R/calib.plot.R

In J0vid/Colormesh: Functions for Processing Image Color Data for Statistical Analysis

#' Diagnostic tool for looking at calibration images and the sampling landmarks
#'
#' @param imagedir path to calibration images
#' @param image.names A vector of image names to look for in imagedir.
#' @param calib.file tps2array object with the sampled color standard. Make sure the IMAGE data in the tps file matches the names of the images exactly. It's okay if it still has a path attached to the name.
#' @param cex change the point size on the image
#' @param col change point colors
#' @param individual which specimen do you want to plot? Defaults to the first specimen
#' @param flip.y.values logical value to try flipping the Y values of the coordinates to see if the landmarks will match up with the color standard
#' @return a plot to check if you should flip the y-axis of the color standard landmarks
#' @examples
#' #load covariates and calibration file
#' specimen.factors <- read.csv(system.file("extdata", "specimen_factors.csv", package = "Colormesh"), header = F)
#' calib.file <- tps2array(system.file("extdata", "calib_LM_coords.TPS", package = "Colormesh"))
#'
#' calib.plot(paste0(path.package("Colormesh"),"/extdata/original_images/"), image.names = specimen.factors[,1], calib.file = calib.file)
#'
#' @export


calib.plot <- function(imagedir, image.names, calib.file, cex = 2, col = "red", individual = 1, flip.y.values = F){

  image.files <- list.files(imagedir, pattern = "*.JPG|*.jpg|*.TIF|*.tif|*.png|*.PNG|*.bmp|*.BMP|*.cr2|*.nef|*.orf|*.crw")
  image.files.san.ext <- tools::file_path_sans_ext(image.files)
  image.names <- tools::file_path_sans_ext(image.names)
  dimnames(calib.file)[[3]] <-  basename(dimnames(calib.file)[[3]])
  dimnames(calib.file)[[3]] <-  tools::file_path_sans_ext(dimnames(calib.file)[[3]])

  corresponding.image <- image_reader(imagedir, image.files[image.files.san.ext == image.names[individual]])
  img.dim <- dim(corresponding.image)

  plot(corresponding.image)
  if(flip.y.values) calib.file[,2,] <- -calib.file[,2,] + img.dim[2]
  points(calib.file[,, dimnames(calib.file)[[3]] == image.names[individual]][,1], -calib.file[,,dimnames(calib.file)[[3]] == image.names[individual]][,2] + dim(corresponding.image)[2], col = col, pch = 19, cex = cex)

  if(flip.y.values == F) print("If the landmarks look flipped relative to the image, set flip.y.values to T in rgb.calibrate")
    else{ print("If the landmarks look flipped relative to the image, set flip.y.values to F in rgb.calibrate")}
}