locaR (version 0.1.2)

omniSpectro: Generate grid of spectrograms for detecting sounds of interest.

Description

omniSpectro creates a grid of time-synchronized spectrograms, to facilitate the manual detection of birds across a microphone array. By opening the resulting jpeg images in an image viewing program (e.g. the standard Microsoft Photos app), short clips of sounds can be viewed across an entire microphone array at once. The authors of this package have found this to be an efficient way to view spectrograms, while effectively eliminating the likelihood of double-counting sound sources that may be clearly detectable on many microphones at the same time. At the present time, this function only works when a settings object, st, is provided.

Usage

omniSpectro(st, lm, intervalLength = 5, intervals = "all")

Value

No return value.

Arguments

st

List. Localization settings object generated using processSettings.

lm

layout matrix generated using the `layoutMatrix()` function, or a user-generated matrix in the same format. This matrix controls how the spectrograms from each station are mapped to rows and columns.

intervalLength

Integer The length of each view interval to be generated, in seconds. Consecutive windows overlap, by default by 1 second. Setting intervalLength = 5 will therefore create 6-second spectrogram views, with one second overlap (e.g. 0 to 6, then 5 to 11, 10 to 16, etc.).

intervals

Integer or 'all'. Which intervals to write to jpeg. For testing purposes, it is often desirable to set this to, e.g. intervals = 1:5, which will create only the first five view windows, to ensure the function is working.

Examples

    # \donttest{
    #First need to convert mp3 example data to wav.
    #list mp3 files.
    f.in <- list.files(system.file('extdata', package = 'locaR'), full.names = TRUE, pattern='mp3$')
    #create wav names.
    f.out <- file.path(tempdir(), basename(f.in))
    #change extension.
    substr(f.out, nchar(f.out)-2, nchar(f.out)) <- 'wav'
    #Convert mp3 to wav, as required for this particular example.
    for(i in 1:length(f.in)) {
      y <- tuneR::readMP3(f.in[i])
      tuneR::writeWave(y, filename = f.out[i])
    }
    #Set up survey.
    survey <- setupSurvey(folder = tempdir(), projectName = 'Ex', run = 1,
               coordinatesFile = system.file('extdata', 'Vignette_Coordinates.csv',
                                             package = 'locaR'),
               siteWavsFolder = tempdir(), date = '20200617', time = '090000', surveyLength = 7)
    #Process settings.
    st <- processSettings(settings = survey, getFilepaths = TRUE, types = 'wav')
    #Set up layout matrix.
    lm <- layoutMatrix(st = st, start = 'topleft', byrow = TRUE, nrow = 3, ncol = 3)
    #create detection spectrograms.
    omniSpectro(st, lm, intervalLength = 7)
    # }