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Rename accelerometer features names

pull/95/head
Meng Li 2020-06-22 13:47:25 -04:00
parent a121c0fe7b
commit 99fe86ac2a
3 changed files with 10 additions and 10 deletions
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4
config.yaml
View File

@ -102,8 +102,8 @@ ACCELEROMETER:
DAY_SEGMENTS: *day_segments
FEATURES:
MAGNITUDE: ["maxmagnitude", "minmagnitude", "avgmagnitude", "medianmagnitude", "stdmagnitude"]
EXERTIONAL_ACTIVITY_EPISODE: ["sumexertionalactivityepisode", "maxexertionalactivityepisode", "minexertionalactivityepisode", "avgexertionalactivityepisode", "medianexertionalactivityepisode", "stdexertionalactivityepisode"]
NONEXERTIONAL_ACTIVITY_EPISODE: ["sumnonexertionalactivityepisode", "maxnonexertionalactivityepisode", "minnonexertionalactivityepisode", "avgnonexertionalactivityepisode", "mediannonexertionalactivityepisode", "stdnonexertionalactivityepisode"]
EXERTIONAL_ACTIVITY_EPISODE: ["sumduration", "maxduration", "minduration", "avgduration", "medianduration", "stdduration"]
NONEXERTIONAL_ACTIVITY_EPISODE: ["sumduration", "maxduration", "minduration", "avgduration", "medianduration", "stdduration"]
VALID_SENSED_MINUTES: True
APPLICATIONS_FOREGROUND:

12
src/features/accelerometer/accelerometer_base.py
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@ -36,10 +36,10 @@ def dropRowsWithCertainThreshold(data, threshold):
def statsFeatures(acc_data, day_segment, features_to_compute, features_type, acc_features):
if features_type == "magnitude":
col_name = features_type
elif features_type == "exertionalactivityepisode" or features_type == "nonexertionalactivityepisode":
elif features_type == "durationexertionalactivityepisode" or features_type == "durationnonexertionalactivityepisode":
col_name = "duration"
else:
raise ValueError("features_type can only be one of ['magnitude', 'exertionalactivityepisode', 'nonexertionalactivityepisode'].")
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()
@ -61,8 +61,8 @@ def statsFeatures(acc_data, day_segment, features_to_compute, features_type, acc
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 = ["sumexertionalactivityepisode", "maxexertionalactivityepisode", "minexertionalactivityepisode", "avgexertionalactivityepisode", "medianexertionalactivityepisode", "stdexertionalactivityepisode"]
base_features_names_nonexertionalactivityepisode = ["sumnonexertionalactivityepisode", "maxnonexertionalactivityepisode", "minnonexertionalactivityepisode", "avgnonexertionalactivityepisode", "mediannonexertionalactivityepisode", "stdnonexertionalactivityepisode"]
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))
@ -99,10 +99,10 @@ def base_accelerometer_features(acc_data, day_segment, requested_features, valid
activity_episode = getActivityEpisodes(acc_minute)
exertionalactivity_episodes = activity_episode[activity_episode["isexertionalactivity"] == 1]
acc_features = statsFeatures(exertionalactivity_episodes, day_segment, features_to_compute_exertionalactivityepisode, "exertionalactivityepisode", acc_features)
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, "nonexertionalactivityepisode", acc_features)
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)

4
src/features/accelerometer_features.py
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@ -8,8 +8,8 @@ day_segment = snakemake.params["day_segment"]
requested_features = {}
requested_features["magnitude"] = snakemake.params["magnitude"]
requested_features["exertional_activity_episode"] = snakemake.params["exertional_activity_episode"]
requested_features["nonexertional_activity_episode"] = snakemake.params["nonexertional_activity_episode"]
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"]