Refactor fitbit_heartrate feature: replace "metrics" with "features"
Co-authored-by: Meng Li <AnnieLM1996@gmail.com>pull/95/head
Mingze Cao
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@ -113,7 +113,7 @@ APPLICATIONS_FOREGROUND:
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HEARTRATE:
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DAY_SEGMENTS: *day_segments
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METRICS: ["maxhr", "minhr", "avghr", "medianhr", "modehr", "stdhr", "diffmaxmodehr", "diffminmodehr", "entropyhr", "lengthoutofrange", "lengthfatburn", "lengthcardio", "lengthpeak"]
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FEATURES: ["maxhr", "minhr", "avghr", "medianhr", "modehr", "stdhr", "diffmaxmodehr", "diffminmodehr", "entropyhr", "lengthoutofrange", "lengthfatburn", "lengthcardio", "lengthpeak"]
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STEP:
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DAY_SEGMENTS: *day_segments
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@ -985,7 +985,7 @@ See `Fitbit: Heart Rate Config Code`_
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| ``pid=config["PIDS"],``
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| ``fitbit_sensor=config["FITBIT_SENSORS"]),``
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- Extract Sensor Metrics:
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- Extract Sensor Features:
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| ``expand("data/processed/{pid}/fitbit_heartrate_{day_segment}.csv",``
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| ``pid=config["PIDS"],``
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@ -1001,9 +1001,9 @@ See `Fitbit: Heart Rate Config Code`_
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- **Script:** ``src/data/fitbit_readable_datetime.py`` - See the fitbit_readable_datetime.py_ script.
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- **Rule:** ``rules/features.snakefile/fitbit_heartrate_metrics`` - See the fitbit_heartrate_metrics_ rule.
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- **Rule:** ``rules/features.snakefile/fitbit_heartrate_features`` - See the fitbit_heartrate_features_ rule.
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- **Script:** ``src/features/fitbit_heartrate_metrics.py`` - See the fitbit_heartrate_metrics.py_ script.
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- **Script:** ``src/features/fitbit_heartrate_features.py`` - See the fitbit_heartrate_features.py_ script.
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.. _fitbit-heart-rate-parameters:
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@ -1014,15 +1014,15 @@ See `Fitbit: Heart Rate Config Code`_
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Name Description
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============ ===================
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day_segment The particular ``day_segments`` that will be analyzed. The available options are ``daily``, ``morning``, ``afternoon``, ``evening``, ``night``
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metrics The different measures that can be retrieved from the Fitbit: Heart Rate dataset.
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See :ref:`Available Fitbit: Heart Rate Metrics <fitbit-heart-rate-available-metrics>` Table below
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features The different measures that can be retrieved from the Fitbit: Heart Rate dataset.
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See :ref:`Available Fitbit: Heart Rate Features <fitbit-heart-rate-available-features>` Table below
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============ ===================
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.. _fitbit-heart-rate-available-metrics:
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.. _fitbit-heart-rate-available-features:
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**Available Fitbit: Heart Rate Metrics**
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**Available Fitbit: Heart Rate Features**
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The following table shows a list of the available metrics for the Fitbit: Heart Rate dataset.
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The following table shows a list of the available features for the Fitbit: Heart Rate dataset.
