U g{jH4 @sFdZddlmZddlmZddlZddlZdZdZ dZ dZ d Z d d d d gZ d)eeeeeeddd Zd*eeeeeeddd Zd+eeeeedddZd,eeeeeefdddZd-eeeeefdddZd.eeeeed!d"d Zdddd de dfeeeeeeeeeeed# d$d Zd/eeeeed&d'd(ZdS)0zPThis script provides several methods to clean abnormal and ectopic RR-intervals.)Tuple)ListNmalikZkarlssonZkamathZacarZcustomremove_outliersremove_ectopic_beatsinterpolate_nan_valuesget_nn_intervalsT,) rr_intervalsverboselow_rrihigh_rrireturncsfdd|D}|rg}|D](}|kr8kr>qHnq ||q tt|}|dkrptd|ntd|td||S)a' Function that replace RR-interval outlier by nan. Parameters --------- rr_intervals : list raw signal extracted. low_rri : int lowest RrInterval to be considered plausible. high_rri : int highest RrInterval to be considered plausible. verbose : bool Print information about deleted outliers. Returns --------- rr_intervals_cleaned : list list of RR-intervals without outliers References ---------- .. [1] O. Inbar, A. Oten, M. Scheinowitz, A. Rotstein, R. Dlin, R.Casaburi. Normal cardiopulmonary responses during incremental exercise in 20-70-yr-old men. .. [2] W. C. Miller, J. P. Wallace, K. E. Eggert. Predicting max HR and the HR-VO2 relationship for exercise prescription in obesity. .. [3] H. Tanaka, K. D. Monahan, D. R. Seals. Age-predictedmaximal heart rate revisited. .. [4] M. Gulati, L. J. Shaw, R. A. Thisted, H. R. Black, C. N. B.Merz, M. F. Arnsdorf. Heart rate response to exercise stress testing in asymptomatic women. cs.g|]&}|krkr$nn|ntjqS)npnan).0rrirr rX/var/www/html/bwave/python/venv/lib/python3.8/site-packages/hrvanalysis/preprocessing.py <sz#remove_outliers..rz {} outlier(s) have been deleted.z The outlier(s) value(s) are : {})appendsumrisnanprintformat)r r r rrr_intervals_cleanedZ outliers_listrZ nan_countrrrrs% 皙?)r methodcustom_removing_ruler rc Cs|tttttfkrtd|tkr4t||d\}}n|tkrLt|d\}}nd}d}|dg}t|ddD]h\}}|r| ||dd}qnt |||d||d r| ||dqn| t j |d7}d }qn|rt d |||S) aN RR-intervals differing by more than the removing_rule from the one proceeding it are removed. Parameters --------- rr_intervals : list list of RR-intervals method : str method to use to clean outlier. malik, kamath, karlsson, acar or custom. custom_removing_rule : int Percentage criteria of difference with previous RR-interval at which we consider that it is abnormal. If method is set to Karlsson, it is the percentage of difference between the absolute mean of previous and next RR-interval at which to consider the beat as abnormal. verbose : bool Print information about ectopic beats. Returns --------- nn_intervals : list list of NN Interval outlier_count : int Count of outlier detected in RR-interval list References ---------- .. [5] Kamath M.V., Fallen E.L.: Correction of the Heart Rate Variability Signal for Ectopics and Miss- ing Beats, In: Malik M., Camm A.J. .. [6] Geometric Methods for Heart Rate Variability Assessment - Malik M et al zNot a valid method. Please choose between malik, kamath, karlsson, acar. You can also choose your own removing critera with custom_rule parameter.)r removing_rule)r rFN)r custom_ruleTz2{} ectopic beat(s) have been deleted with {} rule.) MALIK_RULE KAMATH_RULE KARLSSON_RULE ACAR_RULE CUSTOM_RULE ValueError_remove_outlier_karlsson_remove_outlier_acar enumerater is_outlierrrrr) r rr r nn_intervals outlier_countZprevious_outlieri rr_intervalrrrrOs4!   )r2next_rr_intervalrr$rcCs|tkrt||d|k}n^|tkrhd||ko@d|knpdd||ko`d|kn}nt||||k}|S)a Test if the rr_interval is an outlier Parameters ---------- rr_interval : int RrInterval next_rr_interval : int consecutive RrInterval method : str method to use to clean outlier. malik, kamath, karlsson, acar or custom custom_rule : int percentage criteria of difference with previous RR-interval at which we consider that it is abnormal Returns ---------- outlier : bool True if RrInterval is valid, False if not rrg?g\(\?)r%absr&)r2r3rr$Zoutlierrrrr.s" r.)r r!rcCs|dg}d}tt|D]}|t|dkrD|||dq||||dd}t|||d||kr|||dq|tj|d7}q||fS)u RR-intervals differing by more than the 20 % of the mean of previous and next RR-interval are removed. Parameters --------- rr_intervals : list list of RR-intervals removing_rule : float Percentage of difference between the absolute mean of previous and next RR-interval at which to consider the beat as abnormal. Returns --------- nn_intervals : list list of NN Interval References ---------- .. [7] Automatic filtering of outliers in RR-intervals before analysis of heart rate variability in Holter recordings: a comparison with carefully edited data - Marcus Karlsson, Rolf Hörnsten, Annika Rydberg and Urban Wiklund rr#)rangelenrr4rr)r r!r/r0r1Zmean_prev_next_rrirrrr+s   r+)r rcCs|g}d}t|D]b\}}|dkr,||qt|dd}t||||kr^||q|tj|d7}q||fS)aq RR-intervals differing by more than the 20 % of the mean of last 9 RrIntervals are removed. Parameters --------- rr_intervals : list list of RR-intervals custom_rule : int percentage criteria of difference with mean of 9 previous RR-intervals at which we consider that RR-interval is abnormal. By default, set to 20 % Returns --------- nn_intervals : list list of NN Interval References ---------- .. [8] Automatic ectopic beat elimination in short-term heart rate variability measurements Acar B., Irina S., Hemingway H., Malik M. r iNr#)r-rrZnanmeanr4r)r r$r/r0r1r2Z acar_rule_eltrrrr,s    r,linearforward)r interpolation_method limit_arealimit_directionrcCs&t|}|j||||d}|jS)a` Function that interpolate Nan values with linear interpolation Parameters --------- rr_intervals : list RrIntervals list. interpolation_method : str Method used to interpolate Nan values of series. limit_area: str If limit is specified, consecutive NaNs will be filled with this restriction. limit_direction: str If limit is specified, consecutive NaNs will be filled in this direction. limit: int TODO Returns --------- interpolated_rr_intervals : list new list with outliers replaced by interpolated values. )rlimitr<r=)pdZSeriesZ interpolatevaluestolist)r r;r<r=r>Zseries_rr_intervals_cleanedinterpolated_rr_intervalsrrrrs ) r r rr<r=r;ectopic_beats_removal_methodr rc CsBt||||d}t||||d} t| ||d} t| |||d} | S)au Function that computes NN Intervals from RR-intervals. Parameters --------- rr_intervals : list RrIntervals list. interpolation_method : str Method used to interpolate Nan values of series. ectopic_beats_removal_method : str method to use to clean outlier. malik, kamath, karlsson, acar or custom. low_rri : int lowest RrInterval to be considered plausible. high_rri : int highest RrInterval to be considered plausible. limit_area: str If limit is specified, consecutive NaNs will be filled with this restriction. limit_direction: str If limit is specified, consecutive NaNs will be filled in this direction. verbose : bool Print information about deleted outliers. Returns --------- interpolated_nn_intervals : list list of NN Interval interpolated )r rr )r<r=)rr )rrr) r r rr<r=r;rCr rrBr/Zinterpolated_nn_intervalsrrrr's {Gz?)r/r0r!rcCs<d}|t||kr tdd}t|dkr8tdd}|S)a Test if the sample meet the condition to be used for analysis Parameters ---------- nn_intervals : list list of Normal to Normal Interval outlier_count : int count of outliers or ectopic beats removed from the interval removing_rule : str rule to follow to determine whether the sample is valid or not Returns ---------- bool True if sample is valid, False if not Tz>Too much outlier for analyses ! You should descard the sample.Fz-Not enough Heart beat for Nyquist criteria ! )r7r)r/r0r!resultrrris_valid_sampleRs rG)Tr r )rrT)rr)r)r)r9Nr:N)rD)__doc__typingrrZpandasr?numpyrr%r'r&r(r)__all__floatboolintlistrstrrr.r+r,rrrGrrrrsr     8  F *' "  +