Merge branch 'day_segments' of https://github.com/carissalow/rapids into day_segments
JulioV
commit
10b0386c8f
13
Snakefile
13
Snakefile
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@ -65,12 +65,15 @@ if config["ACTIVITY_RECOGNITION"]["COMPUTE"]:
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files_to_compute.extend(expand("data/processed/{pid}/{sensor}_deltas.csv", pid=pids, sensor=table))
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files_to_compute.extend(expand("data/processed/{pid}/activity_recognition_{day_segment}.csv",pid=config["PIDS"], day_segment = config["ACTIVITY_RECOGNITION"]["DAY_SEGMENTS"]))
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if config["BATTERY"]["COMPUTE"]:
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for provider in config["BATTERY"]["PROVIDERS"].keys():
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if config["BATTERY"]["PROVIDERS"][provider]["COMPUTE"]:
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files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["BATTERY"]["DB_TABLE"]))
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files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["BATTERY"]["DB_TABLE"]))
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files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime_unified.csv", pid=config["PIDS"], sensor=config["BATTERY"]["DB_TABLE"]))
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files_to_compute.extend(expand("data/processed/{pid}/battery_deltas.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/processed/{pid}/battery_{day_segment}.csv", pid = config["PIDS"], day_segment = config["BATTERY"]["DAY_SEGMENTS"]))
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files_to_compute.extend(expand("data/interim/{pid}/battery_episodes.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/interim/{pid}/battery_episodes_resampled.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/interim/{pid}/battery_episodes_resampled_with_datetime.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/interim/{pid}/{sensor_key}_features/{sensor_key}_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["SCREEN"]["PROVIDERS"][provider]["SRC_LANGUAGE"], provider_key=provider, sensor_key="BATTERY".lower()))
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files_to_compute.extend(expand("data/processed/features/{pid}/{sensor_key}.csv", pid=config["PIDS"], sensor_key="BATTERY".lower()))
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for provider in config["SCREEN"]["PROVIDERS"].keys():
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if config["SCREEN"]["PROVIDERS"][provider]["COMPUTE"]:
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@ -121,10 +121,13 @@ ACTIVITY_RECOGNITION:
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FEATURES: ["count","mostcommonactivity","countuniqueactivities","activitychangecount","sumstationary","summobile","sumvehicle"]
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BATTERY:
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COMPUTE: False
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DB_TABLE: battery
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DAY_SEGMENTS: *day_segments
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PROVIDERS:
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RAPIDS:
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COMPUTE: False
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FEATURES: ["countdischarge", "sumdurationdischarge", "countcharge", "sumdurationcharge", "avgconsumptionrate", "maxconsumptionrate"]
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SRC_FOLDER: "rapids" # inside src/features/battery
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SRC_LANGUAGE: "python"
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SCREEN:
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DB_TABLE: screen
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@ -73,16 +73,14 @@ rule screen_episodes:
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rule resample_episodes:
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input:
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"data/interim/{pid}/{sensor}_episodes.csv"
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params:
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sensor = "{sensor}"
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output:
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"data/interim/{pid}/{sensor}_episodes_resampled.csv"
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script:
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"../src/features/utils/resample_episodes.R"
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rule resample_screen_episodes_with_datetime:
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rule resample_episodes_with_datetime:
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input:
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sensor_input = "data/interim/{pid}/screen_episodes_resampled.csv",
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sensor_input = "data/interim/{pid}/{sensor}_episodes_resampled.csv",
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day_segments = "data/interim/day_segments/{pid}_day_segments.csv"
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params:
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timezones = None,
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@ -90,7 +88,7 @@ rule resample_screen_episodes_with_datetime:
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day_segments_type = config["DAY_SEGMENTS"]["TYPE"],
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include_past_periodic_segments = config["DAY_SEGMENTS"]["INCLUDE_PAST_PERIODIC_SEGMENTS"]
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output:
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"data/interim/{pid}/screen_episodes_resampled_with_datetime.csv"
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"data/interim/{pid}/{sensor}_episodes_resampled_with_datetime.csv"
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script:
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"../src/data/readable_datetime.R"
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@ -170,16 +168,29 @@ rule activity_features:
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script:
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"../src/features/activity_recognition.py"
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rule battery_features:
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rule battery_r_features:
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input:
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"data/interim/{pid}/battery_episodes.csv"
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battery_episodes = "data/interim/{pid}/battery_episodes_resampled_with_datetime.csv",
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day_segments_labels = "data/interim/day_segments/{pid}_day_segments_labels.csv"
