Add INCLUDE_ZERO_STEP_ROWS flag for step sensor
parent
529d6e4bf8
commit
b23bb0e402
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@ -122,6 +122,7 @@ STEP:
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SEDENTARY_BOUT: ["countsedentarybout", "maxdurationsedentarybout", "mindurationsedentarybout", "avgdurationsedentarybout", "stddurationsedentarybout"]
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ACTIVE_BOUT: ["countactivebout", "maxdurationactivebout", "mindurationactivebout", "avgdurationactivebout", "stddurationactivebout"]
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THRESHOLD_ACTIVE_BOUT: 10 # steps
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INCLUDE_ZERO_STEP_ROWS: True
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METRICS_FOR_ANALYSIS:
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SOURCES: &sources ["phone_metrics", "fitbit_metrics", "phone_fitbit_metrics"]
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@ -168,7 +168,8 @@ rule fitbit_step_metrics:
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metrics_all_steps = config["STEP"]["METRICS"]["ALL_STEPS"],
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metrics_sedentary_bout = config["STEP"]["METRICS"]["SEDENTARY_BOUT"],
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metrics_active_bout = config["STEP"]["METRICS"]["ACTIVE_BOUT"],
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threshold_active_bout = config["STEP"]["THRESHOLD_ACTIVE_BOUT"]
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threshold_active_bout = config["STEP"]["THRESHOLD_ACTIVE_BOUT"],
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include_zero_step_rows = config["STEP"]["INCLUDE_ZERO_STEP_ROWS"]
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output:
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"data/processed/{pid}/fitbit_step_{day_segment}.csv"
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script:
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@ -8,6 +8,7 @@ all_steps = snakemake.params["metrics_all_steps"]
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sedentary_bout = snakemake.params["metrics_sedentary_bout"]
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active_bout = snakemake.params["metrics_active_bout"]
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threshold_active_bout = snakemake.params['threshold_active_bout']
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include_zero_step_rows = snakemake.params["include_zero_step_rows"]
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#Read csv into a pandas dataframe
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data = pd.read_csv(snakemake.input['steps_data'],parse_dates=['local_date_time'])
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@ -93,5 +94,11 @@ else:
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if("stddurationactivebout" in active_bout):
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finalDataset["step_" + str(day_segment) + "_stddurationactivebout"] = statsMinutes[statsMinutes['active_sedentary']== 'active']['std']
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#Exclude data when the total step count is ZERO during the whole epoch
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if not include_zero_step_rows:
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finalDataset["sumallsteps_aux"] = resampledData["steps"].resample("D").sum()
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finalDataset = finalDataset.query("sumallsteps_aux != 0")
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del finalDataset["sumallsteps_aux"]
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finalDataset.index.names = ['local_date']
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finalDataset.to_csv(snakemake.output[0])
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