Working_directory ="T:\\TimelapseData\\201029GA14"
setwd(Working_directory)

require(EBImage)

csv_raw = read.table("allquant.csv", header = TRUE, sep = ",")
csv_raw = csv_raw[which(csv_raw$TimePoint==2),]
csv_raw= as.data.frame(csv_raw)


  
  # get position folders in directory 
  all.files <- list.files(rec=F)
  foldersInDIR = all.files[file.info(all.files)$isdir]
  
  # get the valid position folders
  positionFolders = grep('_p', foldersInDIR, value=TRUE)
  
  # for each position folder
  for (posFolder in positionFolders) {
    print(posFolder)
    # get the position id
    posID = as.numeric(strsplit(posFolder,"_p")[[1]][2])
    cellsInPositionDF = subset(csv_raw, Position==posID
                               ) # get the info about this position
    
    # load the image on which to plot the clusterID
    if (nrow(cellsInPositionDF)>0){
      setwd(paste(posFolder, sep = "\\"))
      
      imgFilename =  paste(posFolder, "_t00001_z001_w04.png", sep = "")
      imgFilenameOut = paste(posFolder,"_t00001_z001_w05.png", sep = "")
      
      img = readImage(imgFilename)
      imgEnhanced = img * 2000
      
      h<-dim(img)[1]
      w<-dim(img)[2]
      
      
      
      png(imgFilenameOut, width=w, height=h)
      display(img, method="raster")
      
      for (i in 1:length(rownames(cellsInPositionDF))) {
        Xcoord = as.numeric(as.character(cellsInPositionDF$SeedX[i]))
        Ycoord = as.numeric(as.character(cellsInPositionDF$SeedY[i]))
        ClusterID = paste(cellsInPositionDF$M1[i],cellsInPositionDF$mCh[i],sep="")
        #add cluster id on the image
        text(x = Xcoord, y = Ycoord, label = ClusterID, col = "white", cex = 2)
      }
      
      
      #close image
      dev.off()
      Working_directory ="T:\\TimelapseData\\200616GA13"
      setwd(Working_directory)
    }
    
    
  }