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Fix small misalignments in the time position of test sounds

Source: R/auto_realign.R
auto_realign.Rd

auto_realign() fixes small misalignments in the time position of test sounds in an extended selection table using spectrographic cross-correlation.

Usage

auto_realign(
  X,
  Y,
  cores = getOption("mc.cores", 1),
  pb = getOption("pb", TRUE),
  hop.size = getOption("hop.size", 11.6),
  wl = getOption("wl", NULL),
  ovlp = getOption("ovlp", 90),
  wn = c("hanning", "hamming", "bartlett", "blackman", "flattop", "rectangle"),
  bp = NULL
)

Arguments

X

Object of class extended_selection_table (created by warbleR::selection_table() from the warbleR package) with the test sound files' annotations to be aligned. Must contain the following columns: 1) sound.files: name of the .wav files, 2) selec: unique selection identifier (within a sound file), 3) start: start time and 4) end: end time of selections, 5) bottom.freq: low frequency for bandpass, 6) top.freq: high frequency for bandpass, and 7) sound.id: ID of sounds used to identify counterparts across distances. Each sound must have a unique ID within a given distance.

Y

Object of class extended_selection_table (a class created by warbleR::selection_table() from the warbleR package) with the master sound file annotations. This should be the same data used for finding the position of markers in find_markers(). It should also contain a sound.id column.

cores

Numeric vector of length 1. Controls whether parallel computing is applied by specifying the number of cores to be used. Default 1 (i.e. no parallel computing). Can be set globally for the current R session via the "mc.cores" option (see options()).

pb

Logical argument to control if progress bar is shown. Default TRUE. Can be set globally for the current R session via the "pb" option (see options()).

hop.size

Numeric vector of length 1 specifying the time window duration (in ms). Default 11.6 ms, which is equivalent to 512 wl for a 44.1 kHz sampling rate. Ignored if wl is supplied. Can be set globally for the current R session via the "hop.size" option (see options()).

wl

A vector with a single even integer number specifying the window length of the spectrogram. Default NULL. If supplied, hop.size is ignored. Odd integers will be rounded up to the nearest even number. Can be set globally for the current R session via the "wl" option (see options()).

ovlp

Numeric vector of length 1 specifying the percentage of overlap between two consecutive windows, as in seewave::spectro(). Default 90. High values slow down the function but produce more accurate results. Can be set globally for the current R session via the "ovlp" option (see options()).

wn

Character vector of length 1 specifying the window name, as in seewave::ftwindow().

bp

Numeric vector of length 2 giving the lower and upper limits of a frequency bandpass filter (in kHz). Default NULL.

Value

Object X in which time parameters (columns start and end) have been tailored to more closely match the start and end of the reference sound.

Details

Precise alignment is crucial for downstream measures of sound degradation. This function uses spectrogram cross-correlation to improve the time position alignment of test sounds. The master sound file is used as reference. The function calls warbleR::cross_correlation() internally to align sounds using cross-correlation. The output extended selection table contains the new start and end values after alignment.

Note that 1) this function only works to further improve alignments if the estimated position of the test sound is already close to the actual position, and 2) both X and Y must be extended selection tables sensu warbleR::selection_table(). The function might not work properly with annotations with a small frequency range (e.g. pure tones).

References

Araya-Salas, M., Grabarczyk, E. E., Quiroz-Oliva, M., Garcia-Rodriguez, A., & Rico-Guevara, A. (2025). Quantifying degradation in animal acoustic signals with the R package baRulho. Methods in Ecology and Evolution, 00, 1-12. https://doi.org/10.1111/2041-210X.14481

Clark, C.W., Marler, P. & Beeman K. (1987). Quantitative analysis of animal vocal phonology: an application to Swamp Sparrow song. Ethology. 76:101-115.

See also

blur_ratio() and warbleR::cross_correlation().

Other test sound alignment: align_test_files(), find_markers(), manual_realign(), plot_aligned_sounds()

Author

Marcelo Araya-Salas (marcelo.araya@ucr.ac.cr)

Examples

{
  # load example data
  data("test_sounds_est")
  data("master_est")
  
  # create "unaligned_test_sounds_est" by
  # adding error to "test_sounds_est" start and end
  unaligned_test_sounds_est <- test_sounds_est
  set.seed(123)
  noise_time <- sample(c(0.009, -0.01, 0.03, -0.03, 0, 0.07, -0.007),
  nrow(unaligned_test_sounds_est),
  replace = TRUE)
  
  attr(unaligned_test_sounds_est, "check.res")$start <- 
  unaligned_test_sounds_est$start <- 
  unaligned_test_sounds_est$start + noise_time
  attr(unaligned_test_sounds_est, "check.res")$end <- 
  unaligned_test_sounds_est$end  <- 
  unaligned_test_sounds_est$end + noise_time

# re align
realigned_est <- auto_realign(X = unaligned_test_sounds_est, Y = master_est)
}