Add accelerometer features of PANDA provider

pull/103/head
Meng Li 2020-10-13 17:54:53 -04:00
parent 29dcd1f284
commit ac9cf92732
4 changed files with 98 additions and 133 deletions

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@ -167,6 +167,15 @@ ACCELEROMETER:
SRC_FOLDER: "rapids" # inside src/features/accelerometer SRC_FOLDER: "rapids" # inside src/features/accelerometer
SRC_LANGUAGE: "python" SRC_LANGUAGE: "python"
PANDA:
COMPUTE: False
VALID_SENSED_MINUTES: False
FEATURES:
exertional_activity_episode: ["sumduration", "maxduration", "minduration", "avgduration", "medianduration", "stdduration"]
nonexertional_activity_episode: ["sumduration", "maxduration", "minduration", "avgduration", "medianduration", "stdduration"]
SRC_FOLDER: "panda" # inside src/features/accelerometer
SRC_LANGUAGE: "python"
APPLICATIONS_FOREGROUND: APPLICATIONS_FOREGROUND:
DB_TABLE: applications_foreground DB_TABLE: applications_foreground
PROVIDERS: PROVIDERS:

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@ -1,111 +0,0 @@
import pandas as pd
import numpy as np
def getActivityEpisodes(acc_minute):
# rebuild local date time for resampling
acc_minute["local_datetime"] = pd.to_datetime(acc_minute["local_date"].dt.strftime("%Y-%m-%d") + \
" " + acc_minute["local_hour"].apply(str) + ":" + acc_minute["local_minute"].apply(str) + ":00")
# resample the data into 1 minute bins, set "isexertionalactivity" column to be NA if it is missing
resampled_acc_minute = pd.DataFrame(acc_minute.resample("1T", on="local_datetime")["isexertionalactivity"].sum(min_count=1))
# group rows by consecutive values of "isexertionalactivity" column
group = pd.DataFrame(resampled_acc_minute["isexertionalactivity"] != resampled_acc_minute["isexertionalactivity"].shift()).cumsum().rename(columns={"isexertionalactivity": "group_idx"})
# combine resampled_acc_minute and group column
resampled_acc_minute = pd.concat([resampled_acc_minute, group], axis=1)
# drop rows where "isexertionalactivity" column is missing and reset the index
resampled_acc_minute.dropna(subset=["isexertionalactivity"], inplace=True)
resampled_acc_minute.reset_index(inplace=True)
resampled_acc_minute.loc[:, "local_date"] = resampled_acc_minute["local_datetime"].dt.date
# duration column contains the number of minutes (rows) of exertional and nonexertional activity for each episode
activity_episode = resampled_acc_minute.groupby(["isexertionalactivity", "group_idx", "local_date"]).count().rename(columns={"local_datetime": "duration"}).reset_index()
return activity_episode
def dropRowsWithCertainThreshold(data, threshold):
data_grouped = data.groupby(["local_date", "local_hour", "local_minute"]).count()
drop_dates = data_grouped[data_grouped["timestamp"] == threshold].index
data.set_index(["local_date", "local_hour", "local_minute"], inplace = True)
if not drop_dates.empty:
data.drop(drop_dates, axis = 0, inplace = True)
return data.reset_index()
def statsFeatures(acc_data, day_segment, features_to_compute, features_type, acc_features):
if features_type == "magnitude":
col_name = features_type
elif features_type == "durationexertionalactivityepisode" or features_type == "durationnonexertionalactivityepisode":
col_name = "duration"
else:
raise ValueError("features_type can only be one of ['magnitude', 'durationexertionalactivityepisode', 'durationnonexertionalactivityepisode'].")
