

@ -66,7 +66,7 @@ rule overall_compliance_heatmap:
pid_files = expand("data/external/{pid}", pid=config["PIDS"]) pid_files = expand("data/external/{pid}", pid=config["PIDS"])
params: params:
only_show_valid_days = config["OVERALL_COMPLIANCE_HEATMAP"]["ONLY_SHOW_VALID_DAYS"], only_show_valid_days = config["OVERALL_COMPLIANCE_HEATMAP"]["ONLY_SHOW_VALID_DAYS"],
local_timezone = config["READABLE_DATETIME"]["FIXED_TIMEZONE"], local_timezone = config["SENSOR_DATA"]["PHONE"]["TIMEZONE"]["VALUE"],
expected_num_of_days = config["OVERALL_COMPLIANCE_HEATMAP"]["EXPECTED_NUM_OF_DAYS"], expected_num_of_days = config["OVERALL_COMPLIANCE_HEATMAP"]["EXPECTED_NUM_OF_DAYS"],
bin_size = config["OVERALL_COMPLIANCE_HEATMAP"]["BIN_SIZE"], bin_size = config["OVERALL_COMPLIANCE_HEATMAP"]["BIN_SIZE"],
min_bins_per_hour = "{min_valid_bins_per_hour}" min_bins_per_hour = "{min_valid_bins_per_hour}"

40
src/data/download_fitbit_data.R 100644
View File

@ -0,0 +1,40 @@
source("renv/activate.R")
library(RMySQL)
library(dplyr)
library(readr)
library(stringr)
library(yaml)
participant_file <- snakemake@input[[1]]
source <- snakemake@params[["source"]]
sensor <- snakemake@params[["sensor"]]
table <- snakemake@params[["table"]]
sensor_file <- snakemake@output[[1]]
participant <- read_yaml(participant_file)
if(! "FITBIT" %in% names(participant)){
stop(paste("The following participant file does not have a FITBIT section, create one manually or automatically (see the docs):", participant_file))
}
device_ids <- participant$FITBIT$DEVICE_IDS
unified_device_id <- tail(device_ids, 1)
# As opposed to phone data, we dont' filter by date here because data can still be in JSON format, we need to parse it first
if(source$TYPE == "DATABASE"){
dbEngine <- dbConnect(MySQL(), default.file = "./.env", group = source$DATABASE_GROUP)
query <- paste0("SELECT * FROM ", table, " WHERE ",source$DEVICE_ID_COLUMN," IN ('", paste0(device_ids, collapse = "','"), "')")
sensor_data <- dbGetQuery(dbEngine, query)
dbDisconnect(dbEngine)
sensor_data <- sensor_data %>%
rename(device_id = source$DEVICE_ID_COLUMN) %>%
mutate(device_id = unified_device_id) # Unify device_id
if(FALSE) # For MoSHI use, we didn't split fitbit sensors into different tables
sensor_data <- sensor_data %>% filter(fitbit_data_type == str_split(sensor, "_", simplify = TRUE)[[2]])
# Droping duplicates on all columns except for _id or id
sensor_data <- sensor_data %>% distinct(!!!syms(setdiff(names(sensor_data), c("_id", "id"))))
write_csv(sensor_data, sensor_file)
}

