rhrv-master.zip_ECG ST_ST ECG_st segment

# rhrv Matlab tools for calculating Heart-Rate Variability (HRV) metrics on ECG signals. Supports working with the [PhysioNet](https://physionet.org/) data format. ## Features * WFDB wrappers: A small subset of the WFDB tools are wrapped with matlab functions. * `gqrs` - A QRS detection algorithm. * `rdsamp` - For reading PhysioNet signal data into matlab. * `rdann` - For reading PhysioNet annotation data into matlab. * QRS detection: Finding the beats in ECG signals. * `rqrs` - Detection of R-peaks in ECG signals (based on PhysioNet's `gqrs`). Configurable for use with both human and animal ECGs. * `qrs_compare` - Comparison of QRS detections to reference annotations and calculation of quality indices like Sensitivity, PPV. * ECG signal processing * `egcrr` - Construction of RR intervals from ECG data in PhysioNet format. * `filtrr` - Filtering of RR interval time series to detect ectopic (out of place) beats. * HRV Metrics: Calculating quantative measures that indicate the activity of the heart based on RR intervals. * `hrv_time` - Time Domain: AVNN, SDNN, pXNN. * `hrv_freq` - Frequency Domain: * Total and normalized power in VLF, LF and HF bands. * Spectral power estimation using Lomb, Auto Regressive, Welch and FFT methods. * `hrv_nonlinear` - Nonlinear methods: * Detrended fluctuation analysis (DFA), with short- and long-term scaling exponents (alpha1, alpha2). * Spectral power-law scaling exponent (beta). * Multiscale sample entropy (MSE). * Poincaré plot metrics (SD1, SD2). * `hrv_fragmentation` - Time-domain RR interval fragmentation analysis. ## Requirements * Matlab with Signal Processing toolbox. Should work on Matlab R2014b or newer. * The Pysionet WFDB tools. The toolbox can install this for you. ## Installation 1. Clone the repo or download the source code. 2. From MATLAB, run the `rhrv_init` function. This function will: * Check for the presence of the WFDB tools in your system `PATH`. If WFDB tools are not detected, it will attempt to automatically download them for you into the folder `bin/wfdb` under the repository root. * Set up your MATLAB path to include the code from this toolbox. ### Manual WFDB Installation (Optional) The above steps should be enough to get most users started. If however you don't want `rhrv_init` to download the WFDB tools for you, or the automatic installation fails for some reason, you can install them yourself. * On OSX, you can use [homebrew](http://brew.sh) to install it easily with `brew install homebrew/science/wfdb`. * On Windows and Linux, you should either [download the WFDB binaries](https://physionet.org/physiotools/binaries/) for your OS or compile them [from source](https://physionet.org/physiotools/wfdb.shtml#downloading) using the instructions on their website. Once you have the binaries, place them in some folder on your `$PATH` or somewere under the repo's root folder (`bin/wfdb` would be a good choice as it's `.gitignore`d) and they will be found and used automatically. Or, if you would like to manually specify a path outside the repo which contains the WFDB binaries (e.g. `/usr/local/bin` for a homebrew install), you can edit [`cfg/defaults.yml`](https://github.com/avivrosenberg/rhrv/blob/master/cfg/defaults.yml) and set the `rhrv.paths.wfdb_path` variable to the desired path. For linux users it's recommended to install from source as the binaries provided on the PhysioNet website