import pandas as pd import numpy as np import datetime import math, sys, yaml from esm_preprocess import clean_up_esm from esm import classify_sessions_by_completion_time, preprocess_esm input_data_files = dict(snakemake.input) def format_timestamp(x): tstring="" space = False if x//3600 > 0: tstring += f"{x//3600}H" space = True if x % 3600 // 60 > 0: tstring += f" {x % 3600 // 60}M" if "H" in tstring else f"{x % 3600 // 60}M" if x % 60 > 0: tstring += f" {x % 60}S" if "M" in tstring or "H" in tstring else f"{x % 60}S" return tstring def extract_ers_from_file(esm_df, device_id): pd.set_option("display.max_rows", None) pd.set_option("display.max_columns", None) # extracted_ers = pd.DataFrame(columns=["label", "event_timestamp", "length", "shift", "shift_direction", "device_id"]) # esm_df = clean_up_esm(preprocess_esm(esm_df)) esm_preprocessed = clean_up_esm(preprocess_esm(esm_df)) # Take only during work sessions # during_work = esm_df[esm_df["esm_trigger"].str.contains("during_work", na=False)] # esm_trigger_group = esm_df.groupby("esm_session").agg(pd.Series.mode)['esm_trigger'] # Get most frequent esm_trigger within particular session # esm_filtered_sessions = list(esm_trigger_group[esm_trigger_group == 'during_work'].index) # Take only sessions that contains during work # Take only ema_completed sessions responses classified = classify_sessions_by_completion_time(esm_preprocessed) esm_filtered_sessions = classified[classified["session_response"] == 'ema_completed'].reset_index()['esm_session'] esm_df = esm_preprocessed[esm_preprocessed["esm_session"].isin(esm_filtered_sessions)] # Extract time-relevant information extracted_ers = esm_df.groupby(["device_id", "esm_session"])['timestamp'].apply(lambda x: math.ceil((x.max() - x.min()) / 1000)).reset_index() # in rounded up seconds extracted_ers = extracted_ers[extracted_ers["timestamp"] <= 15 * 60].reset_index(drop=True) # ensure that the longest duration of the questionnaire anwsering is 15 min time_before_questionnaire = 30 * 60 # in seconds (30 minutes) extracted_ers["label"] = "straw_event_" + snakemake.params["pid"] + "_" + extracted_ers.index.astype(str).str.zfill(3) extracted_ers["event_timestamp"] = esm_df.groupby("esm_session")['timestamp'].min().reset_index()['timestamp'] extracted_ers["length"] = (extracted_ers["timestamp"] + time_before_questionnaire).apply(lambda x: format_timestamp(x)) extracted_ers["shift"] = time_before_questionnaire extracted_ers["shift"] = extracted_ers["shift"].apply(lambda x: format_timestamp(x)) extracted_ers["shift_direction"] = -1 extracted_ers["device_id"] = device_id return extracted_ers[["label", "event_timestamp", "length", "shift", "shift_direction", "device_id"]] if snakemake.params["stage"] == "extract": esm_df = pd.read_csv(input_data_files['esm_raw_input']) with open(input_data_files['pid_file'], 'r') as stream: pid_file = yaml.load(stream, Loader=yaml.FullLoader) extracted_ers = extract_ers_from_file(esm_df, pid_file["PHONE"]["DEVICE_IDS"][0]) extracted_ers.to_csv(snakemake.output[0], index=False) elif snakemake.params["stage"] == "merge": input_data_files = dict(snakemake.input) straw_events = pd.DataFrame(columns=["label", "event_timestamp", "length", "shift", "shift_direction", "device_id"]) for input_file in input_data_files["ers_files"]: ers_df = pd.read_csv(input_file) straw_events = pd.concat([straw_events, ers_df], axis=0, ignore_index=True) straw_events.to_csv(snakemake.output[0], index=False)