if "sum" + features_type in features_to_compute:
acc_features["acc_" + day_segment + "_sum" + features_type] = acc_data.groupby(["local_date"])[col_name].sum()
if "max" + features_type in features_to_compute:
acc_features["acc_" + day_segment + "_max" + features_type] = acc_data.groupby(["local_date"])[col_name].max()
if "min" + features_type in features_to_compute:
acc_features["acc_" + day_segment + "_min" + features_type] = acc_data.groupby(["local_date"])[col_name].min()
if "avg" + features_type in features_to_compute:
acc_features["acc_" + day_segment + "_avg" + features_type] = acc_data.groupby(["local_date"])[col_name].mean()
if "median" + features_type in features_to_compute:
acc_features["acc_" + day_segment + "_median" + features_type] = acc_data.groupby(["local_date"])[col_name].median()
if "std" + features_type in features_to_compute:
acc_features["acc_" + day_segment + "_std" + features_type] = acc_data.groupby(["local_date"])[col_name].std()
return acc_features
def base_accelerometer_features(acc_data, day_segment, requested_features, valid_sensed_minutes):
# name of the features this function can compute
base_features_names_magnitude = ["maxmagnitude", "minmagnitude", "avgmagnitude", "medianmagnitude", "stdmagnitude"]
base_features_names_exertionalactivityepisode = ["sumdurationexertionalactivityepisode", "maxdurationexertionalactivityepisode", "mindurationexertionalactivityepisode", "avgdurationexertionalactivityepisode", "mediandurationexertionalactivityepisode", "stddurationexertionalactivityepisode"]
base_features_names_nonexertionalactivityepisode = ["sumdurationnonexertionalactivityepisode", "maxdurationnonexertionalactivityepisode", "mindurationnonexertionalactivityepisode", "avgdurationnonexertionalactivityepisode", "mediandurationnonexertionalactivityepisode", "stddurationnonexertionalactivityepisode"]
# the subset of requested features this function can compute
features_to_compute_magnitude = list(set(requested_features["magnitude"]) & set(base_features_names_magnitude))
features_to_compute_exertionalactivityepisode = list(set(requested_features["exertional_activity_episode"]) & set(base_features_names_exertionalactivityepisode))
features_to_compute_nonexertionalactivityepisode = list(set(requested_features["nonexertional_activity_episode"]) & set(base_features_names_nonexertionalactivityepisode))
features_to_compute = features_to_compute_magnitude + features_to_compute_exertionalactivityepisode + features_to_compute_nonexertionalactivityepisode + (["validsensedminutes"] if valid_sensed_minutes else [])
acc_features = pd.DataFrame(columns=["local_date"] + ["acc_" + day_segment + "_" + x for x in features_to_compute])
if not acc_data.empty:
if day_segment != "daily":
acc_data = acc_data[acc_data["local_day_segment"] == day_segment]
if not acc_data.empty:
acc_features = pd.DataFrame()
# get magnitude related features: magnitude = sqrt(x^2+y^2+z^2)
magnitude = acc_data.apply(lambda row: np.sqrt(row["double_values_0"] ** 2 + row["double_values_1"] ** 2 + row["double_values_2"] ** 2), axis=1)
acc_data = acc_data.assign(magnitude = magnitude.values)
acc_features = statsFeatures(acc_data, day_segment, features_to_compute_magnitude, "magnitude", acc_features)
# get extertional activity features
# reference: https://jamanetwork.com/journals/jamasurgery/fullarticle/2753807
# drop rows where we only have one row per minute (no variance)
acc_data = dropRowsWithCertainThreshold(acc_data, 1)
if not acc_data.empty:
# check if the participant performs exertional activity for each minute
acc_minute = pd.DataFrame()
acc_minute["isexertionalactivity"] = (acc_data.groupby(["local_date", "local_hour", "local_minute"])["double_values_0"].var() + acc_data.groupby(["local_date", "local_hour", "local_minute"])["double_values_1"].var() + acc_data.groupby(["local_date", "local_hour", "local_minute"])["double_values_2"].var()).apply(lambda x: 1 if x > 0.15 * (9.807 ** 2) else 0)
acc_minute.reset_index(inplace=True)
if valid_sensed_minutes:
acc_features["acc_" + day_segment + "_validsensedminutes"] = acc_minute.groupby(["local_date"])["isexertionalactivity"].count()
activity_episode = getActivityEpisodes(acc_minute)
