get_envelopes: Extract absolute amplitude envelopes

In maRce10/ohun: Optimizing Acoustic Signal Detection

Extract absolute amplitude envelopes

Description

get_envelopes extracts absolute amplitude envelopes to speed up energy detection

Usage

get_envelopes(path = ".", files = NULL, bp = NULL, hop.size = 11.6, wl = NULL,
cores = 1, thinning = 1, pb = TRUE, smooth = 5, normalize = TRUE)

Arguments

path	Character string containing the directory path where the sound files are located. The current working directory is used as default.
files	character vector or indicating the sound files that will be analyzed. Supported file formats:'.wav', '.mp3', '.flac' and '.wac'. If not supplied the function will work on all sound files (in the supported format) in 'path'.
bp	Numeric vector of length 2 giving the lower and upper limits of a frequency bandpass filter (in kHz). Default is NULL. Bandpass is done using the function ffilter, which applies a short-term Fourier transformation to first create a spectrogram in which the target frequencies are filtered and then is back transformed into a wave object using a reverse Fourier transformation.
hop.size	A numeric vector of length 1 specifying the time window duration (in ms). Default is 11.6 ms, which is equivalent to 512 wl for a 44.1 kHz sampling rate. Ignored if 'wl' is supplied.
wl	A numeric vector of length 1 specifying the window length of the spectrogram. Default is NULL. If supplied, 'hop.size' is ignored. Used internally for bandpass filtering (so only applied when 'bp' is supplied).
cores	Numeric. Controls whether parallel computing is applied. It specifies the number of cores to be used. Default is 1 (i.e. no parallel computing).
thinning	Numeric vector of length 1 in the range 0~1 indicating the proportional reduction of the number of samples used to represent amplitude envelopes (i.e. the thinning of the envelopes). Usually amplitude envelopes have many more samples than those needed to accurately represent amplitude variation in time, which affects the size of the output (usually very large R objects / files). Default is 1 (no thinning). Higher sampling rates can afford higher size reduction (e.g. lower thinning values). Reduction is conducted by linear interpolation using approx. Note that thinning may decrease time precision and that the higher the thinning the less precise the time detection. It's generally not advised if no smoothing ('smooth' argument) is applied.
pb	Logical argument to control progress bar. Default is TRUE.
smooth	A numeric vector of length 1 to smooth the amplitude envelope with a sum smooth function. It controls the time 'neighborhood' (in ms) in which amplitude samples are smoothed (i.e. averaged with neighboring samples). Default is 5. 0 means no smoothing is applied. Note that smoothing is applied before thinning (see 'thinning' argument). The function envelope is used internally which is analogous to sum smoothing in env. This argument is used internally by get_envelopes.
normalize	Logical argument to control if envelopes are normalized to a 0-1 range.

Details

This function extracts the absolute amplitude envelopes of sound files. Can be used to manipulate envelopes before running energy_detector.

Value

An object of class 'envelopes'.

Author(s)

Marcelo Araya-Salas ([e-mail]).

References

Araya-Salas, M., Smith-Vidaurre, G., Chaverri, G., Brenes, J. C., Chirino, F., Elizondo-Calvo, J., & Rico-Guevara, A. 2022. ohun: an R package for diagnosing and optimizing automatic sound event detection. BioRxiv, 2022.12.13.520253. https://doi.org/10.1101/2022.12.13.520253

See Also

energy_detector

Examples

{
  # Save to temporary working directory
  data(list = c("lbh1", "lbh2"))
  tuneR::writeWave(lbh1, file.path(tempdir(), "lbh1.wav"))
  tuneR::writeWave(lbh2, file.path(tempdir(), "lbh2.wav"))

  # get raw absolute amplitude envelopes
  envs <- get_envelopes(path = tempdir())

  # extract segment for the first sound event in the first sound file
  x <- envs[[1]]$envelope

  # and plot it
  plot(x[(length(x) / 9):(length(x) / 4)], type = "l", xlab = "samples", ylab = "amplitude")

  # smoothing envelopes
  envs <- get_envelopes(path = tempdir(), smooth = 6.8)
  x <- envs[[1]]$envelope
  plot(x[(length(x) / 9):(length(x) / 4)], type = "l", xlab = "samples", ylab = "amplitude")

  # smoothing and thinning
  envs <- get_envelopes(path = tempdir(), thinning = 1 / 10, smooth = 6.8)
  x <- envs[[1]]$envelope
  plot(x[(length(x) / 9):(length(x) / 4)], type = "l", xlab = "samples", ylab = "amplitude")

  # no normalization
  envs <- get_envelopes(path = tempdir(), thinning = 1 / 10, smooth = 6.8)
  x <- envs[[1]]$envelope
  plot(x[(length(x) / 9):(length(x) / 4)],
    type = "l", xlab = "samples", ylab = "amplitude",
    normalize = FALSE
  )
}

maRce10/ohun documentation built on Oct. 25, 2024, 6:22 p.m.