rapids/rules/reports.snakefile

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def optional_heatmap_days_by_sensors_input(wildcards):
with open("data/external/"+wildcards.pid, encoding="ISO-8859-1") as external_file:
external_file_content = external_file.readlines()
platforms = external_file_content[1].strip().split(",")
if platforms[0] == "multiple" or (len(platforms) > 1 and "android" in platforms and "ios" in platforms):
platform = "android"
else:
platform = platforms[0]
if platform not in ["android", "ios"]:
raise ValueError("Platform (line 2) in a participant file should be 'android', 'ios', or 'multiple'. You typed '" + platforms + "'")
input_for_heatmap_days_by_sensors, tables = [], config["HEATMAP_DAYS_BY_SENSORS"]["DB_TABLES"]
for sensor in ["ACTIVITY_RECOGNITION", "CONVERSATION"]:
table = config[sensor]["DB_TABLE"][platform.upper()]
if table in tables:
input_for_heatmap_days_by_sensors.append("data/raw/{pid}/" + table + "_with_datetime.csv")
tables = [x for x in tables if x not in config[sensor]["DB_TABLE"].values()]
for table in tables:
input_for_heatmap_days_by_sensors.append("data/raw/{pid}/" + table + "_with_datetime.csv")
return input_for_heatmap_days_by_sensors
rule heatmap_features_correlations:
input:
features = expand("data/processed/{pid}/{sensor}_{day_segment}.csv", pid=config["PIDS"], sensor=config["HEATMAP_FEATURES_CORRELATIONS"]["PHONE_FEATURES"]+config["HEATMAP_FEATURES_CORRELATIONS"]["FITBIT_FEATURES"], day_segment=config["DAY_SEGMENTS"]),
phone_valid_sensed_days = expand("data/interim/{pid}/phone_valid_sensed_days_{{min_valid_hours_per_day}}hours_{{min_valid_bins_per_hour}}bins.csv", pid=config["PIDS"])
params:
min_rows_ratio = config["HEATMAP_FEATURES_CORRELATIONS"]["MIN_ROWS_RATIO"],
corr_threshold = config["HEATMAP_FEATURES_CORRELATIONS"]["CORR_THRESHOLD"],
corr_method = config["HEATMAP_FEATURES_CORRELATIONS"]["CORR_METHOD"]
output:
"reports/data_exploration/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/heatmap_features_correlations.html"
script:
"../src/visualization/heatmap_features_correlations.py"
rule histogram_valid_sensed_hours:
input:
phone_valid_sensed_days = expand("data/interim/{pid}/phone_valid_sensed_days_{{min_valid_hours_per_day}}hours_{{min_valid_bins_per_hour}}bins.csv", pid=config["PIDS"])
output:
"reports/data_exploration/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/histogram_valid_sensed_hours.html"
script:
"../src/visualization/histogram_valid_sensed_hours.py"
rule heatmap_days_by_sensors:
input:
sensors = optional_heatmap_days_by_sensors_input,
phone_valid_sensed_days = "data/interim/{pid}/phone_valid_sensed_days_{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins.csv"
params:
pid = "{pid}",
expected_num_of_days = config["HEATMAP_DAYS_BY_SENSORS"]["EXPECTED_NUM_OF_DAYS"]
output:
"reports/interim/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/{pid}/heatmap_days_by_sensors.html"
script:
"../src/visualization/heatmap_days_by_sensors.py"
rule heatmap_days_by_sensors_all_participants:
input:
heatmap_rows = expand("reports/interim/{{min_valid_hours_per_day}}hours_{{min_valid_bins_per_hour}}bins/{pid}/heatmap_days_by_sensors.html", pid=config["PIDS"])
output:
"reports/data_exploration/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/heatmap_days_by_sensors_all_participants.html"
script:
"../src/visualization/heatmap_days_by_sensors_all_participants.Rmd"
rule heatmap_sensed_bins:
input:
sensor = "data/interim/{pid}/phone_sensed_bins.csv",
pid_file = "data/external/{pid}"
params:
pid = "{pid}",
bin_size = config["HEATMAP_SENSED_BINS"]["BIN_SIZE"]
output:
"reports/interim/heatmap_sensed_bins/{pid}/heatmap_sensed_bins.html"
script:
"../src/visualization/heatmap_sensed_bins.py"
rule heatmap_sensed_bins_all_participants:
input:
heatmap_sensed_bins = expand("reports/interim/heatmap_sensed_bins/{pid}/heatmap_sensed_bins.html", pid=config["PIDS"])
output:
"reports/data_exploration/heatmap_sensed_bins_all_participants.html"
script:
"../src/visualization/heatmap_sensed_bins_all_participants.Rmd"
rule overall_compliance_heatmap:
input:
phone_sensed_bins = expand("data/interim/{pid}/phone_sensed_bins.csv", pid=config["PIDS"]),
phone_valid_sensed_days = expand("data/interim/{pid}/phone_valid_sensed_days_{{min_valid_hours_per_day}}hours_{{min_valid_bins_per_hour}}bins.csv", pid=config["PIDS"]),
pid_files = expand("data/external/{pid}", pid=config["PIDS"])
params:
only_show_valid_days = config["OVERALL_COMPLIANCE_HEATMAP"]["ONLY_SHOW_VALID_DAYS"],
local_timezone = config["READABLE_DATETIME"]["FIXED_TIMEZONE"],
expected_num_of_days = config["OVERALL_COMPLIANCE_HEATMAP"]["EXPECTED_NUM_OF_DAYS"],
bin_size = config["OVERALL_COMPLIANCE_HEATMAP"]["BIN_SIZE"],
min_bins_per_hour = "{min_valid_bins_per_hour}"
output:
"reports/data_exploration/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/overall_compliance_heatmap.html"
script:
"../src/visualization/overall_compliance_heatmap.py"
# rule heatmap_rows:
# input:
# sensor = "data/raw/{pid}/{sensor}_with_datetime.csv",
# pid_file = "data/external/{pid}"
# params:
# table = "{sensor}",
# pid = "{pid}",
# bin_size = config["PHONE_VALID_SENSED_BINS"]["BIN_SIZE"]
# output:
# "reports/figures/{pid}/{sensor}_heatmap_rows.html"
# script:
# "../src/visualization/heatmap_rows.py"
# rule battery_consumption_rates_barchart:
# input:
# sensor = "data/processed/{pid}/battery_daily.csv",
# pid_file = "data/external/{pid}"
# params:
# pid = "{pid}"
# output:
# "reports/figures/{pid}/battery_consumption_rates_barchart.html"
# script:
# "../src/visualization/battery_consumption_rates_barchart.py"
# rule compliance_report:
# input:
# sensor_heatmaps = expand("reports/figures/{{pid}}/{sensor}_heatmap_rows.html", sensor=PHONE_SENSORS),
# compliance_heatmap = rules.compliance_heatmap.output
# output:
# "reports/compliance/{pid}/compliance_report.html",
# script:
# "../src/visualization/compliance_report.Rmd"