inst/script/ImageView_for_v02.R

In kumeS/rMiW: rMiW - R package for providing the analysis workflow for microscopy-based images

#This script for the v02 dataset

####################################################################################
#An image visualization function to create an animation for the 5D array.
####################################################################################
ImageView3D <- function(ImgArray, Sample=1,
                        Lab01="Original", Lab02="Merge", Lab03="Supervised",
                        Name=paste0(DataFolder, "_train_dataset"),
                        Interval = 0.1, Dpi=72,Thres=0.4,
                        Width = 500, Height=250){
    options(EBImage.display = "raster")
    XYsize = 256
    names(ImgArray) <- c("Original", "GroundTruth")

    saveGIF({
    for(n in seq_len(dim(ImgArray$Original)[4])){
      #n <- 1
      par(bg = 'grey')
      Image_color01 <- paintObjects(resize(ImgArray$GroundTruth[Sample,,,n,], XYsize, XYsize, filter="none")/2,
                                      toRGB(resize(ImgArray$Original[Sample,,,n,], XYsize, XYsize, filter="none")), opac=c(0.25, 0.25),
                                      col=c("red","red"), thick=TRUE, closed=FALSE)
      EBImage::display(EBImage::combine(resize(toRGB(ImgArray$Original[Sample,,,n,]), XYsize, XYsize, filter="none"),
                                          resize(Image_color01, XYsize, XYsize, filter="none"),
                                          resize(toRGB(ImgArray$GroundTruth[Sample,,,n,]), XYsize, XYsize, filter="none")),
                         nx=3, all=TRUE, spacing = 0.01, margin = 70)
      text(x = XYsize*0.5, y = -XYsize*0.175,
             label = Lab01, adj = c(0,1), col = "black", cex = 1.2, pos=1, srt=0)
      text(x = XYsize*0.5+XYsize, y = -XYsize*0.175,
             label = Lab02, adj = c(0,1), col = "black", cex = 1.2, pos=1, srt=0)
      text(x = XYsize*0.5+XYsize*2, y = -XYsize*0.175,
             label = Lab03, adj = c(0,1), col = "black", cex = 1.2, pos=1, srt=0)
      text(x = XYsize*0.5+XYsize, y = XYsize + XYsize*0.05,
             label = paste("Image section: ", n),
             adj = c(0,1), col = "black", cex = 1.2, pos=1, srt=0)
    }}, movie.name = paste0(Name, ".gif"), interval = Interval, dpi=Dpi,
    nmax = dim(ImgArray$Original)[4], ani.width = Width, ani.height=Height, ani.type="png")
}

####################################################################################
#An image visualization function to create an animation for the 4D array.
####################################################################################
ImageView2D <- function(ImgArray, Name, Interval = 0.25, N=100 ){
    Lab01="Original"; Lab02="Merge"; Lab03="Supervised"
    Opac=c(0.2, 0.2); Dpi=72
    Width = 500; Height=250; XYsize = 256; Thres=0.4
    options(EBImage.display = "raster")
    names(ImgArray) <- c("Original", "GroundTruth")
    ImgArray$GroundTruth[ImgArray$GroundTruth < Thres] <- 0
    ImgArray$GroundTruth[ImgArray$GroundTruth >= Thres] <- 1
    if(dim(ImgArray$Original)[1] > N){
      Seq0 <- 1:N
    }else{
      Seq0 <- seq_len(dim(ImgArray$Original)[1])
    }
    if(dim(ImgArray$Original)[4] != dim(ImgArray$GroundTruth)[4]){
    animation::saveGIF({
    for(n in Seq0){
      #n <- 1
      par(bg = 'grey')
      X0 <- EBImage::Image(ImgArray$GroundTruth[n,,,], colormode="Grayscale")
      X <- resize(X0, XYsize, XYsize, filter="none")
      Y0 <- EBImage::channel(EBImage::Image(ImgArray$Original[n,,,], colormode="Color"), mode="grey")
      Y <- resize(Y0, XYsize, XYsize, filter="none")
      Image_color01 <- EBImage::paintObjects(X, toRGB(Y), opac=Opac, col=c("red","red"), thick=TRUE, closed=FALSE)
      EBImage::display(EBImage::combine(toRGB(Y),
                                        resize(Image_color01, XYsize, XYsize, filter="none"),
                                        toRGB(X)),
                         nx=3, all=TRUE, spacing = 0.01, margin = 70)
      text(x = XYsize*0.5, y = -XYsize*0.175,
             label = Lab01, adj = c(0,1), col = "black", cex = 1.2, pos=1, srt=0)
      text(x = XYsize*0.5+XYsize, y = -XYsize*0.175,
             label = Lab02, adj = c(0,1), col = "black", cex = 1.2, pos=1, srt=0)
      text(x = XYsize*0.5+XYsize*2, y = -XYsize*0.175,
             label = Lab03, adj = c(0,1), col = "black", cex = 1.2, pos=1, srt=0)
      text(x = XYsize*0.5+XYsize, y = XYsize + XYsize*0.05,
             label = paste("Image section: ", n),
             adj = c(0,1), col = "black", cex = 1.2, pos=1, srt=0)
    }}, movie.name = paste0(Name, ".gif"), interval = Interval, dpi=Dpi,
    nmax = max(Seq0), ani.width = Width, ani.height=Height, ani.type="png")
    }else{
    animation::saveGIF({
    for(n in Seq0){
      #n <- 1
      par(bg = 'grey')
      Image_color01 <- EBImage::paintObjects(resize(ImgArray$GroundTruth[n,,,], XYsize, XYsize, filter="none")/2,
                                      toRGB(resize(ImgArray$Original[n,,,], XYsize, XYsize, filter="none")), opac=Opac,
                                      col=c("red","red"), thick=TRUE, closed=FALSE)
      EBImage::display(EBImage::combine(resize(toRGB(ImgArray$Original[n,,,]), XYsize, XYsize, filter="none"),
                                          resize(Image_color01, XYsize, XYsize, filter="none"),
                                          resize(toRGB(ImgArray$GroundTruth[n,,,]), XYsize, XYsize, filter="none")),
                         nx=3, all=TRUE, spacing = 0.01, margin = 70)
      text(x = XYsize*0.5, y = -XYsize*0.175,
             label = Lab01, adj = c(0,1), col = "black", cex = 1.2, pos=1, srt=0)
      text(x = XYsize*0.5+XYsize, y = -XYsize*0.175,
             label = Lab02, adj = c(0,1), col = "black", cex = 1.2, pos=1, srt=0)
      text(x = XYsize*0.5+XYsize*2, y = -XYsize*0.175,
             label = Lab03, adj = c(0,1), col = "black", cex = 1.2, pos=1, srt=0)
      text(x = XYsize*0.5+XYsize, y = XYsize + XYsize*0.05,
             label = paste("Image section: ", n),
             adj = c(0,1), col = "black", cex = 1.2, pos=1, srt=0)
    }}, movie.name = paste0(Name, ".gif"), interval = Interval, dpi=Dpi,
    nmax = max(Seq0), ani.width = Width, ani.height=Height, ani.type="png")
    }
}

####################################################################################
# Read and display GIF animations
####################################################################################
Display.GIF <- function(GifFileName, View=TRUE){
a <- magick::image_read(GifFileName)
if(View){print(a); return(a)}else{return(a)}
}