vital_sqi.data package

Submodules

vital_sqi.data.removal_utilities module

Trimming raw signals using: invalid values, noise at start/end of recordings etc.

vital_sqi.data.removal_utilities.concate_removed_index(start_list, end_list, remove_sliding_window=0)

handy :param start_list: :param end_list: :param remove_sliding_window: :return:

vital_sqi.data.removal_utilities.cut_by_frequency_partition(df_examine, window_size=None, peak_threshold_ratio=None, lower_bound_threshold=None, remove_sliding_window=None, overlap_rate=None)

Expose

Parameters

• df_examine –

• window_size –

• peak_threshold_ratio –

• lower_bound_threshold –

• remove_sliding_window –

• overlap_rate –

Returns

vital_sqi.data.removal_utilities.cut_invalid_rr_peak(df)

expose :param df: :return:

vital_sqi.data.removal_utilities.fill_missing_value(s, missing_index, missing_len, method='arima', lag_ratio=10)

Parameters

• s – array of input time series

• missing_index – array of list of starting indices missing data

• missing_len – array of number of missing instances,

matching with the index list :param method: :return:

Example: > missing_index = np.where(np.diff(df.TIMESTAMP_MS) > 10)[0] > missing_len = [int((df.TIMESTAMP_MS.iloc[i+1] - df.TIMESTAMP_MS.iloc[i])/10-1)

for i in missing]

> filled_s = fill_missing_value(np.array(df1.PLETH),missing,missing_len)

vital_sqi.data.removal_utilities.get_start_end_points(start_cut_pivot, end_cut_pivot, length_df)

handy :param start_cut_pivot: array of starting points of the removal segment :param end_cut_pivot: array of relevant ending points of removal segment :param length_df: the length of the origin signal :return:

vital_sqi.data.removal_utilities.remove_invalid(df, as_dataframe=True)

Exposed Remove the list of invalid data signal :param df: :param as_dataframe: :return:

vital_sqi.data.removal_utilities.remove_unchanged_squences(df, unchanged_seconds=10, sampling_rate=100, as_dataframe=True)

vital_sqi.data.removal_utilities.trim_data(data, minute_remove=1, sampling_rate=100)

Expose :param data: :param minute_remove: :param sampling_rate: :return:

vital_sqi.data.segment_split module

Splitting long recordings into segments

vital_sqi.data.segment_split.get_split_rr_index(segment_seconds, sequence)

handy Return the index of the splitting points :param segment_seconds: the length of each cut split (in seconds) :param sequence: :return:

vital_sqi.data.segment_split.get_split_time_index(segment_seconds, sequence)

handy Return the index of splitting points :param segment_seconds: the length of each cut split (in seconds) :param sequence: :return:

vital_sqi.data.segment_split.save_each_segment(filename, segment_list, save_file_folder, save_image, save_img_folder, display_trough_peak)

Save each n-second segment into csv and the relevant image :param filename: str, the origin file name :param segment_list: list, the list all split 30-second segments :param display_trough_peak: bool, default = False, display to trough and peak in the saved images :return:

vital_sqi.data.segment_split.save_segment_image(segment, saved_filename, save_img_folder, display_trough_peak)

handy :param segment: :param saved_filename: :param save_img_folder: :param display_trough_peak: :return:

vital_sqi.data.segment_split.split_to_subsegments(signal_data, filename=None, sampling_rate=100.0, segment_length_second=30.0, minute_remove=5.0, wave_type='ecg', split_type='time', is_trim=False, save_file_folder=None, save_image=False, save_img_folder=None, display_trough_peak=True)

Expose Split the data after applying bandpass filter and removing the first and last n-minutes (High pass filter with cutoff at 1Hz) The signal is split according to time domain - default is 30s :param filename: str, path to load file :param sampling_rate:float, default = 100.0. The sampling rate of the wearable device :param segment_length:float, default = 30.0. The length of the segment (in seconds) :param minute_remove: float, default = 5.0. The first and last of n-minutes to be removed :return:

Module contents

vital_sqi.data

A subpackage for all raw waveform data manipulation such as read/write, edit, resample.