R/plot.ijroi.R

In davidcsterratt/RImageJROI: Read 'ImageJ' Region of Interest (ROI) Files

##' @title Plot ijroi object
##' @description Plots ImageJ ROI objects using the \link[=graphics]{'base' graphics} package.
##' @param x The \code{ijroi} object.
##' @param add Whether to add to an existing plot.
##' @param main an overall title for the plot: \code{\link{title}}.
##' @param xlab a title for the x axis: \code{\link{title}}.
##' @param ylab a title for the y axis: \code{\link{title}}.
##' @param asp numeric defining the aspect ratio y/x: see \code{\link{plot.window}}. Defaults to 1.
##' @param ... Additional parameters.
##' @importFrom graphics axis plot
##' @method plot ijroi
##' @details ImageJ ROI objects created with following tools are plotted using following graphics commands:
##' \itemize{
##' \item{Rectangle tool ("rect")} \code{\link{rect}}. Plotted based on coordinates.
##' \item{Oval selections ("oval")} \code{\link{polygon}}. Plotted based on equation.
##' \item{Freehand selections ("freehand")} \code{\link{lines}}. Plotted based on coordinates.
##' \item{Elliptical selections ("freehand", "ELLIPSE")} \code{\link{lines}}. Plotted based on equation.
##' \item{Point Tool and Multi-Point Tool ("point")} \code{\link{points}}. Plotted based on coordinates.
##' \item{Straight Line ("line")} \code{\link{lines}}. Plotted based on coordinates.
##' \item{Arrow tool ("line", "ARROW")} \code{\link{arrows}}. Plotted based on coordinates. Stroke width passed to \code{\link[=par]{lwd}} argument.
##' \item{Segmented Line ("polyline")} \code{\link{lines}}. Plotted based on coordinates.
##' \item{Freehand Line ("freeline")} \code{\link{lines}}. Plotted based on coordinates.
##' }
##' All graphics allow the additional parameters from appropriate functions. Aspect ratio (\code{asp}) is 1 by default leading to correct representation of ImageJ objects. If correct representation is not important, set \code{asp = NA} to use the R base-graphics default setting.
##' 
##' @export
##' @author David Sterratt, Mikko Vihtakari
##' @seealso \code{\link{read.ijroi}}, \code{\link{read.ijzip}}, \code{\link{plot.ijzip}}
##' @examples
##' # type 0 'polygon' ROIs are plotted using lines()
##' file <- file.path(system.file(package = "RImageJROI"), "extdata", "ijroi", "polygon.roi")
##' x <- read.ijroi(file)
##' plot(x, col = "red")
##' 
##' # type 1 'rect' ROIs are plotted using rect()
##' file <- file.path(system.file(package = "RImageJROI"), "extdata", "ijroi", "rect.roi")
##' x <- read.ijroi(file)
##' plot(x, border = "red")
##' 
##' # type 2 'oval' ROIs are plotted using polygon()
##' file <- file.path(system.file(package = "RImageJROI"), "extdata", "ijroi", "oval.roi")
##' x <- read.ijroi(file)
##' plot(x, border = "red")
##' 
##' # type 3 'line' ROIs (among others listed in 'details') are plotted using lines()
##' file <- file.path(system.file(package = "RImageJROI"), "extdata", "ijroi", "line.roi")
##' x <- read.ijroi(file)
##' plot(x, col = "red")
##' 
##' # type 3 arrows are a subtype of 'line'. Plotted using arrows(). The stroke width is
##' # carried over. To change width, use lwd argument
##' file <- file.path(system.file(package = "RImageJROI"), "extdata", "ijroi", "arrow.roi")
##' x <- read.ijroi(file)
##' plot(x, col = "red")
##' 
##' # type 4 'freeline' ROIs are plotted using lines()
##' file <- file.path(system.file(package = "RImageJROI"), "extdata", "ijroi", "freehand_line.roi")
##' x <- read.ijroi(file)
##' plot(x, col = "red")
##' 
##' # type 5 'polyline' ROIs are plotted using lines()
##' file <- file.path(system.file(package = "RImageJROI"), "extdata", "ijroi", "segmented_line.roi")
##' x <- read.ijroi(file)
##' plot(x, col = "red")
##' 
##' # type 7 'freehand' selection ROIs are plotted using lines()
##' file <- file.path(system.file(package = "RImageJROI"), "extdata", "ijroi", "freehand_selection.roi")
##' x <- read.ijroi(file)
##' plot(x, col = "red")
##' 
##' # type 7 Objects created using 'Elliptical selections' tool are also saved as
##' # 'freehand', but with subtype 'ELLIPSE'. The coordinates for this type are flawed
##' # and plotting is done using equation for an ellipse
##' file <- file.path(system.file(package = "RImageJROI"), "extdata", "ijroi", "elliptical.roi")
##' x <- read.ijroi(file)
##' plot(x, border = "red")
##' lines(x$coords[,1], x$coords[,2]) ## plotted based on coordinates.
##'
##' # type 10 'point' ROIs are plotted using points()
##' file <- file.path(system.file(package = "RImageJROI"), "extdata", "ijroi", "multi_point.roi")
##' x <- read.ijroi(file)
##' plot(x, col = "red")
##'
##' # If following is shown as a (round) circle, asp = 1
##' file <- file.path(system.file(package = "RImageJROI"), "extdata", "ijroi", "circle.roi")
##' x <- read.ijroi(file)
##' plot(x, border = "red")
##' 
##' # text is stored as type 'rect' with subtype 'TEXT'. Currently
##' # only the outlining rectangle is returned
##' file <- file.path(system.file(package = "RImageJROI"), "extdata", "ijroi", "text.roi")
##' x <- read.ijroi(file)
##' plot(x, border = "red")
##' 