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params:
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day_segment = "{day_segment}",
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features = config["BATTERY"]["FEATURES"]
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provider = lambda wildcards: config["BATTERY"]["PROVIDERS"][wildcards.provider_key],
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provider_key = "{provider_key}"
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output:
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"data/processed/{pid}/battery_{day_segment}.csv"
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"data/interim/{pid}/battery_features/battery_r_{provider_key}.csv"
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script:
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"../src/features/battery_features.py"
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"../src/features/battery/battery_entry.R"
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rule battery_python_features:
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input:
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battery_episodes = "data/interim/{pid}/battery_episodes_resampled_with_datetime.csv",
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day_segments_labels = "data/interim/day_segments/{pid}_day_segments_labels.csv"
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params:
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provider = lambda wildcards: config["BATTERY"]["PROVIDERS"][wildcards.provider_key],
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provider_key = "{provider_key}"
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output:
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"data/interim/{pid}/battery_features/battery_python_{provider_key}.csv"
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script:
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"../src/features/battery/battery_entry.py"
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rule screen_r_features:
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input:
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@ -1,48 +0,0 @@
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import pandas as pd
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from datetime import datetime, timedelta, time
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from features_utils import splitOvernightEpisodes, splitMultiSegmentEpisodes
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def base_battery_features(battery_data, day_segment, requested_features):
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# name of the features this function can compute
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base_features_names = ["countdischarge", "sumdurationdischarge", "countcharge", "sumdurationcharge", "avgconsumptionrate", "maxconsumptionrate"]
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# the subset of requested features this function can compute
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features_to_compute = list(set(requested_features) & set(base_features_names))
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battery_features = pd.DataFrame(columns=["local_date"] + ["battery_" + day_segment + "_" + x for x in features_to_compute])
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if not battery_data.empty:
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battery_data = splitOvernightEpisodes(battery_data, ["battery_diff"], [])
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if day_segment != "daily":
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battery_data = splitMultiSegmentEpisodes(battery_data, day_segment, ["battery_diff"])
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if not battery_data.empty:
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battery_data["battery_consumption_rate"] = battery_data["battery_diff"] / battery_data["time_diff"]
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# for battery_data_discharge:
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battery_data_discharge = battery_data[battery_data["battery_diff"] > 0]
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battery_discharge_features = pd.DataFrame()
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if "countdischarge" in features_to_compute:
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battery_discharge_features["battery_"+day_segment+"_countdischarge"] = battery_data_discharge.groupby(["local_start_date"])["local_start_date"].count()
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if "sumdurationdischarge" in features_to_compute:
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battery_discharge_features["battery_"+day_segment+"_sumdurationdischarge"] = battery_data_discharge.groupby(["local_start_date"])["time_diff"].sum()
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if "avgconsumptionrate" in features_to_compute:
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battery_discharge_features["battery_"+day_segment+"_avgconsumptionrate"] = battery_data_discharge.groupby(["local_start_date"])["battery_consumption_rate"].mean()
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if "maxconsumptionrate" in features_to_compute:
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battery_discharge_features["battery_"+day_segment+"_maxconsumptionrate"] = battery_data_discharge.groupby(["local_start_date"])["battery_consumption_rate"].max()
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# for battery_data_charge:
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battery_data_charge = battery_data[battery_data["battery_diff"] <= 0]
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battery_charge_features = pd.DataFrame()
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if "countcharge" in features_to_compute:
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battery_charge_features["battery_"+day_segment+"_countcharge"] = battery_data_charge.groupby(["local_start_date"])["local_start_date"].count()
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if "sumdurationcharge" in features_to_compute:
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battery_charge_features["battery_"+day_segment+"_sumdurationcharge"] = battery_data_charge.groupby(["local_start_date"])["time_diff"].sum()
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# combine discharge features and charge features; fill the missing values with ZERO
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battery_features = pd.concat([battery_discharge_features, battery_charge_features], axis=1, sort=True).fillna(0)
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battery_features.index.rename("local_date", inplace=True)
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battery_features = battery_features.reset_index()
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return battery_features
