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Migrate wifi to new file structure

pull/103/head
JulioV 2020-08-31 18:51:06 -04:00
parent 77d9d8f025
commit eda58d9d2c
9 changed files with 109 additions and 38 deletions
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24
Snakefile
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@ -99,16 +99,20 @@ if config["APPLICATIONS_FOREGROUND"]["COMPUTE"]:
files_to_compute.extend(expand("data/interim/{pid}/{sensor}_with_datetime_with_genre.csv", pid=config["PIDS"], sensor=config["APPLICATIONS_FOREGROUND"]["DB_TABLE"]))
files_to_compute.extend(expand("data/processed/{pid}/applications_foreground_{day_segment}.csv", pid = config["PIDS"], day_segment = config["APPLICATIONS_FOREGROUND"]["DAY_SEGMENTS"]))
if config["WIFI"]["COMPUTE"]:
if len(config["WIFI"]["DB_TABLE"]["VISIBLE_ACCESS_POINTS"]) > 0:
files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["WIFI"]["DB_TABLE"]["VISIBLE_ACCESS_POINTS"]))
files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["WIFI"]["DB_TABLE"]["VISIBLE_ACCESS_POINTS"]))
files_to_compute.extend(expand("data/processed/{pid}/wifi_{day_segment}.csv", pid = config["PIDS"], day_segment = config["WIFI"]["DAY_SEGMENTS"]))
if len(config["WIFI"]["DB_TABLE"]["CONNECTED_ACCESS_POINTS"]) > 0:
files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["WIFI"]["DB_TABLE"]["CONNECTED_ACCESS_POINTS"]))
files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["WIFI"]["DB_TABLE"]["CONNECTED_ACCESS_POINTS"]))
files_to_compute.extend(expand("data/processed/{pid}/wifi_{day_segment}.csv", pid = config["PIDS"], day_segment = config["WIFI"]["DAY_SEGMENTS"]))
for provider in config["WIFI"]["PROVIDERS"].keys():
if config["WIFI"]["PROVIDERS"][provider]["COMPUTE"]:
if len(config["WIFI"]["DB_TABLE"]["VISIBLE_ACCESS_POINTS"]) > 0:
files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["WIFI"]["DB_TABLE"]["VISIBLE_ACCESS_POINTS"]))
files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["WIFI"]["DB_TABLE"]["VISIBLE_ACCESS_POINTS"]))
files_to_compute.extend(expand("data/raw/{pid}/{sensor_key}_with_datetime_visibleandconnected.csv", pid=config["PIDS"], sensor_key="WIFI".lower()))
files_to_compute.extend(expand("data/interim/{pid}/{sensor_key}_features/{sensor_key}_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["WIFI"]["PROVIDERS"][provider]["SRC_LANGUAGE"], provider_key=provider, sensor_key="WIFI".lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/{sensor_key}.csv", pid=config["PIDS"], sensor_key="WIFI".lower()))
if len(config["WIFI"]["DB_TABLE"]["CONNECTED_ACCESS_POINTS"]) > 0:
files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["WIFI"]["DB_TABLE"]["CONNECTED_ACCESS_POINTS"]))
files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["WIFI"]["DB_TABLE"]["CONNECTED_ACCESS_POINTS"]))
files_to_compute.extend(expand("data/raw/{pid}/{sensor_key}_with_datetime_visibleandconnected.csv", pid=config["PIDS"], sensor_key="WIFI".lower()))
files_to_compute.extend(expand("data/interim/{pid}/{sensor_key}_features/{sensor_key}_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["WIFI"]["PROVIDERS"][provider]["SRC_LANGUAGE"], provider_key=provider, sensor_key="WIFI".lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/{sensor_key}.csv", pid=config["PIDS"], sensor_key="WIFI".lower()))
if config["HEARTRATE"]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["HEARTRATE"]["DB_TABLE"]))

10
config.yaml
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@ -106,7 +106,6 @@ BLUETOOTH:
PROVIDERS:
RAPIDS:
COMPUTE: False
DAY_SEGMENTS: *day_segments
FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
SRC_FOLDER: "rapids" # inside src/features/bluetooth
SRC_LANGUAGE: "r"
@ -197,12 +196,15 @@ SLEEP:
SUMMARY_FEATURES: ["sumdurationafterwakeup", "sumdurationasleep", "sumdurationawake", "sumdurationtofallasleep", "sumdurationinbed", "avgefficiency", "countepisode"]
WIFI:
COMPUTE: False
DB_TABLE:
VISIBLE_ACCESS_POINTS: "wifi" # if you only have a CONNECTED_ACCESS_POINTS table, set this value to ""
CONNECTED_ACCESS_POINTS: "sensor_wifi" # if you only have a VISIBLE_ACCESS_POINTS table, set this value to ""
DAY_SEGMENTS: *day_segments
FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
PROVIDERS:
RAPIDS:
COMPUTE: False
FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
SRC_FOLDER: "rapids" # inside src/features/bluetooth
SRC_LANGUAGE: "r"
CONVERSATION:
COMPUTE: False

