seltailor: Interactive view of spectrograms to tailor start and end of selections

Description

seltailor produces an interactive spectrographic view (similar to manualoc) in which the start and end times of acoustic signals listed in a data frame can be adjusted.

Usage

seltailor(X = NULL, wl = 512, flim = c(0,22), wn = "hanning", mar = 0.5,
 osci = TRUE, pal = reverse.gray.colors.2, ovlp = 70, auto.next = FALSE, pause = 1,
  comments = TRUE, path = NULL, frange = FALSE, fast.spec = FALSE, ext.window = TRUE,
  width = 15, height = 5, ...)

Arguments

data frame with the following columns: 1) "sound.files": name of the .wav files, 2) "selec": number of the selections, 3) "start": start time of selections, 4) "end": end time of selections. The ouptut of manualoc or autodetec can be used as the input data frame. Other data frames can be used as input, but must have at least the 4 columns mentioned above. Required. Notice that, if an output file ("seltailor_output.csv") is found in the working directory it will be given priority over an input data frame.

A numeric vector of length 1 specifying the spectrogram window length. Default is 512.

flim

A numeric vector of length 2 specifying the frequency limit (in kHz) of the spectrogram, as in the function spectro. Default is c(0,22).

A character vector of length 1 specifying the window function (by default "hanning"). See function ftwindow for more options.

mar

Numeric vector of length 1. Specifies the margins adjacent to the start and end points of the selections to define spectrogram limits. Default is 0.5.

osci

Logical argument. If TRUE adds a oscillogram whenever the spectrograms are produced with higher resolution (see seltime). Default is TRUE. The external program must be closed before resuming analysis. Default is NULL.

pal

A color palette function to be used to assign colors in the plot, as in spectro. Default is reverse.gray.colors.2. See Details.

ovlp

Numeric vector of length 1 specifying the percent overlap between two consecutive windows, as in spectro. Default is 70.

auto.next

Logical argument to control whether the functions moves automatically to the next selection. The time interval before moving to the next selection is controled by the 'pause' argument.

pause

Numeric vector of length 1. Controls the duration of the waiting period before moving to the next selection (in seconds). Default is 1.

comments

Logical argument specifying if 'sel.comment' (when in data frame) should be included in the title of the spectrograms. Default is TRUE.

path

Character string containing the directory path where the sound files are located.

frange

Logical argument specifying whether limits on frequency range should be recorded. If NULL (default) then only the time limits are recorded.

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' spectograms. Palette colors gray.1, gray.2, gray.3 offer decreasing darkness levels. THIS IS STILL BEING TESTED.

ext.window

Logical. If TRUE then and external graphic window is used. Default dimensions can be set using the 'width' and 'height' arguments. Default is TRUE.

width

Numeric of length 1 controling the width of the external graphic window. Ignored if ext.window = FALSE. Default is 15.

height

Numeric of length 1 controling the height of the external graphic window. Ignored if ext.window = FALSE. Default is 5.

...

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

.csv file saved in the working directory with start and end time of selections.

Details

This function produces an interactive spectrographic view (similar to manualoc) in which users can select a new start and end of a vocalization unit (e.g. elements) by clicking at the end and at the start of the signal (in any order). In addition, 2 "buttons" are provided at the upper right side of the spectrogram that allow to stop the analysis ("Stop") or go to the next sound file ("next sel"). When a unit has been selected, the function plots red dotted lines in the start and end of the selection in the spectrogram. The lines "disappear" when a new selections is made. Only the last selection is kept for each selection that is adjusted. The function produces a .csv file (seltailor_output.csv) with the same information than the input data frame, except for the new time coordinates, plus a new column (X$tailored) indicating if the selection has been tailored. The file is saved in the working directory and is updated every time the user moves into the next sound file (next sel "button") or stop the process (Stop "button"). If no selection (by clicking on the 'next' buttom) the original time coordinates are kept. When resuming the process (after "stop" and re-running the function in the same working directory), the function will continue working on the selections that have not been analyzed. Windows length (wl) controls the temporal and frequency precision of the spectrogram. A high "wl" value increases the frequency resolution but reduces the temporal resolution, and vice versa. Any color palette that comes with the seewave package can be used: temp.colors, reverse.gray.colors.1, reverse.gray.colors.2, reverse.heat.colors, reverse.terrain.colors, reverse.topo.colors, reverse.cm.colors, heat.colors, terrain.colors, topo.colors, cm.colors. Note that, unlike manualoc, you cannot zoom in the spectrogram seltailor. The zoom can be adjusted by setting the mar argument.

Examples

Run this code

## Not run: ------------------------------------
# #Set temporary working directory
# setwd(tempdir())
# 
# data(list = c("Phae.long1", "Phae.long2", "Phae.long3", "Phae.long4", "selec.table"))
# writeWave(Phae.long1,"Phae.long1.wav")
# writeWave(Phae.long2,"Phae.long2.wav")
# writeWave(Phae.long3,"Phae.long3.wav")
# writeWave(Phae.long4,"Phae.long4.wav")
# 
# seltailor(X =  selec.table, flim = c(1,12), wl = 300, auto.next = TRUE)
# 
# # Read output .csv file
# seltailor.df <- read.csv("seltailor_output.csv")
# seltailor.df
# 
# # check this directory for .csv file after stopping function
# getwd()
## ---------------------------------------------