Plot spectrograms to check test sound files alignment

manual_realign() plots spectrograms to visually inspect, and interactively adjust, alignment precision on test sound files.

Usage

manual_realign(
  X,
  Y,
  hop.size = getOption("hop.size", 11.6),
  wl = getOption("wl", NULL),
  ovlp = getOption("ovlp", 0),
  path = getOption("sound.files.path", "."),
  collevels = seq(-120, 0, 5),
  palette = viridis::viridis,
  duration = 2,
  mar = 0.2,
  step.lengths = c(5, 30),
  flim = NULL,
  label.col = "white",
  ext.window = TRUE,
  width = 10,
  height = 5,
  srt = 0,
  cex = 1,
  fast.spec = TRUE,
  marker = "start_marker",
  grid = 0.2,
  ...
)

Arguments

X: Object of class data.frame, selection_table, or extended_selection_table (the last 2 classes are created by warbleR::selection_table() from the warbleR package) with the test sound files' annotations (typically the output of align_test_files()) 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 data.frame, selection_table, or extended_selection_table (the last 2 classes are 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.
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 0. Can be set globally for the current R session via the "ovlp" option (see options()).
path: Character string containing the directory path where the sound files are found. Only needed when X is not an extended selection table. If not supplied the current working directory is used. Can be set globally for the current R session via the "sound.files.path" option (see options()).
collevels: Numeric vector of length 3. Specifies levels to partition the amplitude range of the spectrogram (in dB). The more levels, the higher the resolution of the spectrogram. Default seq(-120, 0, 1).
palette: Color palette function for the spectrogram. Default viridis::viridis(). See seewave::spectro() for more palettes. Palettes such as monitoR::gray.2 may work better when fast.spec = TRUE (an argument that can be passed to the internal spectrogram function using ...).
duration: Numeric vector of length 1. Specifies the overall duration of the clip that will be plotted. Notice that only the initial part of the test files is plotted, as this is usually enough to tell the precision of the alignment.
mar: Numeric vector of length 1. Specifies the minimum margins adjacent (before and after) to the start of the marker used for checking alignments (see the marker argument). Default 0.2.
step.lengths: Numeric vector of length 2 indicating the time length (in ms) of short (min(step.lengths)) and long (max(step.lengths)) steps for manually aligning spectrograms. Default c(5, 30).
flim: Numeric vector of length 2 indicating the highest and lowest frequency limits (kHz) of the spectrogram, as in seewave::spectro(). Default NULL, which will plot spectrograms in the full frequency range (0 - nyquist frequency).
label.col: Character string controlling the color of lines and sound ID labels.
ext.window: Logical. If TRUE, an external graphic window is used. Dimensions can be set using the width and height arguments. Default TRUE.
width: Numeric vector of length 1. Single value (in inches) indicating the width of the output image files. Default 10.
height: Numeric vector of length 1. Single value (in inches) indicating the height of the output image files. Default 5.
srt: Numeric argument of length 1. The rotation (in degrees) of the sound ID labels. Default 0.
cex: Numeric argument of length 1 controlling the size of sound ID text labels. Default 1.
fast.spec: Logical. If TRUE, the image function is used internally to create spectrograms, which substantially increases performance (much faster), although some options become unavailable, such as collevels (amplitude scale). Default FALSE.
marker: Character string with the name of the marker to be used as the main reference for checking/adjusting time alignments. Default "start_marker". Note that this can take any of the sound IDs in Y$sound.id.
grid: Numeric vector of length 1 controlling the spacing between vertical lines on the spectrogram. Default 0.2 s. Use 0 to remove the grid.
...: Additional arguments to be passed to the internal spectrogram-creating function for customizing graphical output. The function is a modified version of seewave::spectro(), so it takes the same arguments.

Value

Creates a multipanel graph with spectrograms of master and test sound files in which users can interactively adjust their alignment in time. Returns an object similar to the input object X, in which the start and end of the sounds have been adjusted.

Details

This function allows the interactive adjustment of the alignment of test sound files produced by align_test_files(). The function generates a multipanel graph with the spectrogram of the master sound file on top of that from test sound files, highlighting the position of corresponding test sounds on both in order to simplify assessing and adjusting their alignment. Spectrograms include the first few seconds of the sound files (controlled by duration), which is usually enough to tell the precision of the alignment. The lower spectrogram shows a series of "buttons" that users can click on to control if the test sound file spectrogram (lower panel) needs to be moved to the left ("<") or right (">"). Users can also reset the spectrogram to its original position ("reset"), move on to the next sound file in X (test sound file annotations), or stop the process (stop button).

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

Author

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

Examples

{
  # load example data
  data(list = c("master_est", "test_sounds_est"))

  # save example files in working director to recreate a case in which working
  # with sound files instead of extended selection tables.
  # This doesn't have to be done with your own data as you will
  # have them as sound files already.
  for (i in unique(test_sounds_est$sound.files)[1:2]) {
  writeWave(object = attr(test_sounds_est, "wave.objects")[[i]], file.path(tempdir(), i))
  }

  # save master file
  writeWave(object = attr(master_est, "wave.objects")[[1]], file.path(tempdir(), "master.wav"))

  # get marker position
  markers <- find_markers(X = master_est, test.files = unique(test_sounds_est$sound.files)[2], 
  path = tempdir())

  # align all test sounds
  alg.tests <- align_test_files(X = master_est, Y = markers, path = tempdir())

  # add error to alignment
  lag <- (as.numeric(as.factor(alg.tests$sound.files)) - 2) / 30
  alg.tests$start <- alg.tests$start + lag
  alg.tests$end <- alg.tests$end + lag

  if(interactive()){
  realigned_est <- manual_realign(X = alg.tests, Y = master_est, duration = 2,
  ovlp = 50, hop.size = 14, collevels = seq(-140, 0, 5), palette = viridis::mako,
  ext.window = FALSE)
 }
}