////////////////////////////////////////////////////////////////////////////////////////////////
//
// Karl Bellve
// Biomedical Imaging Group
// University of Massachusetts Medical School
// Karl.Bellve@umassmed.edu
// 
// Ben Czech 
// czechben@gmail.com
//
////////////////////////////////////////////////////////////////////////////////////////////////
//********************************************************************************************//
// Edit below
                              //           {column,row}
int[] firstWell = {1,1};      // 1 indexed {min 1,1}
int[] lastWell = {12,8};      // 1 indexed {max 12,8}
int plateType = 96;           // could be 24, 96, 384, 1536, must conform to SBS standard

// Edit above
//********************************************************************************************//
////////////////////////////////////////////////////////////////////////////////////////////////

import edu.umassmed.big.SBSPlate;
import ij.gui.*;
import java.lang.Math;
import org.micromanager.navigation.PositionList;
import org.micromanager.api.Autofocus;
import org.micromanager.api.AcquisitionOptions;
import org.micromanager.PositionListDlg;

/////////////////////////////////////////////////////////////////////////////////////

move(double x, double y, double z)
{
	print("Moving to " + (x - startX) + "," + (y - startY) + "," + (z - startZ));

	mmc.setXYPosition(xystage,x,y);
  	mmc.waitForDevice(xystage);

	mmc.setPosition(zstage,z); 
	mmc.waitForDevice(zstage);
	// add an extra second...
	mmc.sleep(1000);
}

gui.clearMessageWindow();
gui.closeAllAcquisitions();

/////////////////////////////////////////////////////////////////////////////////////
// Variables
// 0 indexed in microns
// X, Y and Z
double[] position = {0.0,0.0,0.0}; 
double x0,y0,z0,z1,startX,startY,startZ;
// End Variables
/////////////////////////////////////////////////////////////////////////////////////

//sets starting position
startX = mmc.getXPosition(xystage);
startY = mmc.getYPosition(xystage);
startZ = mmc.getPosition(zstage);

// Plate and position list setup
PositionListDlg plg=gui.getXYPosListDlg();
PositionList pl=new PositionList();
gui.setPositionList(pl);
plg.setVisible(true);
SBSPlate plate = new SBSPlate(plateType,startX,startY);
plate.setFirstWell(firstWell[0],firstWell[1]);
plate.setLastWell(lastWell[0],lastWell[1]);
numberOfWells = plate.getNumberOfWells();

// if first well is not {1,1}, move to that position
position = plate.getPlatePosition(firstWell[0],firstWell[1]);
x0 = position[0];
y0 = position[1];
z1 = z0 = mmc.getPosition(zstage);

move(x0,y0,z0);

// This loop cycles through all the wells so you can set multiple X, Y and Z positions
// within each well

int index=0;
int countPositions=0;

for (well = 0; well < numberOfWells;) {
   GenericDialog dialog = new GenericDialog("Mark Positions");
   dialog.addMessage(plate.getWellLabel(well));
   dialog.enableYesNoCancel("Mark","Next Well");
   dialog.showDialog();
   if (dialog.wasOKed()) {
      // set a position within this well
      gui.markCurrentPosition();
      print("Position has been marked at "+plate.getWellLabel(well)+"_"+index);
      pl=gui.getPositionList();
      pl.setLabel(countPositions,plate.getWellLabel(well)+"_"+index);
      countPositions++;
      gui.setPositionList(pl);
      index++;
   } else if (dialog.wasCanceled()) {
      //ends the script	
      GenericDialog dialog2 = new GenericDialog("Cancel?");
      dialog2.addMessage("Select OK if you really want to cancel");
      dialog2.showDialog();
      if (dialog2.wasOKed()) {
         done();
         print("User cancelled, exiting script");
         return false;
      }
   } else {
      // Move to next well
      print("Next Well: " + (well + 1));
      if (dialog.getNextBoolean() != true) {		
         print("Skipping well " + well + " with label " + plate.getWellLabel(well));
      }
      // move the stage to the next well
      position = plate.getNextPlatePosition(); // 0 indexed in microns
      x0 = position[0];
      y0 = position[1];
      z0 = position[2];
      // using last Z and not the default Z
      move(x0,y0,z1);
      index=0;
      well++;
   }
}

pl=gui.getPositionList();
gui.setPositionList(pl);
print("Positions have been marked... Moving back to start position");
move (startX, startY, startZ);
print("Finished");