56
src/data/download_dataset.R → src/data/download_phone_data.R
View File

@ -4,6 +4,9 @@ library(RMySQL)
library(stringr) library(stringr)
library(dplyr) library(dplyr)
library(readr) library(readr)
library(yaml)
library(lubridate)
options(scipen=999)
validate_deviceid_platforms <- function(device_ids, platforms){ validate_deviceid_platforms <- function(device_ids, platforms){
if(length(device_ids) == 1){ if(length(device_ids) == 1){
@ -37,38 +40,57 @@ is_multiplaform_participant <- function(dbEngine, device_ids, platforms){
return(FALSE) return(FALSE)
} }
participant <- snakemake@input[[1]] get_timestamp_filter <- function(device_ids, participant, timezone){
group <- snakemake@params[["group"]] # Read start and end date from the participant file to filter data within that range
start_date <- ymd_hms(paste(participant$PHONE$START_DATE,"00:00:00"), tz=timezone, quiet=TRUE)
end_date <- ymd_hms(paste(participant$PHONE$END_DATE, "23:59:59"), tz=timezone, quiet=TRUE)
start_timestamp = as.numeric(start_date) * 1000
end_timestamp = as.numeric(end_date) * 1000
if(is.na(start_timestamp)){
message(paste("PHONE[START_DATE] was not provided or failed to parse (", participant$PHONE$START_DATE,"), all data for", paste0(device_ids, collapse=","),"is returned"))
return("")
}else if(is.na(end_timestamp)){
message(paste("PHONE[END_DATE] was not provided or failed to parse (", participant$PHONE$END_DATE,"), all data for", paste0(device_ids, collapse=","),"is returned"))
return("")
} else if(start_timestamp > end_timestamp){
stop(paste("Start date has to be before end date in PHONE[TIME_SPAN] (",start_date,",", date(end_date),"), all data for", paste0(device_ids, collapse=","),"is returned"))
return("")
} else {
message(paste("Filtering data between", start_date, "and", end_date, "in", timezone, "for",paste0(device_ids, collapse=",")))
return(paste0("AND timestamp BETWEEN ", start_timestamp, " AND ", end_timestamp))
}
}
participant_file <- snakemake@input[[1]]
source <- snakemake@params[["source"]]
group <- source$DATABASE_GROUP
table <- snakemake@params[["table"]] table <- snakemake@params[["table"]]
sensor <- snakemake@params[["sensor"]] sensor <- snakemake@params[["sensor"]]
timezone <- snakemake@params[["timezone"]] timezone <- snakemake@params[["timezone"]]
aware_multiplatform_tables <- str_split(snakemake@params[["aware_multiplatform_tables"]], ",")[[1]] aware_multiplatform_tables <- str_split(snakemake@params[["aware_multiplatform_tables"]], ",")[[1]]
sensor_file <- snakemake@output[[1]] sensor_file <- snakemake@output[[1]]
device_ids <- strsplit(readLines(participant, n=1), ",")[[1]] participant <- read_yaml(participant_file)
if(! "PHONE" %in% names(participant)){
stop(paste("The following participant file does not have a PHONE section, create one manually or automatically (see the docs):", participant_file))
}
device_ids <- participant$PHONE$DEVICE_IDS
unified_device_id <- tail(device_ids, 1) unified_device_id <- tail(device_ids, 1)
platforms <- strsplit(readLines(participant, n=2)[[2]], ",")[[1]] platforms <- participant$PHONE$PLATFORMS
validate_deviceid_platforms(device_ids, platforms) validate_deviceid_platforms(device_ids, platforms)
timestamp_filter <- get_timestamp_filter(device_ids, participant, timezone)
# Read start and end date from the participant file to filter data within that range
start_date <- strsplit(readLines(participant, n=4)[4], ",")[[1]][1]
end_date <- strsplit(readLines(participant, n=4)[4], ",")[[1]][2]
start_datetime_utc = format(as.POSIXct(paste0(start_date, " 00:00:00"),format="%Y/%m/%d %H:%M:%S",origin="1970-01-01",tz=timezone), tz="UTC")
end_datetime_utc = format(as.POSIXct(paste0(end_date, " 23:59:59"),format="%Y/%m/%d %H:%M:%S",origin="1970-01-01",tz=timezone), tz="UTC")
dbEngine <- dbConnect(MySQL(), default.file = "./.env", group = group) dbEngine <- dbConnect(MySQL(), default.file = "./.env", group = group)
if(is_multiplaform_participant(dbEngine, device_ids, platforms)){ if(is_multiplaform_participant(dbEngine, device_ids, platforms)){
sensor_data <- unify_raw_data(dbEngine, table, sensor, start_datetime_utc, end_datetime_utc, aware_multiplatform_tables, device_ids, platforms) sensor_data <- unify_raw_data(dbEngine, table, sensor, timestamp_filter, aware_multiplatform_tables, device_ids, platforms)
}else { }else {
# table has two elements for conversation and activity recognition (they store data on a different table for ios and android) # table has two elements for conversation and activity recognition (they store data on a different table for ios and android)
if(length(table) > 1){ if(length(table) > 1)
table <- table[[toupper(platforms[1])]] table <- table[[toupper(platforms[1])]]
} query <- paste0("SELECT * FROM ", table, " WHERE ",source$DEVICE_ID_COLUMN," IN ('", paste0(device_ids, collapse = "','"), "')", timestamp_filter)
query <- paste0("SELECT * FROM ", table, " WHERE device_id IN ('", paste0(device_ids, collapse = "','"), "')") sensor_data <- dbGetQuery(dbEngine, query) %>%
if(!(is.na(start_datetime_utc)) && !(is.na(end_datetime_utc)) && start_datetime_utc < end_datetime_utc) rename(device_id = source$DEVICE_ID_COLUMN)
query <- paste0(query, "AND timestamp BETWEEN 1000*UNIX_TIMESTAMP('", start_datetime_utc, "') AND 1000*UNIX_TIMESTAMP('", end_datetime_utc, "')")
sensor_data <- dbGetQuery(dbEngine, query)
} }
sensor_data <- sensor_data %>% arrange(timestamp) sensor_data <- sensor_data %>% arrange(timestamp)

4
src/data/unify_ios_android.R
View File

@ -1,11 +1,13 @@
source("renv/activate.R") source("renv/activate.R")
source("src/data/unify_utils.R") source("src/data/unify_utils.R")
library(yaml)
sensor_data <- read.csv(snakemake@input[["sensor_data"]], stringsAsFactors = FALSE) sensor_data <- read.csv(snakemake@input[["sensor_data"]], stringsAsFactors = FALSE)
participant_info <- snakemake@input[["participant_info"]] participant_info <- snakemake@input[["participant_info"]]
sensor <- snakemake@params[["sensor"]] sensor <- snakemake@params[["sensor"]]
platforms <- strsplit(readLines(participant_info, n=2)[[2]], ",")[[1]] participant <- read_yaml(participant_info)
platforms <- participant$PHONE$PLATFORMS
platform <- ifelse(platforms[1] == "multiple" | (length(platforms) > 1 & "android" %in% platforms & "ios" %in% platforms), "android", platforms[1]) platform <- ifelse(platforms[1] == "multiple" | (length(platforms) > 1 & "android" %in% platforms & "ios" %in% platforms), "android", platforms[1])
sensor_data <- unify_data(sensor_data, sensor, platform) sensor_data <- unify_data(sensor_data, sensor, platform)