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@ -0,0 +1,13 @@
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source("renv/activate.R")
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source("src/features/utils/utils.R")
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library("dplyr")
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library("tidyr")
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sensor_data_file <- snakemake@input[["battery_episodes"]]
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day_segments_file <- snakemake@input[["day_segments_labels"]]
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provider <- snakemake@params["provider"][["provider"]]
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provider_key <- snakemake@params["provider_key"]
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sensor_features <- fetch_provider_features(provider, provider_key, "battery", sensor_data_file, day_segments_file)
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write.csv(sensor_features, snakemake@output[[1]], row.names = FALSE)
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@ -0,0 +1,18 @@
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import pandas as pd
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from importlib import import_module, util
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from pathlib import Path
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# import fetch_provider_features from src/features/utils/utils.py
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spec = util.spec_from_file_location("util", str(Path(snakemake.scriptdir).parent / "utils" / "utils.py"))
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mod = util.module_from_spec(spec)
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spec.loader.exec_module(mod)
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fetch_provider_features = getattr(mod, "fetch_provider_features")
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battery_episodes_file = snakemake.input["battery_episodes"]
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day_segments_file = snakemake.input["day_segments_labels"]
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provider = snakemake.params["provider"]
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provider_key = snakemake.params["provider_key"]
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sensor_features = fetch_provider_features(provider, provider_key, "battery", battery_episodes_file, day_segments_file)
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sensor_features.to_csv(snakemake.output[0], index=False)
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@ -0,0 +1,56 @@
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import pandas as pd
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from datetime import datetime, timedelta, time
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def rapids_features(battery_data, day_segment, provider, filter_data_by_segment, *args, **kwargs):
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# name of the features this function can compute
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base_features_names = ["countdischarge", "sumdurationdischarge", "countcharge", "sumdurationcharge", "avgconsumptionrate", "maxconsumptionrate"]
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# the subset of requested features this function can compute
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requested_features = provider["FEATURES"]
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features_to_compute = list(set(requested_features) & set(base_features_names))
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battery_features = pd.DataFrame(columns=["local_segment"] + ["battery_rapids_" + x for x in features_to_compute])
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if not battery_data.empty:
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battery_data = filter_data_by_segment(battery_data, day_segment)
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battery_data = kwargs["deduplicate_episodes"](battery_data)
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if not battery_data.empty:
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# chunk_episodes
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battery_data = kwargs["chunk_episodes"](battery_data)
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if not battery_data.empty:
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battery_data["episode_id"] = ((battery_data.battery_status != battery_data.battery_status.shift()) | (battery_data.start_timestamp - battery_data.end_timestamp.shift() > 1)).cumsum()
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grouped = battery_data.groupby(by=["local_segment", "episode_id", "battery_status"])
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battery_episodes= grouped[["time_diff"]].sum()
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battery_episodes["battery_diff"] = grouped["battery_level"].first() - grouped["battery_level"].last()
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battery_episodes["battery_consumption_rate"] = battery_episodes["battery_diff"] / battery_episodes["time_diff"]
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battery_episodes.reset_index(inplace=True)
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# for discharge episodes
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battery_discharge_episodes = battery_episodes[(battery_episodes["battery_status"] == 3) | (battery_episodes["battery_status"] == 4)]
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battery_discharge_features = pd.DataFrame()
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if "countdischarge" in features_to_compute:
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battery_discharge_features["battery_rapids_countdischarge"] = battery_discharge_episodes.groupby(["local_segment"])["episode_id"].count()
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if "sumdurationdischarge" in features_to_compute:
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battery_discharge_features["battery_rapids_sumdurationdischarge"] = battery_discharge_episodes.groupby(["local_segment"])["time_diff"].sum()
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if "avgconsumptionrate" in features_to_compute:
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battery_discharge_features["battery_rapids_avgconsumptionrate"] = battery_discharge_episodes.groupby(["local_segment"])["battery_consumption_rate"].mean()
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if "maxconsumptionrate" in features_to_compute:
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battery_discharge_features["battery_rapids_maxconsumptionrate"] = battery_discharge_episodes.groupby(["local_segment"])["battery_consumption_rate"].max()
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# for charge episodes
