Added Light Bugfix, testing and testcase docs

docs/develop/test_cases.rst

@@ -72,3 +72,10 @@ WIFI
     - An option of 5 access point devices is randomly distributed throughout the data records.
     - There is one raw WIFI data file each, for testing both iOS and Android data formats.
     - There is also an additional empty data file for both android and iOS for testing empty data files.
+
+Light
+"""""""
+
+    - The raw light data file contains data for 1 day. 
+    - The raw light data contains 3 or 4 rows of data for each ``epoch`` except ``night``. The single row of data for ``night`` is for testing features for single values inputs. (Example testing the standard deviation of one input value)
+    - Since light is only available for Android there is only one file that constains data for Android. All other files (i.e. for iPhone) are empty data files.

src/features/light/light_base.py

@@ -1,4 +1,5 @@
 import pandas as pd
+import numpy as np
 
 def base_light_features(light_data, day_segment, requested_features):
     # name of the features this function can compute
@@ -26,7 +27,7 @@ def base_light_features(light_data, day_segment, requested_features):
             if "medianlux" in features_to_compute:
                 light_features["light_" + day_segment + "_medianlux"] = light_data.groupby(["local_date"])["double_light_lux"].median()
             if "stdlux" in features_to_compute:
-                light_features["light_" + day_segment + "_stdlux"] = light_data.groupby(["local_date"])["double_light_lux"].std()
+                light_features["light_" + day_segment + "_stdlux"] = light_data.groupby(["local_date"])["double_light_lux"].std().fillna('NA')
             
             light_features = light_features.reset_index()
 

tests/Snakefile

@@ -47,6 +47,11 @@ if config["WIFI"]["COMPUTE"]:
     files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["WIFI"]["DB_TABLE"]))
     files_to_compute.extend(expand("data/processed/{pid}/wifi_{day_segment}.csv", pid = config["PIDS"], day_segment = config["WIFI"]["DAY_SEGMENTS"]))
 
+if config["LIGHT"]["COMPUTE"]:
+    files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["LIGHT"]["DB_TABLE"]))
+    files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["LIGHT"]["DB_TABLE"]))
+    files_to_compute.extend(expand("data/processed/{pid}/light_{day_segment}.csv", pid = config["PIDS"], day_segment = config["LIGHT"]["DAY_SEGMENTS"]))
+
 rule all:
     input:
         files_to_compute

tests/data/processed/test01/light_afternoon.csv

@@ -0,0 +1,2 @@
+local_date,light_afternoon_count,light_afternoon_maxlux,light_afternoon_minlux,light_afternoon_avglux,light_afternoon_medianlux,light_afternoon_stdlux
+2020-07-04,4,97656.0,10351.0,55761.5,57519.5,44778.68551368311

tests/data/processed/test01/light_daily.csv

@@ -0,0 +1,2 @@
+local_date,light_daily_count,light_daily_maxlux,light_daily_minlux,light_daily_avglux,light_daily_medianlux,light_daily_stdlux
+2020-07-04,12,114615.0,0.065,40207.89508333333,19836.0,44686.69422566498

tests/data/processed/test01/light_evening.csv

@@ -0,0 +1,2 @@
+local_date,light_evening_count,light_evening_maxlux,light_evening_minlux,light_evening_avglux,light_evening_medianlux,light_evening_stdlux
+2020-07-04,3,15258.0,84.156,5603.718666666667,1469.0,8389.476102441995

tests/data/processed/test01/light_morning.csv

@@ -0,0 +1,2 @@
+local_date,light_morning_count,light_morning_maxlux,light_morning_minlux,light_morning_avglux,light_morning_medianlux,light_morning_stdlux
+2020-07-04,4,114615.0,472.52,60659.38,63775.0,51510.58234386665

tests/data/processed/test01/light_night.csv

@@ -0,0 +1,2 @@
+local_date,light_night_count,light_night_maxlux,light_night_minlux,light_night_avglux,light_night_medianlux,light_night_stdlux
+2020-07-04,1,0.065,0.065,0.065,0.065,NA

tests/data/processed/test02/light_afternoon.csv

@@ -0,0 +1 @@
+local_date,light_afternoon_maxlux,light_afternoon_medianlux,light_afternoon_avglux,light_afternoon_stdlux,light_afternoon_minlux,light_afternoon_count

tests/data/processed/test02/light_daily.csv

@@ -0,0 +1 @@
+local_date,light_daily_maxlux,light_daily_count,light_daily_minlux,light_daily_stdlux,light_daily_avglux,light_daily_medianlux

tests/data/processed/test02/light_evening.csv

@@ -0,0 +1 @@
+local_date,light_evening_count,light_evening_avglux,light_evening_medianlux,light_evening_minlux,light_evening_maxlux,light_evening_stdlux

tests/data/processed/test02/light_morning.csv

@@ -0,0 +1 @@
+local_date,light_morning_count,light_morning_stdlux,light_morning_minlux,light_morning_maxlux,light_morning_medianlux,light_morning_avglux

tests/data/processed/test02/light_night.csv

@@ -0,0 +1 @@
+local_date,light_night_stdlux,light_night_maxlux,light_night_avglux,light_night_count,light_night_medianlux,light_night_minlux

tests/data/processed/test03/light_afternoon.csv

@@ -0,0 +1 @@
+local_date,light_afternoon_maxlux,light_afternoon_medianlux,light_afternoon_minlux,light_afternoon_stdlux,light_afternoon_count,light_afternoon_avglux