27
rules/features.smk
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@ -227,16 +227,29 @@ rule applications_foreground_features:
script:
"../src/features/applications_foreground_features.py"
rule wifi_features:
input:
expand("data/raw/{{pid}}/{sensor}_with_datetime.csv", sensor=config["WIFI"]["DB_TABLE"]),
day_segments = expand("data/interim/{sensor}_day_segments.csv", sensor=config["WIFI"]["DB_TABLE"])
rule wifi_r_features:
input:
sensor_data = expand("data/raw/{{pid}}/{sensor_key}_with_datetime_visibleandconnected.csv", sensor_key="WIFI".lower()),
day_segments_labels = "data/interim/day_segments_labels.csv"
params:
features = config["WIFI"]["FEATURES"]
provider = lambda wildcards: config["WIFI"]["PROVIDERS"][wildcards.provider_key],
provider_key = "{provider_key}"
output:
"data/processed/{pid}/wifi_features.csv"
"data/interim/{pid}/wifi_features/wifi_r_{provider_key}.csv"
script:
"../src/features/wifi_features.R"
"../src/features/wifi/wifi_entry.R"
rule wifi_python_features:
input:
sensor_data = expand("data/raw/{{pid}}/{sensor_key}_with_datetime_visibleandconnected.csv", sensor_key="WIFI".lower()),
day_segments_labels = "data/interim/day_segments_labels.csv"
params:
provider = lambda wildcards: config["WIFI"]["PROVIDERS"][wildcards.provider_key],
provider_key = "{provider_key}"
output:
"data/interim/{pid}/wifi_features/wifi_python_{provider_key}.csv"
script:
"../src/features/wifi/wifi_entry.py"
rule fitbit_heartrate_features:
input:

8
rules/preprocessing.smk
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@ -172,3 +172,11 @@ rule fitbit_sleep_with_datetime:
intraday_data = "data/raw/{pid}/fitbit_sleep_intraday_with_datetime.csv"
script:
"../src/data/fitbit_readable_datetime.py"
rule join_wifi_tables:
input:
unpack(optional_wifi_input)
output:
"data/raw/{pid}/wifi_with_datetime_visibleandconnected.csv"
script:
"../src/data/join_visible_and_connected_wifi.R"

18
src/data/join_visible_and_connected_wifi.R 100644
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@ -0,0 +1,18 @@
source("renv/activate.R")
library("dplyr")
if(!is.null(snakemake@input[["visible_access_points"]]) && is.null(snakemake@input[["connected_access_points"]])){
wifi_data <- read.csv(snakemake@input[["visible_access_points"]], stringsAsFactors = FALSE)
wifi_data <- wifi_data %>% mutate(connected = 0)
} else if(is.null(snakemake@input[["visible_access_points"]]) && !is.null(snakemake@input[["connected_access_points"]])){
wifi_data <- read.csv(snakemake@input[["connected_access_points"]], stringsAsFactors = FALSE)
wifi_data <- wifi_data %>% mutate(connected = 1)
} else if(!is.null(snakemake@input[["visible_access_points"]]) && !is.null(snakemake@input[["connected_access_points"]])){
visible_access_points <- read.csv(snakemake@input[["visible_access_points"]], stringsAsFactors = FALSE)
visible_access_points <- visible_access_points %>% mutate(connected = 0)
connected_access_points <- read.csv(snakemake@input[["connected_access_points"]], stringsAsFactors = FALSE)
connected_access_points <- connected_access_points %>% mutate(connected = 1)
wifi_data <- bind_rows(visible_access_points, connected_access_points) %>% arrange(timestamp)
}
write.csv(wifi_data, snakemake@output[[1]], row.names = FALSE)

