mask.echogram: Mask an echogram

In hvillalo/echogram: Echogram Visualisation and Analysis

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)

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).

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.

Value

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

Author(s)

Héctor Villalobos

Examples

# import 38 kHz data from HAC file
hacfile <- system.file("extdata", "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)

hvillalo/echogram documentation built on Oct. 2, 2023, 7:28 a.m.