exertionalactivity_episodes = activity_episode[activity_episode["isexertionalactivity"] == 1]
acc_features = statsFeatures(exertionalactivity_episodes, day_segment, features_to_compute_exertionalactivityepisode, "durationexertionalactivityepisode", acc_features)
nonexertionalactivity_episodes = activity_episode[activity_episode["isexertionalactivity"] == 0]
acc_features = statsFeatures(nonexertionalactivity_episodes, day_segment, features_to_compute_nonexertionalactivityepisode, "durationnonexertionalactivityepisode", acc_features)
acc_features[[colname for colname in acc_features.columns if "std" not in colname]] = acc_features[[colname for colname in acc_features.columns if "std" not in colname]].fillna(0)
acc_features = acc_features.reset_index()
return acc_features

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@ -0,0 +1,89 @@
import pandas as pd
import numpy as np
def dropRowsWithCertainThreshold(data, threshold):
data_grouped = data.groupby(["local_timezone", "local_segment", "local_date", "local_hour", "local_minute"])
data_cleaned = data_grouped.filter(lambda x: x["timestamp"].count() > threshold)
return data_cleaned
def getActivityEpisodes(acc_minute):
# rebuild local date time for resampling
acc_minute["local_datetime"] = pd.to_datetime(acc_minute["local_date"] + \
" " + acc_minute["local_hour"].apply(str) + ":" + acc_minute["local_minute"].apply(str) + ":00")
# compute time interval between consecutive rows in minutes
acc_minute["rows_interval"] = round(acc_minute["local_datetime"].diff().dt.total_seconds() / 60, 0)
# put consecutive rows into the same group if (1) the interval between two rows is 1 minute and (2) have the same values of "isexertionalactivity", "local_timezone", and "local_segment"
acc_minute["group_idx"] = ((acc_minute[["isexertionalactivity", "local_timezone", "local_segment"]].shift() != acc_minute[["isexertionalactivity", "local_timezone", "local_segment"]]).any(axis=1) | (acc_minute["rows_interval"] != 1)).cumsum()
# get activity episodes: duration column contains the number of minutes (rows) of exertional and nonexertional activity for each episode
grouped = acc_minute.groupby("group_idx")
activity_episodes = grouped["local_segment"].agg(duration="count")
activity_episodes[["local_segment", "isexertionalactivity"]] = grouped[["local_segment", "isexertionalactivity"]].first()
return activity_episodes
def statsFeatures(acc_data, features_to_compute, features_type, acc_features):
if "sum" + features_type in features_to_compute:
acc_features["acc_panda_sum" + features_type] = acc_data.groupby(["local_segment"])["duration"].sum()
if "max" + features_type in features_to_compute:
acc_features["acc_panda_max" + features_type] = acc_data.groupby(["local_segment"])["duration"].max()
if "min" + features_type in features_to_compute:
acc_features["acc_panda_min" + features_type] = acc_data.groupby(["local_segment"])["duration"].min()
if "avg" + features_type in features_to_compute:
acc_features["acc_panda_avg" + features_type] = acc_data.groupby(["local_segment"])["duration"].mean()
if "median" + features_type in features_to_compute:
acc_features["acc_panda_median" + features_type] = acc_data.groupby(["local_segment"])["duration"].median()
if "std" + features_type in features_to_compute:
acc_features["acc_panda_std" + features_type] = acc_data.groupby(["local_segment"])["duration"].std()
return acc_features
def panda_features(sensor_data_files, day_segment, provider, filter_data_by_segment, *args, **kwargs):
acc_data = pd.read_csv(sensor_data_files["sensor_data"])
requested_features = provider["FEATURES"]
valid_sensed_minutes = provider["VALID_SENSED_MINUTES"]
# name of the features this function can compute
base_features_names_exertionalactivityepisode = ["sumdurationexertionalactivityepisode", "maxdurationexertionalactivityepisode", "mindurationexertionalactivityepisode", "avgdurationexertionalactivityepisode", "mediandurationexertionalactivityepisode", "stddurationexertionalactivityepisode"]
base_features_names_nonexertionalactivityepisode = ["sumdurationnonexertionalactivityepisode", "maxdurationnonexertionalactivityepisode", "mindurationnonexertionalactivityepisode", "avgdurationnonexertionalactivityepisode", "mediandurationnonexertionalactivityepisode", "stddurationnonexertionalactivityepisode"]