tests/data/processed/test03/light_daily.csv

@@ -0,0 +1 @@
+local_date,light_daily_maxlux,light_daily_avglux,light_daily_count,light_daily_minlux,light_daily_medianlux,light_daily_stdlux

tests/data/processed/test03/light_evening.csv

@@ -0,0 +1 @@
+local_date,light_evening_stdlux,light_evening_medianlux,light_evening_maxlux,light_evening_count,light_evening_minlux,light_evening_avglux

tests/data/processed/test03/light_morning.csv

@@ -0,0 +1 @@
+local_date,light_morning_stdlux,light_morning_medianlux,light_morning_maxlux,light_morning_minlux,light_morning_count,light_morning_avglux

tests/data/processed/test03/light_night.csv

@@ -0,0 +1 @@
+local_date,light_night_maxlux,light_night_medianlux,light_night_minlux,light_night_stdlux,light_night_count,light_night_avglux

tests/data/processed/test04/light_afternoon.csv

@@ -0,0 +1 @@
+local_date,light_afternoon_avglux,light_afternoon_count,light_afternoon_maxlux,light_afternoon_medianlux,light_afternoon_minlux,light_afternoon_stdlux

tests/data/processed/test04/light_daily.csv

@@ -0,0 +1 @@
+local_date,light_daily_avglux,light_daily_stdlux,light_daily_medianlux,light_daily_minlux,light_daily_maxlux,light_daily_count

tests/data/processed/test04/light_evening.csv

@@ -0,0 +1 @@
+local_date,light_evening_avglux,light_evening_minlux,light_evening_maxlux,light_evening_medianlux,light_evening_stdlux,light_evening_count

tests/data/processed/test04/light_morning.csv

@@ -0,0 +1 @@
+local_date,light_morning_minlux,light_morning_avglux,light_morning_stdlux,light_morning_medianlux,light_morning_count,light_morning_maxlux

tests/data/processed/test04/light_night.csv

@@ -0,0 +1 @@
+local_date,light_night_count,light_night_stdlux,light_night_minlux,light_night_medianlux,light_night_maxlux,light_night_avglux

tests/data/raw/test01/light_raw.csv

@@ -0,0 +1,13 @@
+timestamp,device_id,double_light_lux,accuracy,label
+1593856800461,wYESbVwI-4GfR-G5I6-7iKL-tOmCKs02MBun,472.52,3,
+1593863999053,wYESbVwI-4GfR-G5I6-7iKL-tOmCKs02MBun,37252,3,
+1593871199794,wYESbVwI-4GfR-G5I6-7iKL-tOmCKs02MBun,90298,3,
+1593878399891,wYESbVwI-4GfR-G5I6-7iKL-tOmCKs02MBun,114615,3,
+1593878400002,wYESbVwI-4GfR-G5I6-7iKL-tOmCKs02MBun,97656,3,
+1593885599119,wYESbVwI-4GfR-G5I6-7iKL-tOmCKs02MBun,90625,3,
+1593892799453,wYESbVwI-4GfR-G5I6-7iKL-tOmCKs02MBun,24414,3,
+1593899999082,wYESbVwI-4GfR-G5I6-7iKL-tOmCKs02MBun,10351,3,
+1593900000724,wYESbVwI-4GfR-G5I6-7iKL-tOmCKs02MBun,15258,3,
+1593907199287,wYESbVwI-4GfR-G5I6-7iKL-tOmCKs02MBun,1469,3,
+1593921599301,wYESbVwI-4GfR-G5I6-7iKL-tOmCKs02MBun,84.156,3,
+1593849599654,wYESbVwI-4GfR-G5I6-7iKL-tOmCKs02MBun,0.065,3,

tests/data/raw/test02/light_raw.csv

@@ -0,0 +1 @@
+timestamp,device_id,double_light_lux,accuracy,label

tests/data/raw/test03/light_raw.csv

@@ -0,0 +1 @@
+timestamp,device_id,double_light_lux,accuracy,label

tests/data/raw/test04/light_raw.csv

@@ -0,0 +1 @@
+timestamp,device_id,double_light_lux,accuracy,label

tests/settings/config.yaml

@@ -2,4 +2,4 @@ directory: ./
 configfile: ./tests/settings/testing_config.yaml
 snakefile: ./tests/Snakefile
 cores: 1
-forcerun: [messages_features, call_features, screen_features, battery_features, bluetooth_features, wifi_features]
+forcerun: [messages_features, call_features, screen_features, battery_features, bluetooth_features, wifi_features, light_features]

tests/settings/testing_config.yaml

@@ -2,13 +2,12 @@
 # You must create a file for each participant named pXXX containing their device_id. This can be done manually or automatically
 PIDS: [test01, test02, test03, test04]
 
-
 # Global var with common day segments
 DAY_SEGMENTS: &day_segments
   [daily, morning, afternoon, evening, night]
 
 PHONE_VALID_SENSED_BINS:
-  TABLES: [messages, calls, screen, battery, bluetooth, wifi]
+  TABLES: [messages, calls, screen, battery, bluetooth, wifi, light]
 
 # Communication SMS features config, TYPES and FEATURES keys need to match
 MESSAGES:
@@ -56,3 +55,9 @@ WIFI:
   DB_TABLE: wifi
   DAY_SEGMENTS: *day_segments
   FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
+
+LIGHT:
+  COMPUTE: True
+  DB_TABLE: light
+  DAY_SEGMENTS: *day_segments
+  FEATURES: ["count", "maxlux", "minlux", "avglux", "medianlux", "stdlux"]