R/wavelet-onset-search.R

In Teresa00/hfmAnnotation: HFM Internal Package for Annotations

# Teresa updated May 25th 2018

#' @importFrom assertthat assert_that
#' @importFrom magrittr %>% subtract add
#' @importFrom purrr as_vector discard partial reduce
#'
library("magrittr")
library("purrr")
library("assertthat")


first_min_ <- function(signal_slice) {
  x <-
    abs(signal_slice)

  is_lower_than_before <-
    x[-c(1, length(x))] <= x[-c(length(x) - 1, length(x))]

  is_lower_than_after <-
    x[-c(1, length(x))] <= x[-c(1, 2)]

  localmin <-
    is_lower_than_before & is_lower_than_after

  index <-
    which(localmin != 0)[1]
}


#' Search for the onset of a wave using the derivative method
#'
#' TODO: Add details, perhaps better description
#'
#' @param peak_onset An integer. The index of the peak
#' where the onset will be searched around.
#' @param signal_slice A vector of wavelet signal slice
#' which is a search window for wave onset searching.
#' @param K A constant for defining amplitude threshold.
#'
#' @export
#'

wavelet_onset_search <- function(peak_onset, signal_slice, K) {
  amp_peak_onset <-
    signal_slice[length(signal_slice)] %>%
    abs()
    # abs(tail(signal_slice, 1))

  threshold <-
    amp_peak_onset * K

  slice_inverse <-
    signal_slice[(length(signal_slice) - 1):1]

  index1 <-
    which(abs(slice_inverse) < threshold)[1]

  index2 <-
    first_min_(slice_inverse)

  onset <-
    if ((is.na(index1)) & (is.na(index2))) {
      peak_onset - length(signal_slice) + 1
    } else if (is.na(index1)) {
      peak_onset - index2
    } else if (is.na(index2)) {
      peak_onset - index1
    } else {
      peak_onset - min(index1, index2)
    }
}