plot.ijroi <- function(x, add=FALSE, xlab = "", ylab = "", main = "", asp = 1, ...) {
  with(x, {
    if (!add) {
      plot(NA, NA, xlim=xrange, ylim=yrange, xlab = xlab, ylab = ylab, main = main, asp = asp)
    }
    if (strType == "rect") {
      rect(left, bottom, right, top, ...)
    }
    if (strType == "oval") {
      theta <- seq(0, 2*pi, len=360)
      polygon(left + width/2*(1 + sin(theta)),
              top + height/2*(1 + cos(theta)), ...)
    }
    if (strType == "line") {
      if(!exists("strSubtype")){
        lines(coords, ...)
    }}
    if (strType == "line") {
      if(exists("strSubtype")) if(subtype == 2) {
      arrows(x0 = x1, y0 = y1, x1 = x2, y1 = y2, lwd = strokeWidth, ...)
    }}
    if (strType %in% c("polygon", "traced")) {
      coords <- rbind(coords, coords[1,])
      lines(coords, ...)
    }
    if(strType %in% c("freehand")) {
      if(exists("strSubtype")){
      if(strSubtype %in% c("ELLIPSE")) {
      centerX <- (x1 + x2)/2
      centerY <- (y1 + y2)/2
      theta <- seq(0, 2*pi, len=360)
      dx <- x2 - x1
      dy <- y2 - y1
      major <- sqrt(dx^2 + dy^2)
      minor <- major*aspectRatio
      a <- major/2
      b <- minor/2
      phi <- atan2(dy, dx)
      ellipX <- centerX + a*cos(theta)*cos(phi) - b*sin(theta)*sin(phi)
      ellipY <- centerY + a*cos(theta)*sin(phi) + b*sin(theta)*cos(phi)
      polygon(ellipX, ellipY, ...)
    }} else {
      coords <- rbind(coords, coords[1,])
      lines(coords, ...)
      }
    }
    if (strType %in% c("polyline", "freeline", "angle")) {
      lines(coords, ...)
    }
    if (strType == "point") {
      points(coords, ...)
    }
  })
}