spectro {seewave}R Documentation

2D-spectrogram of a time wave

Description

This function returns a two-dimension spectrographic representation of a time wave. The function corresponds to short-term Fourier transform. An amplitude contour plot can be overlaid.

Usage

spectro(wave, f, wl = 512, wn = "hanning", zp = 0,
ovlp = 0, dB = "max0", dBref = NULL, plot = TRUE,
grid = TRUE, osc = FALSE, scale = TRUE, cont = FALSE,
collevels = NULL, palette = spectro.colors,
contlevels = NULL, colcont = "black",
colbg = "white", colgrid = "black",
colaxis = "black", collab="black",
tlab = "Time (s)",
flab = "Frequency (kHz)",
alab = "Amplitude",
scalelab = "Amplitude\n(dB)",
main=NULL,
scalefontlab = 1, scalecexlab =0.75,
axisX = TRUE, axisY = TRUE, tlim = NULL, trel = TRUE,
flim = NULL, flimd = NULL,
widths = c(6,1), heights = c(3,1),
listen=FALSE,
...)

Arguments

wave an R object.
f sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.
wl window length for the analysis (even number of points). (by default = 512)
zp zero-padding (even number of points), see Details.
ovlp overlap between two successive windows (in %).
dB a character string specifying the type dB to return: "max0" (default) for a maximum dB value at 0, "A", "B", "C" and "D" for common dB weights.
dBref a dB reference value when dB is TRUE. NULL by default but should be set to 2*10e-5 for a 20 microPa reference.
wn window name, see ftwindow (by default "hanning").
plot logical, if TRUE plots the spectrogram (by default TRUE).
grid logical, if TRUE plots a y-axis grid (by default TRUE).
osc logical, if TRUE plots an oscillogram beneath the spectrogram (by default FALSE).
scale logical, if TRUE plots a dB colour scale on the right side of the spectrogram (by default TRUE).
cont logical, if TRUE overplots contour lines on the spectrogram (by default FALSE).
collevels a set of levels which are used to partition the amplitude range of the spectrogram (in dB).
palette a color palette function to be used to assign colors in the plot, see Details.
contlevels a set of levels which are used to partition the amplitude range for contour overplot (in dB).
colcont colour for cont plotting.
colbg background colour.
colgrid colour for grid plotting.
colaxis color of the axes.
collab color of the labels.
tlab label of the time axis.
flab label of the frequency axis.
alab label of the amplitude axis.
scalelab amplitude scale label.
main label of the main title.
scalefontlab font of the amplitude scale label.
scalecexlab cex of the amplitude scale label.
axisX logical, if TRUE plots time X-axis (by default TRUE).
axisY logical, if TRUE plots frequency Y-axis (by default TRUE).
tlim modifications of the time X-axis limits.
trel time X-axis with a relative scale when tlim is not null, i.e. relative to wave.
flim modifications of the frequency Y-axis limits.
flimd dynamic modifications of the frequency Y-axis limits. New wl and ovlp arguments are applied to increase time/frequency resolution.
widths a vector of length 2 to control the relative widths of columns on the device when scale is TRUE.
heights a vector of length 2 to control the relative heights of rows on the device when osc is TRUE.
listen if TRUE the sound is played back (by default FALSE).
... other contour and oscillo graphical parameters.

Details

Following Heisenberg uncertainty principle, the short-term Fourier transform cannot be precised in both time and frequency. The temporal and frequency precisions of the function are actually dependent of the wl value. Choosing a high wl value will increase the frequency resolution but reduce the temporal one, and vice versa. The frequency precision is obtained by calculating the ratio f/wl, and the temporal precision is obtained by calculating the reverse ratio wl/f. This problem can be reduced in some way with zp that adds 0 values on both sides of the analysis window. This increases frequency resolution without altering time resolution.
Any colour palette can be used. In particular, it is possible to use other palettes coming with seewave: temp.colors, rev.gray.colors.1, rev.gray.colors.2, rev.heat.colors, rev.terrain.colors, rev.topo.colors, rev.cm.colors corresponding to the reverse of heat.colors, terrain.colors, topo.colors, cm.colors.
Use locator to identify points.

Value

This function returns a list of three items:

time a numeric vector corresponding to the time axis.
freq a numeric vector corresponding to the frequency axis.
amp a numeric matrix corresponding to the amplitude values. Each column is a Fourier transform of length wl.

Note

This function is based on fft, contour and filled.contour

Author(s)

Jerome Sueur sueur@mnhn.fr and Caroline Simonis csimonis@mnhn.fr.

References

Hopp, S. L., Owren, M. J. and Evans, C. S. (Eds) 1998. Animal acoustic communication. Springer, Berlin, Heidelberg.

See Also

spectro3D, dynspec, wf, oscillo, dBscale, fft.

Examples

data(tico)
data(pellucens)
# simple plots
spectro(tico,f=22050)
spectro(tico,f=22050,osc=TRUE)
spectro(tico,f=22050,scale=FALSE)
spectro(tico,f=22050,osc=TRUE,scale=FALSE)
# change the dB scale by setting a different dB reference value (20 microPa)spectro(tico,f=22050, dBref=2*10e-5)
# manipulating wl
op<-par(mfrow=c(2,2))
spectro(tico,f=22050,wl=256,scale=FALSE)
title("wl = 256")
spectro(tico,f=22050,wl=512,scale=FALSE)
title("wl = 512")
spectro(tico,f=22050,wl=1024,scale=FALSE)
title("wl = 1024")
spectro(tico,f=22050,wl=4096,scale=FALSE)
title("wl = 4096")
par(op)
# vertical zoom using flim
spectro(tico,f=22050, ylim=c(2,6))
spectro(tico,f=22050, ylimd=c(2,6))
# a full plot
pellu2<-cutw(pellucens,f=22050,from=1,plot=FALSE)
spectro(pellu2,f=22050,ovlp=85,zp=16,osc=TRUE,
    cont=TRUE,contlevels=seq(-30,0,20),colcont="red",
    lwd=1.5,lty=2,palette=rev.terrain.colors)
# black and white spectrogram 
spectro(pellu2,f=22050,ovlp=85,zp=16,
    palette=rev.gray.colors.1)
# colour modifications
data(sheep)
spectro(sheep,f=8000,palette=temp.colors,collevels=seq(-115,0,1))
spectro(pellu2,f=22050,ovlp=85,zp=16,
palette=rev.cm.colors,osc=TRUE,colwave="orchid1") 
spectro(pellu2,f=22050,ovlp=85,zp=16,osc=TRUE,palette=rev.heat.colors,
colbg="black",colgrid="white", colwave="white",colaxis="white",collab="white")

[Package seewave version 1.5.6 Index]