prep_static_ggspectro: Generate ggplot2-based spectrogram(s), which can be passed to...

In dynaSpec: Dynamic Spectrogram Visualizations

Description

Can be used to generate single or segmented static spectrograms. Works as standalone, but the returned object is also intended to feed into paged_spectro. Workflow: 1) use prep_static_ggspectro to crop, filter, segment and tweak all spectrogram parameters; 2) pass these settings to paged_spectro to generate dynamic spectrogram video.

Usage

prep_static_ggspectro(soundFile,destFolder,outFilename,savePNG=FALSE,colPal="inferno",
crop=NULL,bg=NULL,filter=NULL,xLim=NULL,yLim=c(0,10),plotLegend=FALSE,onlyPlotSpec=TRUE,
ampTrans=1,min_dB=-30,wl=512, ovlp=90,wn="blackman",specWidth=9,specHeight=3,
colbins=30,ampThresh=0,bgFlood=FALSE,fontAndAxisCol=NULL,optim=NULL,...)

Arguments

soundFile	should work with URLs, full and relative paths; handles .mp3 and .wav
destFolder	needs to be like "figures/spectrograms/" to be relative to working directory; goes to soundFile folder by default or working directory if soundFile is a URL; can specify "wd" to output to the working directory
outFilename	if left out, will use input name in output filename
savePNG	save static spectrograms as PNGs? They will be exported to destFolder
colPal	color palette; one of "viridis","magma","plasma","inferno","cividis" from the viridis package OR a 2 value vector (e.g. c("white","black")), defining the start and end of a custom color gradient
crop	subset of recording to include; if crop=NULL, use whole file; if number, interpreted as crop first X.X sec; if c(X1,X2), interpreted as specific time interval in sec
bg	background color (defaults to 1st value of chosen palette)
filter	apply a bandpass filter? Defaults to none (NULL). Expects 'c(0,2)' where sound from 0 to 2kHz would be filtered out
xLim	is the time limit in seconds for all spectrograms; i.e. page width in seconds for multi-page dynamic spectrograms (defaults to WAV file length, unless file duration >5s)
yLim	is the frequency limits (y-axis); default is c(0,10) aka 0-10kHz
plotLegend	include a legend showing amplitude colors?
onlyPlotSpec	do you want to just plot the spec and leave out the legend, axes, and axis labels?
ampTrans	amplitude transform for boosting spectrum contrast; defaults to identity (actual dB values); specify a decimal number for the lambda value of scales::modulus_trans(); 2.5 is a good place to start. (This amplifies your loud values the most, while not increasing background noise much at all)
min_dB	the minimum decibel (quietest sound) to include in the spec; defaults to -30 (-40 would include quieter sounds; -20 would cut out all but very loud sounds)
wl	window length for the spectrogram (low values= higher temporal res; high values= higher freq. res). Default 512 is a good tradeoff
ovlp	how much overlap (as percent) between sliding windows to generate spec? Default 90 looks good, but takes longer
wn	window name (slight tweaks on algorithm that affect smoothness of output) see spectro
specWidth	what width (in inches) would you like to make your PNG output be, if saving a static spec?
specHeight	what height (in inches) would you like to make your PNG output be, if saving a static spec?
colbins	default 30: increasing can smooth the color contours, but take longer to generate spec
ampThresh	amplitude threshold as a percent to cut out of recording (try 5 to start); default= no filtering (high data loss with this; not recommended; play with min_dB and ampTrans first)
bgFlood	do you want the background color to spill into the axis margins? Default=FALSE (i.e. white margins)
fontAndAxisCol	the color of legend text if onlyPlotSpec=TRUE (since margins will be white, with black text); if bgFlood=TRUE, this will be the color of axis margins, labels and legend text. If you don't supply this, it will be picked automatically to be white or black based on supplied bg color
optim	NULL by default; this is an experimental feature to simplify the dataframe of the FFT-processed waveform used to generate the spectrogram (currently does nothing)
...	Other arguments to be passed for rendering the spec (i.e. to seewave::spectro)

Value

a list with all spectrogram parameters, segmented WAV files (segWavs) and spectrograms spec; importantly, spec is a list of n=number of "pages"/segments; the first page is displayed by default

Author(s)

Matthew R Wilkins ([e-mail])

References

Araya-Salas M & Wilkins M R. (2020). *dynaSpec: dynamic spectrogram visualizations in R*. R package version 1.0.0.

See Also

paged_spectro

Examples

## Not run: 
require(dynaSpec)
f <- list.files(pattern=".wav", full.names = TRUE, path = system.file(package="dynaSpec"))

# default behavior should be a decent start for good recordings; doesn't save anything, just plots
prep_static_ggspectro(f[1])

# to use with paged_spectro or to do other stuff, you need to assign the
# resulting object, but it will still always plot the first spec
# let's add axes and boost the signal a smidge
femaleBarnSwallow <- prep_static_ggspectro(f[1],destFolder="wd",
onlyPlotSpec = FALSE, bgFlood=TRUE,ampTrans=2)
 
# feels like we're missing a little bit of the quieter signals; let's lower
# the minimum amplitude threshold a bit
femaleBarnSwallow<-prep_static_ggspectro(f[1],destFolder="wd",
onlyPlotSpec = FALSE, bgFlood=TRUE,ampTrans=2,min_dB=-35)
 
#now for a male song  
maleBarnSwallow<-prep_static_ggspectro(f[2],destFolder="wd",onlyPlotSpec = FALSE, 
bgFlood=TRUE)

#Nice, but the trill is fading out; I'm gonna signal boost and lower the min_dB
maleBarnSwallow<-prep_static_ggspectro(f[2],destFolder="wd",onlyPlotSpec = FALSE, 
bgFlood=TRUE,ampTrans=2,min_dB=-40)

#much stronger, now let's combine them (you need the cowplot package)

# cowplot::plot_grid(femaleBarnSwallow$spec[[1]]+xlim(0,5)+ggtitle("female barn swallow song"),
# maleBarnSwallow$spec[[1]]+xlim(0,5)+ggtitle("male barn swallow song"),ncol=1,labels="auto")

# ggsave("M&F_barn_swallow_song_specs.jpeg")

# see more examples at https://marce10.github.io/dynaSpec/

## End(Not run)

dynaSpec documentation built on March 10, 2021, 1:08 a.m.