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battery_charge_episodes = battery_episodes[(battery_episodes["battery_status"] == 2) | (battery_episodes["battery_status"] == 5)]
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battery_charge_features = pd.DataFrame()
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if "countcharge" in features_to_compute:
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battery_charge_features["battery_rapids_countcharge"] = battery_charge_episodes.groupby(["local_segment"])["episode_id"].count()
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if "sumdurationcharge" in features_to_compute:
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battery_charge_features["battery_rapids_sumdurationcharge"] = battery_charge_episodes.groupby(["local_segment"])["time_diff"].sum()
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# combine discharge features and charge features; fill the missing values with ZERO
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battery_features = pd.concat([battery_discharge_features, battery_charge_features], axis=1, sort=True).fillna(0)
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battery_features.index.rename("local_segment", inplace=True)
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battery_features = battery_features.reset_index()
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return battery_features
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@ -44,7 +44,6 @@ get_screen_episodes <- function(screen){
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filter( (screen_status == 3 & lead(screen_status) == 0) | (screen_status == 0 & lag(screen_status) == 3) ) %>%
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summarise(episode = "unlock",
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screen_sequence = toString(screen_status),
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time_diff = (last(timestamp) - first(timestamp)) / (1000 * 60),
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start_timestamp = first(timestamp),
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end_timestamp = last(timestamp)) %>%
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filter(str_detect(screen_sequence,
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@ -58,7 +57,6 @@ get_screen_episodes <- function(screen){
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if(nrow(screen) < 2){
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episodes <- data.frame(episode = character(),
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screen_sequence = character(),
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time_diff = numeric(),
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start_timestamp = character(),
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end_timestamp = character())
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} else {
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@ -47,6 +47,7 @@ def rapids_features(screen_data, day_segment, provider, filter_data_by_segment,
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if not screen_data.empty:
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screen_data = filter_data_by_segment(screen_data, day_segment)
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screen_data = kwargs["deduplicate_episodes"](screen_data)
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if not screen_data.empty:
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# chunk_episodes
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screen_data = kwargs["chunk_episodes"](screen_data)
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@ -1,44 +0,0 @@
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import pandas as pd
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def resample_screen_deltas(screen_deltas):
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column_names = ("episode_id", "episode", "screen_sequence", "timestamp", "duration")
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records_resampled = []
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for _, row in screen_deltas.iterrows():
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episode_id, episode, screen_sequence = row["episode_id"], row["episode"], row["screen_sequence"]
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start_timestamp, end_timestamp = row["start_timestamp"], row["end_timestamp"]
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for timestamp in range(start_timestamp, end_timestamp, 1000 * 60):
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records_resampled.append((episode_id, episode, screen_sequence, timestamp, min(1, (end_timestamp - timestamp) / (1000 * 60))))
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return records_resampled, column_names
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def resample_battery_deltas(battery_deltas):
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column_names = ("battery_diff", "timestamp")
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records_resampled = []
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for _, row in battery_deltas.iterrows():
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start_timestamp, end_timestamp = row["start_timestamp"], row["end_timestamp"]
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battery_diff = row["battery_diff"] / row["time_diff"]
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for timestamp in range(start_timestamp, end_timestamp, 1000 * 60):
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records_resampled.append((battery_diff, timestamp))
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return records_resampled, column_names
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deltas = pd.read_csv(snakemake.input[0])
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sensor = snakemake.params["sensor"]
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if sensor == "battery":
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records_resampled, column_names = resample_battery_deltas(deltas)
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if sensor == "screen":
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records_resampled, column_names = resample_screen_deltas(deltas)
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deltas_resampled = pd.DataFrame(data=records_resampled, columns=column_names)
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deltas_resampled.to_csv(snakemake.output[0], index=False)
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@ -13,45 +13,47 @@ def filter_data_by_segment(data, day_segment):
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data[["local_segment","timestamps_segment"]] = data["local_segment"].str.split(pat =";",n=1, expand=True)
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return(data)
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# Each minute could fall into two segments.
