oXim (version 1.2.2)

getOxyrange: Takes a matrix of echogram and calculate Oxycline.

Description

This function takes a filter configuration and applies to echograms given on an echoData object.

Usage

getOxyrange(fluidMatrix, filterSettings = NULL, stepBYstep = FALSE, ...)

Arguments

fluidMatrix

Object of class echoData (from readEchograms function) with echogram

filterSettings

List with combination of filters.

stepBYstep

logical. If FALSE (default), returns just original and final echogram, otherwise each echogram (after applying filters one by one) will be returned.

...

Arguments passed to smooth.spline function. See Details.

Details

If filterSettings = NULL, oXim will use filter configuration present on defaultFilterSettings data set. For extra details about image filters, see createFilterSetting help.

Application of filters may produce some gaps in the final matrix. In order to fill them, the function uses smooth.spline whose arguments can be passed using by ....

Examples

# NOT RUN {
fileMode <- list(fish38_file   = system.file("extdata", "fish38.mat", package = "oXim"),
                 fluid120_file = system.file("extdata", "fluid120.mat", package = "oXim"),
                 blue38_file   = system.file("extdata", "blue38.mat", package = "oXim"))
echoData <- readEchograms(fileMode = fileMode)
oxyLimits <- getOxyrange(fluidMatrix = echoData)

# }