are very outdated. ## Usage Exaple of calculating HRV measures for a PhysioNet record (in this case from [`mitdb`](https://www.physionet.org/physiobank/database/mitdb/)): ``` >> rhrv('db/mitdb/111', 'window_minutes', 15, 'plot', true); ``` Will give you: ``` [0.000] >> rhrv: Processing ECG signal from record db/mitdb/111 (ch. 1)... [0.000] >> rhrv: Signal duration: 00:30:05.000 [HH:mm:ss.ms] [0.010] >> rhrv: Analyzing window 1 of 2... [0.010] >> rhrv: [1/2] Detecting QRS end RR intervals... [0.810] >> rhrv: [1/2] Filtering RR intervals... [0.840] >> rhrv: [1/2] 1039 NN intervals, 6 RR intervals were filtered out [0.840] >> rhrv: [1/2] Calculating time-domain metrics... [0.920] >> rhrv: [1/2] Calculating frequency-domain metrics... [1.180] >> rhrv: [1/2] Calculating nonlinear metrics... [1.430] >> rhrv: [1/2] Calculating fragmentation metrics... [1.490] >> rhrv: Analyzing window 2 of 2... [1.490] >> rhrv: [2/2] Detecting QRS end RR intervals... [2.080] >> rhrv: [2/2] Filtering RR intervals... [2.100] >> rhrv: [2/2] 1057 NN intervals, 8 RR intervals were filtered out [2.100] >> rhrv: [2/2] Calculating time-domain metrics... [2.140] >> rhrv: [2/2] Calculating frequency-domain metrics... [2.240] >> rhrv: [2/2] Calculating nonlinear metrics... [2.450] >> rhrv: [2/2] Calculating fragmentation metrics... [2.490] >> rhrv: Building statistics table... [2.520] >> rhrv: Displaying Results... RR NN AVNN SDNN RMSSD pNN50 SEM TOTAL_POWER_LOMB VLF_POWER_LOMB LF_POWER_LOMB HF_POWER_LOMB LF_NORM_LOMB HF_NORM_LOMB LF_TO_HF_LOMB LF_PEAK_LOMB HF_PEAK_LOMB SD1 SD2 alpha1 alpha2 beta SampEn PIP IALS PSS PAS ____ ____ ______ ______ ______ _______ _______ ________________ ______________ _____________ _____________ ____________ ____________ _____________ ____________ ____________ _______ ______ ________ ________ _______ _______ _______ _________ ______ ______ 1 1045 1039 858.96 30.961 33.622 14.162 0.96054 333.22 67.098 23.574 242.55 8.8583 91.142 0.097193 0.046667 0.16667 23.786 36.745 0.65937 0.72845 -1.2471 1.835 53.321 0.53468 61.598 12.512 2 1065 1057 841.86 40.182 32.306 12.784 1.2359 388.66 132.7 32.031 223.93 12.514 87.486 0.14304 0.043333 0.16667 22.855 51.996 0.70064 0.92309 -1.6706 1.6483 52.318 0.52462 57.332 15.137 Mean 1055 1048 850.41 35.572 32.964 13.473 1.0982 360.94 99.899 27.802 233.24 10.686 89.314 0.12012 0.045 0.16667 23.32 44.371 0.68 0.82577 -1.4588 1.7417 52.819 0.52965 59.465 13.825 SE 10 9 8.5503 4.6103 0.6578 0.68888 0.1377 27.723 32.801 4.2286 9.3065 1.8278 1.8278 0.022923 0.0016667 0 0.46545 7.6255 0.020637 0.097316 0.21176 0.09336 0.50131 0.0050304 2.1328 1.3126 Median 1055 1048 850.41 35.572 32.964 13.473 1.0982 360.94 99.899 27.802 233.24 10.686 89.314 0.12012 0.045 0.16667 23.32 44.371 0.68 0.82577 -1.4588 1.7417 52.819 0.52965 59.465 13.825 [2.580] >> rhrv: Generating plots... [4.930] >> rhrv: Finished processing record db/mitdb/111. ``` The `window_minutes` parameter allow splitting the signal into windows and calculating all metrics per window. You can pass in an empty array `[]` to disable spliting. Note that in order to run the example you need to first download the relevant record (`mitdb/111`) from PhysioNet's [`mitdb` database](https://physionet.org/physiobank/database/mitdb/) (both `.dat` and `.hea` files). In the example, they were downloaded to the folder `db/mitdb` relative to MATLABs current folder. Any relative or absolute path can be used. See also [this FAQ](h