// Karl Bellve's Well Plate Test Script
// 20110218 K.H. explicitly add the class path & added some progress messages, 

// for N = 96, generated position will lie on x on [0,99000] microns y on [0, 63000] microns
// for N = 24 only ever 4th well is inspected on a 96 well plate

addClassPath("Big.jar");
import edu.umassmed.big.SBSPlate;
import javax.swing.JOptionPane;
import java.lang.Math;
import org.micromanager.api.Autofocus;
gui.closeAllAcquisitions();
gui.clearMessageWindow();


// coordinates of well A1
double [] x0;
double [] y0;
x0 = new double[1];
y0 = new double[1];

xystage = mmc.getXYStageDevice();
zstage = mmc.getFocusDevice();
Autofocus a2 = gui.getAutofocus();
Double[] xyposition = new Double[2];
xyposition[0] = 0.0;
xyposition[1] = 0.0;
double [] ipos  = new double[2]; 

JOptionPane.showMessageDialog(null, "Please position stage at center of Well A1, then press OK");
mmc.getXYPosition (xystage, x0, y0);
print(" current position : \n");
xyposition[0] += (int)Math.round(x0[0]);
xyposition[1] += (int) Math.round(y0[0]);


mmc.setXYPosition(xystage,xyposition[0],xyposition[1]);
mmc.waitForDevice(xystage);

// ensure an image window is open
mmc.snapImage();
image0 = mmc.getImage();
gui.displayImage(image0);
//ad hoc for the plate I've got I see that there is a rather large incline of the focus plane in Y
// for y = 0, z = -843
// for y = 63000, z =  -1189
// z = -843 - (.00549 * y)

SBSPlate plate = new SBSPlate(24);//(1536);
numberOfWells = plate.getNumberOfWells();
Integer m = new Integer(0);
for (m = 1; m <= numberOfWells; m++) {
  // code to take an image could be here

  a2.fullFocus();
  gui.updateImage();
  // move the stage to the next well
  ipos = plate.getNextPosition(); // 0 indexed in mcrons

  xyposition[0] = ipos[0] + (int)Math.round(x0[0]);
  xyposition[1] = ipos[1] + (int)Math.round(y0[0]);
  mmc.setXYPosition(xystage,xyposition[0],xyposition[1]);
  print("going-> [" + xyposition[0].toString() + ", " + xyposition[1].toString()+"]");
  mmc.waitForDevice(xystage);
/*
  Double zoffcalc = -843. -(0.00549*ipos[1]);
  mmc.setPosition(zstage, zoffcalc);
  print("setting Z to " + zoffcalc.toString());
  mmc.waitForDevice(zstage);
*/
  Double newz = mmc.getPosition(zstage);
print ("reported z position is " + newz.toString());
}
// return stage to starting position
mmc.setXYPosition(xystage,x0[0],y0[0]);
mmc.waitForDevice(xystage);
// this will help you if you ever define any functions in this bean shell script
update();