2
src/features/utils/utils.R
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@ -20,7 +20,7 @@ fetch_provider_features <- function(provider, provider_key, config_key, sensor_d
day_segments_labels <- read.csv(day_segments_file, stringsAsFactors = FALSE)
if(!"FEATURES" %in% names(provider))
stop(paste0("Provider config[CALLS][PROVIDERS][", provider_key,"] is missing a FEATURES attribute in config.yaml"))
stop(paste0("Provider config[", config_key,"][PROVIDERS][", provider_key,"] is missing a FEATURES attribute in config.yaml"))
if(provider[["COMPUTE"]] == TRUE){
code_path <- paste0("src/features/", config_key,"/", provider[["SRC_FOLDER"]], "/main.R")

27
src/features/wifi/wifi_base.R → src/features/wifi/rapids/main.R
View File

@ -1,18 +1,12 @@
library(dplyr)
filter_by_day_segment <- function(data, day_segment) {
if(day_segment != "daily")
data <- data %>% filter(local_day_segment == day_segment)
return(data %>% group_by(local_date))
}
compute_wifi_feature <- function(data, feature, day_segment){
data <- data %>% filter_by_day_segment(day_segment)
data <- data %>% filter_data_by_segment(day_segment)
if(feature %in% c("countscans", "uniquedevices")){
data <- data %>% group_by(local_segment)
data <- switch(feature,
"countscans" = data %>% summarise(!!paste("wifi", day_segment, feature, sep = "_") := n()),
"uniquedevices" = data %>% summarise(!!paste("wifi", day_segment, feature, sep = "_") := n_distinct(bssid)))
"countscans" = data %>% summarise(!!paste("wifi_rapids", feature, sep = "_") := n()),
"uniquedevices" = data %>% summarise(!!paste("wifi_rapids", feature, sep = "_") := n_distinct(bssid)))
return(data)
} else if(feature == "countscansmostuniquedevice"){
# Get the most scanned device
@ -25,15 +19,16 @@ compute_wifi_feature <- function(data, feature, day_segment){
pull(bssid)
return(data %>%
filter(bssid == mostuniquedevice) %>%
group_by(local_date) %>%
summarise(!!paste("wifi", day_segment, feature, sep = "_") := n()) %>%
group_by(local_segment) %>%
summarise(!!paste("wifi_rapids", feature, sep = "_") := n()) %>%
replace(is.na(.), 0))
}
}
base_wifi_features <- function(wifi_data, day_segment, requested_features){
rapids_features <- function(wifi_data, day_segment, provider){
requested_features <- provider[["FEATURES"]]
# Output dataframe
features = data.frame(local_date = character(), stringsAsFactors = FALSE)
features = data.frame(local_segment = character(), stringsAsFactors = FALSE)
# The name of the features this function can compute
base_features_names <- c("countscans", "uniquedevices", "countscansmostuniquedevice")
@ -42,8 +37,8 @@ base_wifi_features <- function(wifi_data, day_segment, requested_features){
features_to_compute <- intersect(base_features_names, requested_features)
for(feature_name in features_to_compute){
feature <- compute_wifi_feature(wifi_data, feature_name, day_segment)
features <- merge(features, feature, by="local_date", all = TRUE)
feature <- compute_wifi_feature(wifi_data, feature_name, day_segment)
features <- merge(features, feature, by="local_segment", all = TRUE)
}
return(features)

13
src/features/wifi/wifi_entry.R 100644
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@ -0,0 +1,13 @@
source("renv/activate.R")
source("src/features/utils/utils.R")
library("dplyr")
library("tidyr")
sensor_data_file <- snakemake@input[["sensor_data"]]
day_segments_file <- snakemake@input[["day_segments_labels"]]
provider <- snakemake@params["provider"][["provider"]]
provider_key <- snakemake@params["provider_key"]
sensor_features <- fetch_provider_features(provider, provider_key, "wifi", sensor_data_file, day_segments_file)
write.csv(sensor_features, snakemake@output[[1]], row.names = FALSE)

18
src/features/wifi/wifi_entry.py 100644
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@ -0,0 +1,18 @@
import pandas as pd
from importlib import import_module, util
from pathlib import Path
# import fetch_provider_features from src/features/utils/utils.py
spec = util.spec_from_file_location("util", str(Path(snakemake.scriptdir).parent / "utils" / "utils.py"))
mod = util.module_from_spec(spec)
spec.loader.exec_module(mod)
fetch_provider_features = getattr(mod, "fetch_provider_features")
sensor_data_file = snakemake.input["sensor_data"][0]
day_segments_file = snakemake.input["day_segments_labels"]
provider = snakemake.params["provider"]
provider_key = snakemake.params["provider_key"]
sensor_features = fetch_provider_features(provider, provider_key, "wifi", sensor_data_file, day_segments_file)
sensor_features.to_csv(snakemake.output[0], index=False)