R/oXim-main.R

In LuisLauM/oXim: Oxycline Index from Matrix Echograms

# oXim package: Oxycline Index from Matrix Echograms ---------------
#' @importFrom R.matlab readMat
#' @importFrom imagine convolutionQuantile
#' @import graphics
#' @import stats
#' @import sp
#' @importFrom gstat idw
#'
#' @title Oxycline Index from Matrix Echograms
#'
#' @author Wencheng Lau-Medrano, \email{luis.laum@gmail.com}
#' @name oXim-package
#' @description Tools for oxycline depth calculation from echogram matrices
#' @aliases oXim-package oXim
#' @docType package
#' @keywords echograms, oxycline, depth, image-filtering
#' @exportClass echoData
#' @exportClass oxyclineData
NULL

#' @title Takes outputs from Echopen and generates a matrix to calculate Oxycline.
#' @description This function search outputs of Echoopen for Fluid-like, Blue noise
#' and Fish and use them to make a filtered matrix to calculate the Oxycline limits.
#'
#' @param fileMode List with needed variables to read single Matlab files. See details below.
#' @param directoryMode List with needed variables to read Matlab files from directory. See details below.
#' @param validFish38 Range of valid values for Fish-38kHz.
#' @param validBlue38 Range of valid values for Blue-38kHz.
#' @param upLimitFluid120 Upper limit for Fluidlike-120kHz.
#' @param pinInterval Time threshold (in secs) to consider separate two matrices (echograms).
#' @param date.format A character string. The default method is \code{\%Y-\%m-\%d \%H:\%M:\%S}.
#' @param ... Extra arguments (not used for now).
#'
#' @details \code{fileMode} must be a \code{list} with the next structure: \code{fish38_file} (directory for fish38 file),
#' \code{blue38_file} (directory for blue38 file) and \code{fluid120_file} (directory for fluid120 file).
#'
#' Similarly, \code{directoryMode} must be a \code{list} with the next structure: \code{directory} (folder
#' where the files are storaged), \code{fish38_pattern} (text pattern for recognizing fish38 files),
#' \code{blue38_pattern} (text pattern for recognizing blue38 files) and \code{fluid120_pattern}
#' (text pattern for recognizing fluid120 files).
#'
#' @examples
#' 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)
#' print(echoData)
#'
#' @export
readEchograms <- function(fileMode = NULL, directoryMode = NULL,
                          validFish38 = c(-100, -21), validBlue38 = c(-100, -56),
                          upLimitFluid120 = -53, pinInterval = 50, date.format = "%d-%m-%Y %H:%M:%S", ...){

  echoData <- getEchoData(fileMode = fileMode, directoryMode = directoryMode,
                           validFish38 = validFish38, validBlue38 = validBlue38, upLimitFluid120 = upLimitFluid120,
                           pinInterval = pinInterval, date.format = date.format, ...)

  class(echoData) <- "echoData"

  return(echoData)
}

#' @title Takes a matrix of echogram and calculate Oxycline.
#' @description This function takes a filter configuration and applies to echograms given on an \code{echoData} object.
#'
#' @param fluidMatrix Object of class \code{echoData} (from \code{\link{readEchograms}} function) with echogram
#' @param filterSettings List with combination of filters.
#' @param stepBYstep \code{logical}. If \code{FALSE} (default), returns just original and final echogram, otherwise each
#' echogram (after applying filters one by one) will be returned.
#' @param ... Arguments passed to \code{\link{smooth.spline}} function. See Details.
#'
#' @details If \code{filterSettings = NULL}, oXim will use filter configuration present on \code{defaultFilterSettings}
#' data set. For extra details about image filters, see \code{\link{createFilterSetting}} help.
#'
#' Application of filters may produce some gaps in the final matrix. In order to fill them, the function uses
#' \code{\link{smooth.spline}} whose arguments can be passed using by \code{...}.
#'
#' @examples
#' 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)
#'
#' @export
#' @exportClass oxyclineData
getOxyrange <- function(fluidMatrix, filterSettings = NULL, stepBYstep = FALSE, ...){

  nEchograms <- fluidMatrix$info$n_echograms

  # Define 'fluidMatrix' using
  fluidMatrix <- if(all.equal(class(fluidMatrix), "echoData")){
    fluidMatrix$data
  }else{
    list(data = fluidMatrix)
  }

  # Get filtered echograms using filterSettings
  filterSettings <- .checkFilterSettings(filterSettings)

  # Get dimensions (lon, lat, time) of outputs' matrix
  oxyDims <- getOxyDims(oxyclineData = fluidMatrix)

  # Fill outputs' matrix
  oxyclineData <- list()
  for(i in seq_along(fluidMatrix)){
    oxyclineData[[i]] <- getFilteredEchogram(fluidMatrix = fluidMatrix[[i]], filterSettings = filterSettings,
                                              stepBYstep = stepBYstep, ...)
  }
  names(oxyclineData) <- paste0("matrix_", seq_along(fluidMatrix))

  # Get ranges of depth of oxycline using the last matrix of each echogram
  oxyRange <- getOxyrange_int(oxyclineData = oxyclineData, oxyDims = oxyDims, ...)