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# Firstly, we generate two rows for each resampled minute via resample_episodes rule:
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# the first row's timestamp column is the start_timestamp, while the second row's timestamp column is the end_timestamp.
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# Then, we check if the segments of start_timestamp are the same as the segments of end_timestamp:
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# if they are the same (only fall into one segment), we will discard the second row;
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# otherwise (fall into two segments), we will keep both.
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def deduplicate_episodes(sensor_episodes):
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# Drop rows where segments of start_timestamp and end_timestamp are the same
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sensor_episodes = sensor_episodes.drop_duplicates(subset=["start_timestamp", "end_timestamp", "local_segment"], keep="first")
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# Delete useless columns
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for drop_col in ["utc_date_time", "local_date_time", "local_date", "local_time", "local_hour", "local_minute"]:
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del sensor_episodes[drop_col]
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return sensor_episodes
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def chunk_episodes(sensor_episodes):
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import pytz, copy
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import pandas as pd
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from datetime import datetime
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# avoid warning messages: SettingWithCopyWarning
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sensor_episodes = sensor_episodes.copy()
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# Unix timestamp for current segment in milliseconds
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sensor_episodes[["segment_start_timestamp", "segment_end_timestamp"]] = sensor_episodes["timestamps_segment"].str.split(",", expand=True)
|
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|
||||
# convert string to datetime with local timezone
|
||||
sensor_episodes["start_datetime"] = pd.to_datetime(sensor_episodes["local_segment"].str[-39:-20], format="%Y-%m-%d#%H:%M:%S")
|
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sensor_episodes["start_datetime"] = pd.concat([data["start_datetime"].dt.tz_localize(tz) for tz, data in sensor_episodes.groupby("local_timezone")])
|
||||
# Compute chunked timestamp
|
||||
sensor_episodes["chunked_start_timestamp"] = sensor_episodes[["start_timestamp", "segment_start_timestamp"]].max(axis=1)
|
||||
sensor_episodes["chunked_end_timestamp"] = sensor_episodes[["end_timestamp", "segment_end_timestamp"]].min(axis=1)
|
||||
|
||||
sensor_episodes["end_datetime"] = pd.to_datetime(sensor_episodes["local_segment"].str[-19:], format="%Y-%m-%d#%H:%M:%S")
|
||||
sensor_episodes["end_datetime"] = pd.concat([data["end_datetime"].dt.tz_localize(tz) for tz, data in sensor_episodes.groupby("local_timezone")])
|
||||
|
||||
# unix timestamp in milliseconds
|
||||