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================== =========== =============
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Name Units Description
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@ -1192,8 +1192,8 @@ stddurationactivebout minutes Std duration active bout: The standard
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.. _`Fitbit: Heart Rate Config Code`: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/config.yaml#L113
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.. _fitbit_with_datetime: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/rules/preprocessing.snakefile#L94
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.. _fitbit_readable_datetime.py: https://github.com/carissalow/rapids/blob/master/src/data/fitbit_readable_datetime.py
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.. _fitbit_heartrate_metrics: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/rules/features.snakefile#L151
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.. _fitbit_heartrate_metrics.py: https://github.com/carissalow/rapids/blob/master/src/features/fitbit_heartrate_metrics.py
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.. _fitbit_heartrate_features: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/rules/features.snakefile#L151
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.. _fitbit_heartrate_features.py: https://github.com/carissalow/rapids/blob/master/src/features/fitbit_heartrate_features.py
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.. _`Fitbit: Steps Config Code`: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/config.yaml#L117
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.. _fitbit_step_features: https://github.com/carissalow/rapids/blob/765bb462636d5029a05f54d4c558487e3786b90b/rules/features.snakefile#L162
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.. _fitbit_step_features.py: https://github.com/carissalow/rapids/blob/master/src/features/fitbit_step_features.py
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@ -149,16 +149,16 @@ rule applications_foreground_features:
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script:
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"../src/features/applications_foreground_features.py"
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rule fitbit_heartrate_metrics:
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rule fitbit_heartrate_features:
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input:
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"data/raw/{pid}/fitbit_heartrate_with_datetime.csv",
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params:
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day_segment = "{day_segment}",
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metrics = config["HEARTRATE"]["METRICS"],
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features = config["HEARTRATE"]["FEATURES"],
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output:
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"data/processed/{pid}/fitbit_heartrate_{day_segment}.csv"
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script:
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"../src/features/fitbit_heartrate_metrics.py"
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"../src/features/fitbit_heartrate_features.py"
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rule fitbit_step_features:
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input:
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@ -6,10 +6,10 @@ import json
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heartrate_data = pd.read_csv(snakemake.input[0], parse_dates=["local_date_time", "local_date"])
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day_segment = snakemake.params["day_segment"]
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metrics = snakemake.params["metrics"]
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features = snakemake.params["features"]
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heartrate_features = pd.DataFrame(columns=["local_date"] + ["heartrate_" + day_segment + "_" + x for x in metrics])
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heartrate_features = pd.DataFrame(columns=["local_date"] + ["heartrate_" + day_segment + "_" + x for x in features])
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if not heartrate_data.empty:
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device_id = heartrate_data["device_id"][0]
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num_rows_per_minute = heartrate_data.groupby(["local_date", "local_hour", "local_minute"]).count().mean()["device_id"]
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@ -20,27 +20,27 @@ if not heartrate_data.empty:
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heartrate_features = pd.DataFrame()
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# get stats of heartrate
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if "maxhr" in metrics:
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if "maxhr" in features:
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heartrate_features["heartrate_" + day_segment + "_maxhr"] = heartrate_data.groupby(["local_date"])["heartrate"].max()
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if "minhr" in metrics:
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if "minhr" in features:
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heartrate_features["heartrate_" + day_segment + "_minhr"] = heartrate_data.groupby(["local_date"])["heartrate"].min()
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if "avghr" in metrics:
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if "avghr" in features:
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heartrate_features["heartrate_" + day_segment + "_avghr"] = heartrate_data.groupby(["local_date"])["heartrate"].mean()
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if "medianhr" in metrics:
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if "medianhr" in features:
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heartrate_features["heartrate_" + day_segment + "_medianhr"] = heartrate_data.groupby(["local_date"])["heartrate"].median()
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if "modehr" in metrics:
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if "modehr" in features:
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heartrate_features["heartrate_" + day_segment + "_modehr"] = heartrate_data.groupby(["local_date"])["heartrate"].agg(lambda x: pd.Series.mode(x)[0])
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if "stdhr" in metrics:
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if "stdhr" in features:
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heartrate_features["heartrate_" + day_segment + "_stdhr"] = heartrate_data.groupby(["local_date"])["heartrate"].std()
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if "diffmaxmodehr" in metrics:
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if "diffmaxmodehr" in features:
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heartrate_features["heartrate_" + day_segment + "_diffmaxmodehr"] = heartrate_data.groupby(["local_date"])["heartrate"].max() - heartrate_data.groupby(["local_date"])["heartrate"].agg(lambda x: pd.Series.mode(x)[0])
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if "diffminmodehr" in metrics:
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if "diffminmodehr" in features:
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heartrate_features["heartrate_" + day_segment + "_diffminmodehr"] = heartrate_data.groupby(["local_date"])["heartrate"].agg(lambda x: pd.Series.mode(x)[0]) - heartrate_data.groupby(["local_date"])["heartrate"].min()
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if "entropyhr" in metrics:
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if "entropyhr" in features:
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heartrate_features["heartrate_" + day_segment + "_entropyhr"] = heartrate_data.groupby(["local_date"])["heartrate"].agg(entropy)
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# get number of minutes in each heart rate zone
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for feature_name in list(set(["lengthoutofrange", "lengthfatburn", "lengthcardio", "lengthpeak"]) & set(metrics)):
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for feature_name in list(set(["lengthoutofrange", "lengthfatburn", "lengthcardio", "lengthpeak"]) & set(features)):
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heartrate_zone = heartrate_data[heartrate_data["heartrate_zone"] == feature_name[6:]]
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heartrate_features["heartrate_" + day_segment + "_" + feature_name] = heartrate_zone.groupby(["local_date"])["device_id"].count() / num_rows_per_minute
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heartrate_features.fillna(value={"heartrate_" + day_segment + "_" + feature_name: 0}, inplace=True)
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