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Patching IBI with BVP - selecting appropriate pipeline entry point. WIP

sociality-task
Primoz 2022-05-24 11:07:18 +00:00
parent 2a8f58f5c8
commit bb62497ba6
3 changed files with 16 additions and 5 deletions
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2
Snakefile
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@ -359,8 +359,6 @@ for provider in config["EMPATICA_INTER_BEAT_INTERVAL"]["PROVIDERS"].keys():
if config["EMPATICA_INTER_BEAT_INTERVAL"]["PROVIDERS"][provider]["COMPUTE"]: if config["EMPATICA_INTER_BEAT_INTERVAL"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/empatica_inter_beat_interval_raw.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/raw/{pid}/empatica_inter_beat_interval_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/empatica_inter_beat_interval_with_datetime.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/raw/{pid}/empatica_inter_beat_interval_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/empatica_blood_volume_pulse_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/empatica_blood_volume_pulse_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/empatica_inter_beat_interval_features/empatica_inter_beat_interval_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["EMPATICA_INTER_BEAT_INTERVAL"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower())) files_to_compute.extend(expand("data/interim/{pid}/empatica_inter_beat_interval_features/empatica_inter_beat_interval_{language}_{provider_key}.csv", pid=config["PIDS"], language=get_script_language(config["EMPATICA_INTER_BEAT_INTERVAL"]["PROVIDERS"][provider]["SRC_SCRIPT"]), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/empatica_inter_beat_interval.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/processed/features/{pid}/empatica_inter_beat_interval.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))

9
config.yaml
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@ -3,7 +3,7 @@
######################################################################################################################## ########################################################################################################################
# See https://www.rapids.science/latest/setup/configuration/#participant-files # See https://www.rapids.science/latest/setup/configuration/#participant-files
PIDS: [p01] #p02, p03] PIDS: [p01] #p01, p02, p03]
# See https://www.rapids.science/latest/setup/configuration/#automatic-creation-of-participant-files # See https://www.rapids.science/latest/setup/configuration/#automatic-creation-of-participant-files
CREATE_PARTICIPANT_FILES: CREATE_PARTICIPANT_FILES:
@ -43,12 +43,15 @@ TIMEZONE:
# See https://www.rapids.science/latest/setup/configuration/#data-stream-configuration # See https://www.rapids.science/latest/setup/configuration/#data-stream-configuration
PHONE_DATA_STREAMS: PHONE_DATA_STREAMS:
USE: aware_csv USE: aware_postgresql
# AVAILABLE: # AVAILABLE:
aware_mysql: aware_mysql:
DATABASE_GROUP: MY_GROUP DATABASE_GROUP: MY_GROUP
aware_postgresql:
DATABASE_GROUP: PSQL_STRAW
aware_csv: aware_csv:
FOLDER: data/external/aware_csv FOLDER: data/external/aware_csv
@ -177,7 +180,7 @@ PHONE_BLUETOOTH:
# See https://www.rapids.science/latest/features/phone-calls/ # See https://www.rapids.science/latest/features/phone-calls/
PHONE_CALLS: PHONE_CALLS:
CONTAINER: calls.csv CONTAINER: call
PROVIDERS: PROVIDERS:
RAPIDS: RAPIDS:
COMPUTE: False COMPUTE: False

10
src/data/streams/empatica_zip/container.py
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@ -8,6 +8,8 @@ import csv
from collections import OrderedDict from collections import OrderedDict
from io import BytesIO, StringIO from io import BytesIO, StringIO
from cr_features.hrv import get_HRV_features
def processAcceleration(x, y, z): def processAcceleration(x, y, z):
x = float(x) x = float(x)
y = float(y) y = float(y)
@ -94,6 +96,14 @@ def pull_data(data_configuration, device, sensor, container, columns_to_download
print("Extracting {} data from {} for {}".format(sensor, zipfile, device)) print("Extracting {} data from {} for {}".format(sensor, zipfile, device))
with ZipFile(zipfile, 'r') as zipFile: with ZipFile(zipfile, 'r') as zipFile:
listOfFileNames = zipFile.namelist() listOfFileNames = zipFile.namelist()
if sensor == "EMPATICA_INTER_BEAT_INTERVAL":
extracted_bvp_data = extract_empatica_data(zipFile.read('BVP.csv'), "EMPATICA_BLOOD_VOLUME_PULSE")
hrv_time_and_freq_features, sample, bvp_rr, bvp_timings, peak_indx = \
get_HRV_features(extracted_bvp_data['blood_volume_pulse'].to_numpy(), ma=False, detrend=False, m_deternd=False,
low_pass=False, winsorize=True, winsorize_value=25,
hampel_fiter=False, median_filter=False, mod_z_score_filter=True,
sampling=64, feature_names=['meanHr'])
print(bvp_rr, bvp_timings)
for fileName in listOfFileNames: for fileName in listOfFileNames:
if fileName == sensor_csv: if fileName == sensor_csv:
participant_data = pd.concat([participant_data, extract_empatica_data(zipFile.read(fileName), sensor)], axis=0) participant_data = pd.concat([participant_data, extract_empatica_data(zipFile.read(fileName), sensor)], axis=0)