mport ij.ImagePlus;
import ij.IJ;
import org.micromanager.api.MMWindow;

// A simple script to run intelligent acquisition 


// This script will explore an area of your slide and look for interesting cells
// The macro identified with "macroName" will analyze images and return
// the coordinates of the interesting cell through the ImageJ ResultsTable

// You will need to create 2 acquisiton setting files, one for exploration
// the other for high resolution imaging.


// Edit all settings down to the DO NOT EDIT line

// AcqSettings for exploration
acqSetA = "/Users/nico/AcqSettings-A.xml";

// AcqSettings for high-res time lapse imaging
acqSetB = "/Users/nico/AcqSettings-B.xml";

// analysis macro name
macroName = "";

// hard coded x and y width of a single image in microns 
// could be figured out dynamically
xWidthMicron = 100;
yWidthMicron = 100;

// pixel size in microns
// this could also be figured out dynamically
pixelSizeMicron = 0.208;

// fraction of the image that will be set as ROI in the time-lapse imaging
// should be set to a number > 0 and <= 1;
fractionRoi = 0.5;

// Number of locations in X and Y that will be explored
nrImagesX = 2;
nrImagesY = 2;



// Do not edit below this line


imageIndexX = 0;
imageIndexY = 0;
acqNumber = 0;
RoiX = (int) mmc.getImageWidth() * fractionRoi / 2;
RoiY = (int) mmc.getImageHeight() * fractionRoi / 2;
RoiWidth = (int) 2 * RoiX;
RoiHeight = (int) 2 * RoiY;

gui.message ("Roi: " + RoiX + " " + RoiY + " " + RoiWidth + " " + RoiHeight);

xyStage = mmc.getXYStageDevice();

stop = false;

while (!stop) {

   gui.loadAcquisition(acqSetA);

   thisAcq = gui.runAcquisition();

   // get x and y coordinates
   xPos = mmc.getXPosition(xyStage);
   yPos = mmc.getYPosition(xyStage);

   gui.message("Acquisition " + acqNumber + " finished at position: " + xPos + ", " + yPos);
   acqNumber++;


   // Now run the macro
   // ij.IJ.runMacro(macroName);

   gui.closeAcquisitionWindow(thisAcq);

   // determine if an interesting cell was found
   found = false;
   res = ij.measure.ResultsTable.getResultsTable();
   if (res.getCounter() > 0) {
      // X and Y coordinates of object found in pixels
      xPos = res.getValue("X", 0);
      yPos = res.getValue("Y", 0);
      mmc.setRelativeXYPosition(xyStage, xPos * pixelSizeMicron, yPos * pixelSizeMicron);
      mmc.setROI((int) RoiX, (int) RoiY, (int) RoiWidth, (int) RoiHeight);
      gui.message("Imaging interesting cell at position: " + 
         mmc.getXPosition(xyStage) + ", " + mmc.getYPosition(xyStage) );

      gui.loadAcquisition(acqSetB);
      goodStuff = gui.runAcquisition();
      gui.closeAcquisitionWindow(goodStuff);
      mmc.setRelativeXYPosition(xyStage, - xPos * pixelSizeMicron, - yPos * pixelSizeMicron);
      mmc.clearROI();
      org.micromanager.utils.JavaUtils.sleep(200);
   } 

   if (imageIndexX < nrImagesX - 1) {
      mmc.setRelativeXYPosition(xyStage, xWidthMicron, 0);
      imageIndexX++;
   } else {
      if (imageIndexY < nrImagesY - 1) {
         mmc.setRelativeXYPosition(xyStage, - ( (nrImagesX - 1) * xWidthMicron),
             yWidthMicron);
         imageIndexY++;
         imageIndexX = 0;
      } else {  // done
         stop = true;
      }
   }

}