sensor_episodes["start_timestamp"] = sensor_episodes["start_datetime"].apply(lambda dt: dt.timestamp() * 1000)
|
||||
sensor_episodes["end_timestamp"] = sensor_episodes["end_datetime"].apply(lambda dt: dt.timestamp() * 1000)
|
||||
|
||||
# compute chunked timestamp
|
||||
sensor_episodes["chunked_start_timestamp"] = sensor_episodes[["timestamp", "start_timestamp"]].max(axis=1)
|
||||
|
||||
sensor_episodes["timestamp_plus_duration"] = sensor_episodes["timestamp"] + sensor_episodes["duration"] * 1000 * 60
|
||||
sensor_episodes["chunked_end_timestamp"] = sensor_episodes[["timestamp_plus_duration", "end_timestamp"]].min(axis=1)
|
||||
|
||||
# time_diff: intersection of current row and segment
|
||||
# Compute time_diff: intersection of current row and segment
|
||||
sensor_episodes["time_diff"] = (sensor_episodes["chunked_end_timestamp"] - sensor_episodes["chunked_start_timestamp"]) / (1000 * 60)
|
||||
|
||||
# compute chunked datetime
|
||||
# Compute chunked datetime
|
||||
sensor_episodes["chunked_start_datetime"] = pd.to_datetime(sensor_episodes["chunked_start_timestamp"], unit="ms", utc=True)
|
||||
sensor_episodes["chunked_start_datetime"] = pd.concat([data["chunked_start_datetime"].dt.tz_convert(tz) for tz, data in sensor_episodes.groupby("local_timezone")])
|
||||
|
||||
sensor_episodes["chunked_end_datetime"] = pd.to_datetime(sensor_episodes["chunked_end_timestamp"], unit="ms", utc=True)
|
||||
sensor_episodes["chunked_end_datetime"] = pd.concat([data["chunked_end_datetime"].dt.tz_convert(tz) for tz, data in sensor_episodes.groupby("local_timezone")])
|
||||
|
||||
# merge episodes
|
||||
sensor_episodes_grouped = sensor_episodes.groupby(["episode_id", "episode", "screen_sequence"])
|
||||
# Merge episodes
|
||||
cols_for_groupby = [col for col in sensor_episodes.columns if col not in ["local_timezone", "timestamps_segment", "timestamp", "assigned_segments", "start_datetime", "end_datetime", "start_timestamp", "end_timestamp", "time_diff", "segment_start_timestamp", "segment_end_timestamp", "chunked_start_timestamp", "chunked_end_timestamp", "chunked_start_datetime", "chunked_end_datetime"]]
|
||||
|
||||
sensor_episodes_grouped = sensor_episodes.groupby(by=cols_for_groupby)
|
||||
merged_sensor_episodes = sensor_episodes_grouped[["time_diff"]].sum()
|
||||
merged_sensor_episodes["local_segment"] = sensor_episodes_grouped["local_segment"].first()
|
||||
|
||||
merged_sensor_episodes["start_timestamp"] = sensor_episodes_grouped["chunked_start_timestamp"].first()
|
||||
merged_sensor_episodes["end_timestamp"] = sensor_episodes_grouped["chunked_end_timestamp"].last()
|
||||
|
|
@ -80,7 +82,7 @@ def fetch_provider_features(provider, provider_key, config_key, sensor_data_file
|
|||
|
||||
for day_segment in day_segments_labels["label"]:
|
||||
print("{} Processing {} {} {}".format(rapids_log_tag, config_key, provider_key, day_segment))
|
||||
features = feature_function(sensor_data, day_segment, provider, filter_data_by_segment=filter_data_by_segment, chunk_episodes=chunk_episodes)
|
||||
features = feature_function(sensor_data, day_segment, provider, filter_data_by_segment=filter_data_by_segment, deduplicate_episodes=deduplicate_episodes, chunk_episodes=chunk_episodes)
|
||||
sensor_features = sensor_features.merge(features, how="outer")
|
||||
else:
|
||||
for feature in provider["FEATURES"]:
|
||||
|
|
|
|||
Loading…
Reference in New Issue