echogram (version 0.1.3)

mask.echogram: Mask an echogram

Description

This function creates, and optionally applies, a mask by ``blanking'' portions of the Sv data matrix of an echogram.

Usage

mask.echogram(echogram, surf.off = NULL, bott.off = NULL, mask = TRUE)

Value

When mask = FALSE, a masking matrix is returned. When mask = TRUE (the default), an object of class ``echogram'' with the mask applied.

Arguments

echogram

an object of class ``echogram'' as returned by read.echogram.

surf.off

surface offset in m defining the upper layer (refered to the surface) to be masked.

bott.off

bottom offset in m defining the bottom layer (refered to the bottom) to be masked.

mask

logical. If FALSE, the function returns a masking matrix. If TRUE (the default), the function returns a masked echogram (see details).

Author

Héctor Villalobos

Details

The masking process consists in producing a matrix of the same dimensions as the original Sv data matrix with NA's in the masked portion and 1's otherwise. The product of both matrices gives the masked echogram.

Examples

# import 38 kHz data from HAC file
hacfile <- system.file("hac", "D20150510-T202500.hac", package = "echogram")
echo2.038 <- read.echogram(hacfile, channel = 1)

# make a copy of the original echogram
tmp <- echo2.038

# Create a mask, which is a matrix with 1's and NA's 
mask <- mask.echogram(tmp, surf.off = 1, bott.off = -1, mask = FALSE)
image(t(mask[nrow(mask):1, ])) 

# Apply mask to echogram
tmp$Sv <- tmp$Sv * mask 
echogram(tmp)

# By default, the function returns the masked echogram
echo2.038mask <- mask.echogram(echo2.038, surf.off = 2, bott.off = 0.2)
echogram(echo2.038mask)