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Plot spectrograms to check test sound files alignment

Source: R/manual_realign.R
manual_realign.Rd

manual_realign plots spectrograms to visually inspect 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 the function selection_table from the warbleR package) with the reference to the test sounds (typically the output of align_test_files). 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 distance.

Y

object of class 'data.frame', 'selection_table' or 'extended_selection_table' (the last 2 classes are created by the function selection_table from the warbleR package) with the master sound file annotations. This should be the same data than that was used for finding the position of markers in find_markers. It should also contain a 'sound.id' column.

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. 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 is 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 spectro. Default is 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

A 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 is seq(-120, 0, 1).

palette

Color palette function for spectrogram. Default is viridis. See spectro for more palettes. Palettes as gray.2 may work better when fast.spec = TRUE (an argument that can be passed to the internal spectrogram function using "...").

duration

A 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 are plotted as this is 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 'marker' argument). Default is 0.2.

step.lengths

Numeric vector of length 2 indicating the time length (in ms) of short (min(step.lengths)) and long steps (max(step.lengths)) for manually aligning spectrograms. Default is c(5, 30).

flim

A numeric vector of length 2 indicating the highest and lowest frequency limits (kHz) of the spectrogram, as in spectro. Default is 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 then and external graphic window is used.Dimensions can be set using the 'width' and 'height' arguments. Default is TRUE.

width

Numeric vector of length 1. Single value (in inches) indicating the width of the output image files. Default is 10.

height

Numeric vector of length 1. Single value (in inches) indicating the height of the output image files. Default is 5.

srt

Numeric argument of length 1. The rotation (in degrees) of the sound id labels. Default is 0.

cex

Numeric argument of length 1controlling the size of sound id text labels. Default is 1.

fast.spec

Logical. If TRUE then image function is used internally to create spectrograms, which substantially increases performance (much faster), although some options become unavailable, as collevels (amplitude scale). Default is FALSE.

marker

Character string with the name of the marker to be used as the main reference for checking/adjusting time alignments. Default is '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 is 0.2 s. Use 0 to remove grid.

...

Additional arguments to be passed to the internal spectrogram creating function for customizing graphical output. The function is a modified version of 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. Return 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 in top of that from test sound files, highlighting the position of correspondent 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 (low 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). The function returns an object similar to the input object 'X' in which the start and end of the sounds have been adjusted.

References

Araya-Salas M., E. Grabarczyk, M. Quiroz-Oliva, A. Garcia-Rodriguez, A. Rico-Guevara. (2023), baRulho: an R package to quantify degradation in animal acoustic signals .bioRxiv 2023.11.22.568305.

See also

auto_realign; find_markers; align_test_files

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

Author

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

Examples

{
  # load example data
  data("master_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)

  # 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)
 }
}