# the subset of requested features this function can compute
features_to_compute_exertionalactivityepisode = list(set([x + "exertionalactivityepisode" for x in requested_features["exertional_activity_episode"]]) & set(base_features_names_exertionalactivityepisode))
features_to_compute_nonexertionalactivityepisode = list(set([ x + "nonexertionalactivityepisode" for x in requested_features["nonexertional_activity_episode"]]) & set(base_features_names_nonexertionalactivityepisode))
features_to_compute = features_to_compute_exertionalactivityepisode + features_to_compute_nonexertionalactivityepisode + (["validsensedminutes"] if valid_sensed_minutes else [])
acc_features = pd.DataFrame(columns=["local_segment"] + ["acc_panda_" + x for x in features_to_compute])
if not acc_data.empty:
acc_data = filter_data_by_segment(acc_data, day_segment)
if not acc_data.empty:
acc_features = pd.DataFrame()
# drop rows where we only have one row per minute (no variance)
acc_data = dropRowsWithCertainThreshold(acc_data, 1)
if not acc_data.empty:
# check if the participant performs exertional activity for each minute
acc_minute = pd.DataFrame()
acc_minute["isexertionalactivity"] = (acc_data.groupby(["local_timezone", "local_segment", "local_date", "local_hour", "local_minute"])["double_values_0"].var() + acc_data.groupby(["local_timezone", "local_segment", "local_date", "local_hour", "local_minute"])["double_values_1"].var() + acc_data.groupby(["local_timezone", "local_segment", "local_date", "local_hour", "local_minute"])["double_values_2"].var()).apply(lambda x: 1 if x > 0.15 * (9.807 ** 2) else 0)
acc_minute.reset_index(inplace=True)
if valid_sensed_minutes:
acc_features["acc_panda_validsensedminutes"] = acc_minute.groupby(["local_segment"])["isexertionalactivity"].count()
activity_episodes = getActivityEpisodes(acc_minute)
# compute exertional episodes features
exertionalactivity_episodes = activity_episodes[activity_episodes["isexertionalactivity"] == 1]
acc_features = statsFeatures(exertionalactivity_episodes, features_to_compute_exertionalactivityepisode, "durationexertionalactivityepisode", acc_features)
# compute non-exertional episodes features
nonexertionalactivity_episodes = activity_episodes[activity_episodes["isexertionalactivity"] == 0]
acc_features = statsFeatures(nonexertionalactivity_episodes, features_to_compute_nonexertionalactivityepisode, "durationnonexertionalactivityepisode", acc_features)
acc_features[[colname for colname in acc_features.columns if "std" not in colname]] = acc_features[[colname for colname in acc_features.columns if "std" not in colname]].fillna(0)
acc_features = acc_features.reset_index()
return acc_features

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@ -1,22 +0,0 @@
import numpy as np
import pandas as pd
from accelerometer.accelerometer_base import base_accelerometer_features
acc_data = pd.read_csv(snakemake.input[0], parse_dates=["local_date_time", "local_date"])
day_segment = snakemake.params["day_segment"]
requested_features = {}
requested_features["magnitude"] = snakemake.params["magnitude"]
requested_features["exertional_activity_episode"] = [feature + "exertionalactivityepisode" for feature in snakemake.params["exertional_activity_episode"]]
requested_features["nonexertional_activity_episode"] = [feature + "nonexertionalactivityepisode" for feature in snakemake.params["nonexertional_activity_episode"]]
valid_sensed_minutes = snakemake.params["valid_sensed_minutes"]
acc_features = pd.DataFrame(columns=["local_date"])
acc_features = acc_features.merge(base_accelerometer_features(acc_data, day_segment, requested_features, valid_sensed_minutes), on="local_date", how="outer")
assert np.sum([len(x) for x in requested_features.values()]) + (1 if valid_sensed_minutes else 0) + 1 == acc_features.shape[1], "The number of features in the output dataframe (=" + str(acc_features.shape[1]) + ") does not match the expected value (=" + str(np.sum([len(x) for x in requested_features.values()]) + (1 if valid_sensed_minutes else 0)) + " + 1). Verify your accelerometer feature extraction functions"
acc_features.to_csv(snakemake.output[0], index=False)