// Batch script which processes raw images of cell microarrays. Input images should be 32-bit RGB TIFF files.
// This script will convert the raw images to 8-bit TIFF files and optionally rotates them 90 degrees
// clockwise so they're upright, i.e., first arrayed condition at the top left.
// Images are additionally binned to enable quantification by CellProfiler.
// The script will write the selected settings into a file titled "settings.txt" in the destination folder.

// Initial options
setBatchMode(true)

// Create the dialog box to select the desired settings
Dialog.create("Array processing");
Dialog.addNumber("Binning in x:", 4);
Dialog.addNumber("Binning in y:", 4);
Dialog.addCheckbox("Rotate 90 degrees clockwise", true);
Dialog.addCheckbox("Enhance contrast", false);
Dialog.addNumber("% pixels saturated", 0.4);
Dialog.show();

// Capture values from dialog
xBinning = Dialog.getNumber();
yBinning = Dialog.getNumber();
rotate = Dialog.getCheckbox();
enhance = Dialog.getCheckbox();
pixelSaturated = Dialog.getNumber();

// Get source and destination directories
source = getDirectory("Choose Source Directory");
sourceList = getFileList(source);
destination = getDirectory("Choose Destination Directory");

// Perform desired operations
for (i=0; i<sourceList.length; i++) {
  showProgress(i+1, sourceList.length);
  open(source + sourceList[i]);
  run("32-bit");
  run("8-bit");
  if (rotate) run("Rotate 90 Degrees Right");
  run("Bin...", "x=xBinning y=yBinning bin=Average");
  if (enhance) {
    run("Enhance Contrast...", "saturated=pixelSaturated normalize");
  }
  saveAs("tiff", destination + sourceList[i]);
  close();
}

// Save settings
settingsFile = File.open(destination + "settings.txt");
MonthNames = newArray("Jan","Feb","Mar","Apr","May","Jun","Jul","Aug","Sep","Oct","Nov","Dec");
DayNames = newArray("Sun", "Mon","Tue","Wed","Thu","Fri","Sat");
getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second, msec);
TimeString ="Date: "+DayNames[dayOfWeek]+" ";
if (dayOfMonth<10) {TimeString = TimeString+"0";}
TimeString = TimeString+dayOfMonth+"-"+MonthNames[month]+"-"+year+"\nTime: ";
if (hour<10) {TimeString = TimeString+"0";}
TimeString = TimeString+hour+":";
if (minute<10) {TimeString = TimeString+"0";}
TimeString = TimeString+minute+":";
if (second<10) {TimeString = TimeString+"0";}
TimeString = TimeString+second;
print(settingsFile, TimeString);
print(settingsFile, "x binning: " + xBinning + "\n");
print(settingsFile, "y binning: " + yBinning + "\n");
print(settingsFile, "rotate: " + rotate + "\n");
print(settingsFile, "enhance: " + enhance + "\n");
print(settingsFile, "saturated pixels: " + pixelSaturated + "\n");