biopsykit.signals.ecg.event_extraction package

Module for ECG event extraction.

class biopsykit.signals.ecg.event_extraction.BaseEcgExtraction[source]

Bases: BaseExtraction

Base class for ECG event extraction algorithms.

extract(*, ecg, sampling_rate_hz)[source]

Extract events from ECG signal.

This is an abstract method that needs to be implemented in a subclass.

Parameters

  • ecg (DataFrame) – ECG signal

  • sampling_rate_hz (float) – Sampling rate of ECG signal in Hz

Return type

self

Raises

NotImplementedError – If this method is called from the base class

class biopsykit.signals.ecg.event_extraction.BaseEcgExtractionWithHeartbeats[source]

Bases: BaseExtraction

Base class for ECG event extraction algorithms that require segmented heartbeats.

extract(*, ecg, heartbeats, sampling_rate_hz)[source]

Extract events from ECG signal.

This is an abstract method that needs to be implemented in a subclass.

Parameters

  • ecg (DataFrame) – ECG signal

  • heartbeats (DataFrame) – DataFrame containing segmented heartbeats. Each row contains start, end, and R-peak location (in samples from beginning of signal) of that heartbeat, index functions as id of heartbeat

  • sampling_rate_hz (float) – Sampling rate of ECG signal in Hz

Return type

self

Raises

NotImplementedError – If this method is called from the base class

class biopsykit.signals.ecg.event_extraction.QPeakExtractionForouzanfar2018(scaling_factor=2000, handle_missing_events='warn')[source]

Bases: BaseEcgExtractionWithHeartbeats, CanHandleMissingEventsMixin

Initialize new QPeakExtractionForouzanfar2018 algorithm instance.

Parameters

  • scaling_factor (float, optional) – Scaling factor for the threshold used to detect the Q-peak. Default: 2000

  • handle_missing_events (one of {"warn", "raise", "ignore"}, optional) – How to handle missing data in the input dataframes. Default: “warn”

scaling_factor: float
extract(*, ecg, heartbeats, sampling_rate_hz)[source]

Extract Q-peaks from given ECG signal.

The results are saved in the points_ attribute of the super class.

Parameters

  • ecg (DataFrame) – ECG signal

  • heartbeats (DataFrame) – DataFrame containing one row per segmented heartbeat, each row contains start, end, and R-peak location (in samples from beginning of signal) of that heartbeat, index functions as id of heartbeat

  • sampling_rate_hz (float) – Sampling rate of ECG signal in hz

Return type

self

Raises

EventExtractionError – If the event extraction fails and handle_missing is set to “raise”

class biopsykit.signals.ecg.event_extraction.QPeakExtractionMartinez2004Neurokit(handle_missing_events='warn')[source]

Bases: BaseEcgExtractionWithHeartbeats, CanHandleMissingEventsMixin

Initialize new QPeakExtractionMartinez2004Neurokit algorithm instance.

Parameters

handle_missing_events (one of {"warn", "raise", "ignore"}, optional) – How to handle missing data in the input dataframes. Default: “warn”

extract(*, ecg, heartbeats, sampling_rate_hz)[source]

Extract Q-peaks from given ECG signal.

The results are saved in the points_ attribute of the super class.

Parameters

  • ecg (DataFrame) – ECG signal

  • heartbeats (DataFrame) – DataFrame containing one row per segmented heartbeat, each row contains start, end, and R-peak location (in samples from beginning of signal) of that heartbeat, index functions as id of heartbeat

  • sampling_rate_hz (int) – Sampling rate of ECG signal in hz

Return type

self

Raises

EventExtractionError – If the event extraction fails and handle_missing is set to “raise”

class biopsykit.signals.ecg.event_extraction.QPeakExtractionSciPyFindPeaksNeurokit(handle_missing_events='warn')[source]

Bases: BaseEcgExtractionWithHeartbeats, CanHandleMissingEventsMixin

Initialize new QPeakExtractionSciPyFindPeaksNeurokit algorithm instance.

Parameters

handle_missing_events (one of {"warn", "raise", "ignore"}, optional) – How to handle missing data in the input dataframes. Default: “warn”

extract(*, ecg, heartbeats, sampling_rate_hz)[source]

Extract Q-peaks from given ECG signal.

The results are saved in the points_ attribute of the super class.

Parameters

  • ecg (DataFrame) – ECG signal

  • heartbeats (DataFrame) – DataFrame containing one row per segmented heartbeat, each row contains start, end, and R-peak location (in samples from beginning of signal) of that heartbeat, index functions as id of heartbeat

  • sampling_rate_hz (int) – Sampling rate of ECG signal in hz

Return type

self

Raises

EventExtractionError – If the event extraction fails and handle_missing is set to “raise”

class biopsykit.signals.ecg.event_extraction.QPeakExtractionVanLien2013(time_interval_ms=40, handle_missing_events='warn')[source]

Bases: BaseEcgExtractionWithHeartbeats, CanHandleMissingEventsMixin

Initialize new QPeakExtractionVanLien2013 algorithm instance.

Parameters

  • time_interval_ms (int, optional) – Specify the constant time interval in milliseconds which will be subtracted from the R-peak for Q-peak estimation. Default: 40 ms

  • handle_missing_events (one of {"warn", "raise", "ignore"}, optional) – How to handle missing data in the input dataframes. Default: “warn”

time_interval_ms: int
extract(*, ecg, heartbeats, sampling_rate_hz)[source]

Extract Q-peaks from given ECG signal.

The results are saved in the points_ attribute of the super class.

Parameters

  • ecg (DataFrame) – ECG signal. Not used in this function since Q-peak is estimated from the R-peaks in the heartbeats DataFrame.

  • heartbeats (DataFrame) – DataFrame containing one row per segmented heartbeat, each row contains start, end, and R-peak location (in samples from beginning of signal) of that heartbeat, index functions as id of heartbeat

  • sampling_rate_hz (int) – Sampling rate of ECG signal in hz

Return type

self

Raises

EventExtractionError – If the event extraction fails and handle_missing is set to “raise”

class biopsykit.signals.ecg.event_extraction.RPeakExtractionNeurokit(handle_missing_events='warn', method='neurokit')[source]

Bases: BaseEcgExtraction, CanHandleMissingEventsMixin

Initialize new RPeakExtractionNeurokit algorithm instance.

Parameters

  • handle_missing_events (one of {"warn", "raise", "ignore"}, optional) – How to handle missing data in the input dataframes. Default: “warn”

  • method (str) –

ecg_processed_: DataFrame
method: str
extract(*, ecg, sampling_rate_hz)[source]

Extract events from ECG signal.

This is an abstract method that needs to be implemented in a subclass.

Parameters

  • ecg (DataFrame) – ECG signal

  • sampling_rate_hz (float) – Sampling rate of ECG signal in Hz

Return type

self

Raises

NotImplementedError – If this method is called from the base class

biopsykit.signals.ecg.aggregation package biopsykit.signals.ecg.hrv_extraction package