7
src/data/unify_utils.R
View File

@ -138,7 +138,7 @@ unify_ios_conversation <- function(conversation){
} }
# This function is used in download_dataset.R # This function is used in download_dataset.R
unify_raw_data <- function(dbEngine, sensor_table, sensor, start_datetime_utc, end_datetime_utc, aware_multiplatform_tables, device_ids, platforms){ unify_raw_data <- function(dbEngine, sensor_table, sensor, timestamp_filter, aware_multiplatform_tables, device_ids, platforms){
# If platforms is 'multiple', fetch each device_id's platform from aware_device, otherwise, use those given by the user # If platforms is 'multiple', fetch each device_id's platform from aware_device, otherwise, use those given by the user
if(length(platforms) == 1 && platforms == "multiple") if(length(platforms) == 1 && platforms == "multiple")
devices_platforms <- dbGetQuery(dbEngine, paste0("SELECT device_id,brand FROM aware_device WHERE device_id IN ('", paste0(device_ids, collapse = "','"), "')")) %>% devices_platforms <- dbGetQuery(dbEngine, paste0("SELECT device_id,brand FROM aware_device WHERE device_id IN ('", paste0(device_ids, collapse = "','"), "')")) %>%
@ -169,10 +169,7 @@ unify_raw_data <- function(dbEngine, sensor_table, sensor, start_datetime_utc, e
table <- conversation_tables[[platform]] table <- conversation_tables[[platform]]
if(table %in% available_tables_in_db){ if(table %in% available_tables_in_db){
query <- paste0("SELECT * FROM ", table, " WHERE device_id IN ('", device_id, "')") query <- paste0("SELECT * FROM ", table, " WHERE device_id IN ('", device_id, "')", timestamp_filter)
if(!(is.na(start_datetime_utc)) && !(is.na(end_datetime_utc)) && start_datetime_utc < end_datetime_utc){
query <- paste0(query, "AND timestamp BETWEEN 1000*UNIX_TIMESTAMP('", start_datetime_utc, "') AND 1000*UNIX_TIMESTAMP('", end_datetime_utc, "')")
}
sensor_data <- unify_data(dbGetQuery(dbEngine, query), sensor, platform) sensor_data <- unify_data(dbGetQuery(dbEngine, query), sensor, platform)
participants_sensordata <- append(participants_sensordata, list(sensor_data)) participants_sensordata <- append(participants_sensordata, list(sensor_data))
}else{ }else{

37
tools/update_format_participant_files.py 100644
View File

@ -0,0 +1,37 @@
#!/usr/bin/python
from pathlib import Path
import yaml, os
import sys
p = Path(r'data/external/').glob('*')
files = [x for x in p if x.is_file() and x.suffix == "" and "." not in x.stem]
for file in files:
reader = open(file, 'r')
phone = {"DEVICES_IDS" :"", "PLATFORMS" :"", "LABEL" :"", "START_DATE" :"", "END_DATE" :""}
lines = reader.read().splitlines()
if(len(lines) >=1 and len(lines[0]) > 0):
phone["DEVICE_IDS"] = lines[0]
if(len(lines) >=2 and len(lines[1]) > 0):
phone["PLATFORMS"] = lines[1]
if(len(lines) >=3 and len(lines[2]) > 0):
phone["LABEL"] = lines[2]
if(len(lines) >=4 and len(lines[3]) > 0):
phone["START_DATE"] = lines[3].split(",")[0]
phone["END_DATE"] = lines[3].split(",")[1]
new_participant_file = Path(r'data/external/participant_files/') / (file.stem + ".yaml")
os.makedirs(os.path.dirname(new_participant_file), exist_ok=True)
with open(new_participant_file, 'w') as writer:
writer.write("PHONE:\n")
writer.write(" DEVICE_IDS: [{}]\n".format(phone["DEVICE_IDS"]))
writer.write(" PLATFORMS: [{}]\n".format(phone["PLATFORMS"]))
writer.write(" LABEL: {}\n".format(phone["LABEL"]))
writer.write(" START_DATE: {}\n".format(phone["START_DATE"]))
writer.write(" END_DATE: {}\n".format(phone["END_DATE"]))
writer.write("FITBIT:\n")
writer.write(" DEVICE_IDS: [{}]\n".format(phone["DEVICE_IDS"]))
writer.write(" LABEL: {}\n".format(phone["LABEL"]))
writer.write(" START_DATE: {}\n".format(phone["START_DATE"]))
writer.write(" END_DATE: {}\n".format(phone["END_DATE"]))
print("Processed files:")
print(list(map(str, files)))