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Implement AR features for iOS 

Co-authored-by: JulioV <juliovhz@gmail.com>
pull/95/head
Meng Li 2020-04-20 18:05:54 -04:00
parent 77d41639d8
commit 490599c742
6 changed files with 81 additions and 16 deletions
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4
Snakefile
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@ -42,8 +42,8 @@ rule all:
expand("data/processed/{pid}/bluetooth_{segment}.csv",
pid=config["PIDS"],
segment = config["BLUETOOTH"]["DAY_SEGMENTS"]),
expand("data/processed/{pid}/google_activity_recognition_{segment}.csv",pid=config["PIDS"],
segment = config["GOOGLE_ACTIVITY_RECOGNITION"]["DAY_SEGMENTS"]),
expand("data/processed/{pid}/activity_recognition_{segment}.csv",pid=config["PIDS"],
segment = config["ACTIVITY_RECOGNITION"]["DAY_SEGMENTS"]),
expand("data/processed/{pid}/battery_{day_segment}.csv",
pid = config["PIDS"],
day_segment = config["BATTERY"]["DAY_SEGMENTS"]),

6
config.yaml
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@ -1,5 +1,5 @@
# Valid database table names
SENSORS: [applications_crashes, applications_foreground, applications_notifications, battery, bluetooth, calls, locations, messages, plugin_ambient_noise, plugin_device_usage, plugin_google_activity_recognition, screen]
SENSORS: [applications_crashes, applications_foreground, applications_notifications, battery, bluetooth, calls, locations, messages, plugin_ambient_noise, plugin_device_usage, plugin_google_activity_recognition, plugin_ios_activity_recognition, screen]
FITBIT_TABLE: [fitbit_data]
FITBIT_SENSORS: [heartrate, steps, sleep, calories]
@ -78,7 +78,7 @@ BLUETOOTH:
DAY_SEGMENTS: *day_segments
FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
GOOGLE_ACTIVITY_RECOGNITION:
ACTIVITY_RECOGNITION:
DAY_SEGMENTS: *day_segments
FEATURES: ['count','mostcommonactivity','countuniqueactivities','activitychangecount','sumstationary','summobile','sumvehicle']
@ -132,7 +132,7 @@ PARAMS_FOR_ANALYSIS:
GROUNDTRUTH_TABLE: participant_info
SOURCES: &sources ["phone_features", "fitbit_features", "phone_fitbit_features"]
DAY_SEGMENTS: *day_segments
PHONE_FEATURES: [accelerometer, applications_foreground, battery, call_incoming, call_missed, call_outgoing, google_activity_recognition, light, location_barnett, screen, sms_received, sms_sent]
PHONE_FEATURES: [accelerometer, applications_foreground, battery, call_incoming, call_missed, call_outgoing, activity_recognition, light, location_barnett, screen, sms_received, sms_sent]
FITBIT_FEATURES: [fitbit_heartrate, fitbit_step]
PHONE_FITBIT_FEATURES: "" # This array is merged in the input_merge_features_of_single_participant function in models.snakefile
DEMOGRAPHIC_FEATURES: [age, gender, inpatientdays]

32
rules/features.snakefile
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@ -1,3 +1,14 @@
def optional_ar_input(wildcards):
with open("data/external/"+wildcards.pid, encoding="ISO-8859-1") as external_file:
external_file_content = external_file.readlines()
platform = external_file_content[1].strip()
if platform == "android":
return ["data/raw/{pid}/plugin_google_activity_recognition_with_datetime_unified.csv",
"data/processed/{pid}/plugin_google_activity_recognition_deltas.csv"]
else:
return ["data/raw/{pid}/plugin_ios_activity_recognition_with_datetime_unified.csv",
"data/processed/{pid}/plugin_ios_activity_recognition_deltas.csv"]
rule sms_features:
input:
"data/raw/{pid}/messages_with_datetime.csv"
@ -41,11 +52,19 @@ rule screen_deltas:
rule google_activity_recognition_deltas:
input:
"data/raw/{pid}/plugin_google_activity_recognition_with_datetime.csv"
"data/raw/{pid}/plugin_google_activity_recognition_with_datetime_unified.csv"
output:
"data/processed/{pid}/plugin_google_activity_recognition_deltas.csv"
script:
"../src/features/google_activity_recognition_deltas.R"
"../src/features/activity_recognition_deltas.R"
rule ios_activity_recognition_deltas:
input:
"data/raw/{pid}/plugin_ios_activity_recognition_with_datetime_unified.csv"
output:
"data/processed/{pid}/plugin_ios_activity_recognition_deltas.csv"
script:
"../src/features/activity_recognition_deltas.R"
rule location_barnett_features:
input:
@ -75,15 +94,14 @@ rule bluetooth_features:
rule activity_features:
input:
gar_events = "data/raw/{pid}/plugin_google_activity_recognition_with_datetime.csv",
gar_deltas = "data/processed/{pid}/plugin_google_activity_recognition_deltas.csv"
optional_ar_input
params:
segment = "{day_segment}",
features = config["GOOGLE_ACTIVITY_RECOGNITION"]["FEATURES"]
features = config["ACTIVITY_RECOGNITION"]["FEATURES"]
output:
"data/processed/{pid}/google_activity_recognition_{day_segment}.csv"
"data/processed/{pid}/activity_recognition_{day_segment}.csv"
script:
"../src/features/google_activity_recognition.py"
"../src/features/activity_recognition.py"
rule battery_features:
input:

47
src/data/unify_ios_android.R
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@ -1,6 +1,7 @@
source("packrat/init.R")
library(dplyr)
library(stringr)
unify_ios_battery <- function(ios_battery){
# We only need to unify battery data for iOS client V1. V2 does it out-of-the-box
@ -64,6 +65,50 @@ unify_ios_calls <- function(ios_calls){
return(ios_calls)
}
clean_ios_activity_column <- function(ios_gar){
ios_gar <- ios_gar %>%
mutate(activities = str_replace_all(activities, pattern = '("|\\[|\\])', replacement = ""))
existent_multiple_activities <- ios_gar %>%
filter(str_detect(activities, ",")) %>%
group_by(activities) %>%
summarise(mutiple_activities = unique(activities)) %>%
pull(mutiple_activities)
known_multiple_activities <- c("stationary,automotive")
unkown_multiple_actvities <- setdiff(existent_multiple_activities, known_multiple_activities)
if(length(unkown_multiple_actvities) > 0){
stop(paste0("There are unkwown combinations of ios activities, you need to implement the decision of the ones to keep: ", unkown_multiple_actvities))
}
ios_gar <- ios_gar %>%
mutate(activities = str_replace_all(activities, pattern = "stationary,automotive", replacement = "automotive"))
return(ios_gar)
}
unify_ios_gar <- function(ios_gar){
# We only need to unify Google Activity Recognition data for iOS
# discard rows where activities column is blank
ios_gar <- ios_gar[-which(ios_gar$activities == ""), ]
# clean "activities" column of ios_gar
ios_gar <- clean_ios_activity_column(ios_gar)
# make it compatible with android version: generate "activity_name" and "activity_type" columns
ios_gar <- ios_gar %>%
mutate(activity_name = case_when(activities == "automotive" ~ "in_vehicle",
activities == "cycling" ~ "on_bicycle",
activities == "walking" | activities == "running" ~ "on_foot",
activities == "stationary" ~ "still"),
activity_type = case_when(activities == "automotive" ~ 0,
activities == "cycling" ~ 1,
activities == "walking" | activities == "running" ~ 2,
activities == "stationary" ~ 3,
activities == "unknown" ~ 4))
return(ios_gar)
}
sensor_data <- read.csv(snakemake@input[["sensor_data"]], stringsAsFactors = FALSE)
participant_info <- snakemake@input[["participant_info"]]
@ -80,5 +125,7 @@ if(sensor == "calls"){
sensor_data = unify_ios_battery(sensor_data)
}
# android battery remains unchanged
} else if(sensor == "plugin_ios_activity_recognition"){
sensor_data = unify_ios_gar(sensor_data)
}
write.csv(sensor_data, snakemake@output[[1]], row.names = FALSE)

4
src/features/google_activity_recognition.py → src/features/activity_recognition.py
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@ -7,8 +7,8 @@ day_segment = snakemake.params["segment"]
features = snakemake.params["features"]
#Read csv into a pandas dataframe
data = pd.read_csv(snakemake.input['gar_events'],parse_dates=['local_date_time'])
ar_deltas = pd.read_csv(snakemake.input['gar_deltas'],parse_dates=["local_start_date_time", "local_end_date_time", "local_start_date", "local_end_date"])
data = pd.read_csv(snakemake.input[0],parse_dates=["local_date_time"])
ar_deltas = pd.read_csv(snakemake.input[1],parse_dates=["local_start_date_time", "local_end_date_time", "local_start_date", "local_end_date"])
columns = list("ar_" + str(day_segment) + "_" + column for column in features)
if data.empty:

0
src/features/google_activity_recognition_deltas.R → src/features/activity_recognition_deltas.R
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