parent
3d4c26754e
commit
7c240a9613
11
Snakefile
11
Snakefile
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@ -4,9 +4,18 @@ include: "rules/preprocessing.snakefile"
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include: "rules/features.snakefile"
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include: "rules/models.snakefile"
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include: "rules/reports.snakefile"
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include: "rules/mystudy.snakefile" # You can add snakfiles with rules tailored to your project
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rule all:
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input:
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# My study (this is an example of a rule created specifically for a study)
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expand("data/interim/{pid}/days_to_analyse_{days_before_surgery}_{days_in_hospital}_{days_after_discharge}.csv",
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pid=config["PIDS"],
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days_before_surgery = config["METRICS_FOR_ANALYSIS"]["DAYS_BEFORE_SURGERY"],
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days_after_discharge= config["METRICS_FOR_ANALYSIS"]["DAYS_AFTER_DISCHARGE"],
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days_in_hospital= config["METRICS_FOR_ANALYSIS"]["DAYS_IN_HOSPITAL"]),
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# Feature extraction
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expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["SENSORS"]),
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expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["FITBIT_TABLE"]),
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expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["SENSORS"]),
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@ -64,7 +73,7 @@ rule all:
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expand("data/processed/metrics_for_population_model/{source}_{day_segment}.csv",
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source = config["METRICS_FOR_ANALYSIS"]["SOURCES"],
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day_segment = config["METRICS_FOR_ANALYSIS"]["DAY_SEGMENTS"]),
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# Reports
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# Vizualisations
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expand("reports/figures/{pid}/{sensor}_heatmap_rows.html", pid=config["PIDS"], sensor=config["SENSORS"]),
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expand("reports/figures/{pid}/compliance_heatmap.html", pid=config["PIDS"]),
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expand("reports/figures/{pid}/battery_consumption_rates_barchart.html", pid=config["PIDS"]),
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@ -130,4 +130,7 @@ METRICS_FOR_ANALYSIS:
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PHONE_METRICS: [accelerometer, applications_foreground, battery, call_incoming, call_missed, call_outgoing, google_activity_recognition, light, location_barnett, screen, sms_received, sms_sent]
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FITBIT_METRICS: [fitbit_heartrate, fitbit_step]
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PHONE_FITBIT_METRICS: "" # This array is merged in the input_merge_features_of_single_participant function in models.snakefile
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DROP_VALID_SENSED_DAYS: True
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DROP_VALID_SENSED_DAYS: True
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DAYS_BEFORE_SURGERY: 15
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DAYS_AFTER_DISCHARGE: 7
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DAYS_IN_HOSPITAL: F
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@ -0,0 +1,12 @@
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rule days_to_analyse:
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input:
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participant_info = "data/external/participant_info.csv",
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pid_file = "data/external/{pid}"
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params:
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days_before_surgery = config["METRICS_FOR_ANALYSIS"]["DAYS_BEFORE_SURGERY"],
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days_after_discharge = config["METRICS_FOR_ANALYSIS"]["DAYS_AFTER_DISCHARGE"],
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days_in_hospital= config["METRICS_FOR_ANALYSIS"]["DAYS_IN_HOSPITAL"]
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output:
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"data/interim/{pid}/days_to_analyse_{days_before_surgery}_{days_in_hospital}_{days_after_discharge}.csv"
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script:
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"../src/models/select_days_to_analyse.py"
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@ -0,0 +1,34 @@
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import pandas as pd
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from datetime import timedelta
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def appendDaysInRange(days_to_analyse, start_date, end_date):
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num_of_days = (end_date - start_date).days
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for day in range(num_of_days + 1):
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days_to_analyse = days_to_analyse.append({"days_to_analyse": start_date + timedelta(days = day)}, ignore_index=True)
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return days_to_analyse
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days_before_surgery = snakemake.params["days_before_surgery"]
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days_in_hospital = snakemake.params["days_in_hospital"]
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days_after_discharge = snakemake.params["days_after_discharge"]
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participant_info = pd.read_csv(snakemake.input["participant_info"], parse_dates=["surgery_date", "discharge_date"])
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with open(snakemake.input["pid_file"], encoding="ISO-8859-1") as external_file:
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pid_file_content = external_file.readlines()
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device_ids = pid_file_content[0].strip().split(",")
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days_to_analyse = pd.DataFrame(columns = ["days_to_analyse"])
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participant_info = participant_info[participant_info["device_id"].isin(device_ids)]
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try:
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surgery_date, discharge_date = participant_info["surgery_date"].iloc[0].date(), participant_info["discharge_date"].iloc[0].date()
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except:
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pass
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else:
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start_date = surgery_date - timedelta(days = days_before_surgery)
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end_date = discharge_date + timedelta(days = days_after_discharge)
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days_to_analyse = appendDaysInRange(days_to_analyse, start_date, surgery_date - timedelta(days = 1))
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if days_in_hospital == "T":
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days_to_analyse = appendDaysInRange(days_to_analyse, surgery_date, discharge_date)
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days_to_analyse = appendDaysInRange(days_to_analyse, discharge_date + timedelta(days = 1), end_date)
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days_to_analyse.to_csv(snakemake.output[0], index=False)
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