  # Compile outputs on a list
  oxyclineData <- list(info = list(number_echograms = nEchograms,
                                   date_range = lapply(fluidMatrix, function(x) range(x$dimnames$time)),
                                   depth_range = lapply(fluidMatrix, function(x) range(x$dimnames$depth)),
                                   filter_settings = filterSettings),
                       dims = oxyDims,
                       outputs = oxyclineData,
                       oxycline_range = oxyRange)

  # Set class
  class(oxyclineData) <- "oxyclineData"

  return(oxyclineData)
}

#' @export createFilterSetting
#'
#' @title Create filter-settings Object.
#' @description This function allows to create correctly a filter-settings object in order to insert as input on
#' \code{getOxyrange} function.
#'
#' @param name Parameter to indicate prefixed profile of settings. This parameter has priority over the others.
#' @param type Indicates type of filter to use. See details below.
#' @param radius Indicates the size (on pixels) of sides of square used to apply the filters.
#' @param times Indicates number of times to apply the filters.
#' @param tolerance For \code{noiselessFilter}, this parameter indicates proportion of pixels to consider from
#' filter matrix (radius x radius).
#'
#' @details About each parameter:
#' \describe{
#' \item{\strong{name}}{This parameter must be a string and it works as a short way to select an specific set of filter
#' settings. This parameter has priority over the others, so to create a personalized set of filters, `name` will must
#' set as \code{NULL}. (It will be fully available in next version.)}
#' \item{\strong{type}}{This parameter must be a string and indicates what kind of filter method will be applied to the
#' echograms. There are two options to select: \code{definerFilter} which works as a reverse-effect median filter
#' and \code{noiselessFilter} which removes  noisy signals on the echograms.}
#' \item{\strong{radius}}{This parameter is useful to specify the size of the filter matrix which will be applied to
#' the echogram. It must be integer, even and greater than 3.}
#' \item{\strong{times}}{This parameter is useful to indicate how many times the filter will be applied to the echogram.
#' It must be integer and greater than 1. The function will remove rows with \code{times=0} values.}
#' \item{\strong{tolerance}}{Internal parameter to modify selected values on a convolution matrix filter. This parameter
#' is meaningful only for \code{noiselessFilter}.}
#' }
#'
#' @examples
#' # Use default profile
#' createFilterSetting(name = "default")
#'
#' # Generate a personalized profile
#' createFilterSetting(type = "definerFilter", radius = c(3, 5, 5))
createFilterSetting <- function(name = "default", type = NULL, radius = NULL, times = NULL, tolerance = NULL){

  defaultFilterSettings <- get("defaultFilterSettings")

  if(is.null(name) || !is.vector(name) || length(name) > 1 || !is.element(name, defaultFilterSettings$name)){
    # Check variables of fileter settings object
    for(i in c("type", "radius", "times", "tolerance")){
     if(is.null(get(x = i))){
       stop("There is no valid value for ", i, ".")
     }
    }

    # Chaeck name
    if(!any(is.element(sort(unique(type)), c("definerFilter", "noiselessFilter"))))
      stop("Problem with 'filterSettings'. There is, at least, one wrong value on 'type' column.")

    # Check radius
    if(any(abs(as.integer(radius) - radius) > 1e-8) | any(.isOdd(radius)) | any(radius < 3))
      stop("Problem with 'filterSettings'. There is, at least, one wrong value on 'radius' column.")

    # Check times
    if(any(abs(as.integer(times) - times) > 1e-8) | any(times < 1))
      stop("Problem with 'filterSettings'. There is, at least, one wrong value on 'times' column.")

    # Check tolerance
    if(!is.numeric(tolerance) | any(tolerance <= 0 | tolerance >= 1))
      stop("Problem with 'filterSettings'. There is, at least, one wrong value on 'times' column.")

    # Get maximum length
    allLength <- max(unlist(lapply(list(type, radius, times, tolerance), length)))

    # Build filter-settings Object
    output <- data.frame(type = rep(type, length.out = allLength),
                         radius = rep(radius, length.out = allLength),
                         times = rep(times, length.out = allLength),
                         tolerance = rep(tolerance, length.out = allLength),
                         stringsAsFactors = FALSE)
  }else{

    output <- subset(defaultFilterSettings, defaultFilterSettings$name == name)
  }

  return(output)
}


#' @title Plot a matrix of a filtered echogram.
#' @description This function takes an echogram matrix and plot it.
#'
#' @param x Object of class \code{oxyclineData}, \code{echoData} or \code{matrix} with information for make
#' an echogram plot. If \code{x} is a \code{matrix}, column names must indicate the time and row names, the
#' depth.
#' @param colEchogram Pallete of colours to plot the echograms. If \code{NULL} (default) the system
#' will use the same combination used on object \code{colPallete}.
#' @param ... Extra arguments passed to \code{\link{echogramPlot}} function.
#'
#' @details Typically, `echogramPlot` can be applied to echogram matrix object, however it also may use
#' `echoData` and `oxyclineData` objects, as a method.
#'
#' @export
#'
#' @examples
#' 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)
#' echogramPlot(x = echoData)
echogramPlot <- function(x, colEchogram = "colPalette", ...){
  UseMethod(generic = "echogramPlot", object = x)
}

#' @title Default color palette most using on acostic echograms.
#' @name colPalette
#' @description Vector with 256 colors commonly used on echograms plots.
#' @aliases colPalette
#' @docType data
#' @usage colPalette
#' @format A vector of 256 colors in RBG format.
#' @references Boletines del Instituto del Mar del Peru.
NULL

#' @title Default set of filter parameters.
#' @name defaultFilterSettings
#' @description \code{data.frame} object containig a settings used by \code{getOxyrange}
#' function to apply echograms' matrix. It can be usefull as example of filter settings.
#' @aliases defaultFilterSettings
#' @docType data
#' @usage defaultFilterSettings
#' @format A \code{data.frame} with columns name, type, radius, times and tolerance.
NULL