Create long spectrograms of entire sound files

full_spectrograms produces image files with spectrograms of entire sound files split into multiple rows.

Usage

full_spectrograms(X = NULL, flim = NULL, sxrow = 5, rows = 10,
collevels = seq(-40, 0, 1), ovlp = 50, parallel = 1, wl = 512, gr = FALSE,
pal = reverse.gray.colors.2, cex = 1, it = "jpeg", flist = NULL,
overwrite = TRUE, path = NULL, pb = TRUE, fast.spec = FALSE, labels = "selec",
 horizontal = FALSE, song = NULL, suffix = NULL, dest.path = NULL,
 only.annotated = FALSE, ...)

Arguments

X: 'selection_table' object or any data frame with columns for sound file name (sound.files), selection number (selec), and start and end time of signal (start and end). If given, a transparent box is plotted around each selection and the selections are labeled with the selection number (and selection comment, if available). Default is NULL. Alternatively, it can also take the output of cross_correlation or auto_detec (when 'output' is a 'list', see cross_correlation or auto_detec). If supplied a secondary row is displayed under each spectrogram showing the detection (either cross-correlation scores or wave envelopes) values across time.
flim: A numeric vector of length 2 indicating the highest and lowest frequency limits (kHz) of the spectrogram, as in spectro. Default is NULL. Alternatively, a character vector similar to c("-1", "1") in which the first number is the value to be added to the minimum bottom frequency in 'X' and the second the value to be added to the maximum top frequency in 'X'. This is computed independently for each sound file so the frequency limit better fits the frequency range of the annotated signals. This is useful when plotting annotated spectrograms with marked differences in the frequency range of annotations among sond files. Note that top frequency adjustment is ignored if 'song' labels are included (argument 'song').
sxrow: A numeric vector of length 1. Specifies seconds of spectrogram per row. Default is 5.
rows: A numeric vector of length 1. Specifies number of rows per image file. Default is 10.
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(-40, 0, 1).
ovlp: Numeric vector of length 1 specifying % of overlap between two consecutive windows, as in spectro. Default is 50. High values of ovlp slow down the function but produce more accurate selection limits (when X is provided).
parallel: Numeric. Controls whether parallel computing is applied. It specifies the number of cores to be used. Default is 1 (i.e. no parallel computing).
wl: A numeric vector of length 1 specifying the window length of the spectrogram, default is 512.
gr: Logical argument to add grid to spectrogram. Default is FALSE.
pal: Color palette function for spectrogram. Default is reverse.gray.colors.2. See spectro for more palettes.
cex: A numeric vector of length 1 giving the amount by which text (including sound file and page number) should be magnified. Default is 1.
it: A character vector of length 1 giving the image type to be used. Currently only "tiff" and "jpeg" are admitted. Default is "jpeg".
flist: character vector or factor indicating the subset of files that will be analyzed. Ignored if X is provided.
overwrite: Logical argument. If TRUE all selections will be analyzed again when code is rerun. If FALSE only the selections that do not have a image file in the working directory will be analyzed. Default is FALSE.
path: Character string containing the directory path where the sound files are located. If NULL (default) then the current working directory is used.
pb: Logical argument to control progress bar. Default is TRUE.
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, and sc (amplitude scale). This option is indicated for signals with high background noise levels. Palette colors gray.1, gray.2, gray.3, topo.1 and rainbow.1 (which should be imported from the package monitoR) seem to work better with 'fast' spectrograms. Palette colors gray.1, gray.2, gray.3 offer decreasing darkness levels.
labels: Character string with the name of the column(s) for selection labeling. Default is 'selec'. Set to NULL to remove labels.
horizontal: Logical. Controls if the images are produced as horizontal or vertical pages. Default is FALSE.
song: Character string with the name of the column to used as a label a for higher organization level in the song (similar to 'song_colm' in song_analysis). If supplied then lines above the selections belonging to the same 'song' are plotted. Ignored if 'X' is not provided.
suffix: Character vector of length 1. Suffix for the output image file (to be added at the end of the default file name). Default is NULL.
dest.path: Character string containing the directory path where the image files will be saved. If NULL (default) then the folder containing the sound files will be used instead.
only.annotated: Logical argument to control if only the pages that contained annotated sounds (from 'X') are printed. Only used if 'X' is supplied.
...: Additional arguments for image formatting. It accepts 'width', 'height' (which will overwrite 'horizontal') and 'res' as in png.

Value

image files with spectrograms of entire sound files in the working directory. Multiple pages can be returned, depending on the length of each sound file.

Details

The function creates spectrograms for complete sound files, printing the name of the sound files and the "page" number (p1-p2...) at the upper right corner of the image files. If 'X' is supplied, the function delimits and labels the selections. This function aims to facilitate visual inspection of multiple files as well as visual classification of vocalization units and the analysis of animal vocal sequences.

References

Araya-Salas, M., & Smith-Vidaurre, G. (2017). warbleR: An R package to streamline analysis of animal acoustic signals. Methods in Ecology and Evolution, 8(2), 184-191.

Author

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

Examples

if (FALSE) {
# save sound file examples to temporary working directory
data(list = c("Phae.long1", "Phae.long2", "lbh_selec_table"))
writeWave(Phae.long1, file.path(tempdir(), "Phae.long1.wav"))
writeWave(Phae.long2, file.path(tempdir(), "Phae.long2.wav"))

full_spectrograms(
  sxrow = 2, rows = 8, pal = reverse.heat.colors, wl = 300,
  path = tempdir()
)

# including selections
full_spectrograms(
  sxrow = 2, rows = 8, X = lbh_selec_table,
  pal = reverse.heat.colors, overwrite = TRUE, wl = 300, path = tempdir()
)

# check this floder
# tempdir()
}