// This macro demonstrates how a macro can display a
// data input dialog box. The dialog it creates contains
// one string field, one popup menu, two numeric fields,   
// and one check box.

  Block = "A";
  width=5; height=4; 
  pxlsz = 0.654; diam = 800;
  xCoordNames = "abcdefghiklmnopqr";
  Dialog.create("TMA ROI generator");
  Dialog.addString("Block:", Block);
  Dialog.addNumber("Width:", width);
  Dialog.addNumber("Height:", height);
  Dialog.addNumber("PIxel size:", pxlsz);
  Dialog.addNumber("Diameter[µm]:", diam);
  Dialog.show();
  waitForUser("please mark the first and the last spot with the multipoint tool");
  getSelectionCoordinates(xCoordinates, yCoordinates); 

  Block = Dialog.getString();
  width = Dialog.getNumber();
  height = Dialog.getNumber();
  pxlsz = Dialog.getNumber();
  diam = Dialog.getNumber();
  

  

alpha1 = atan2(yCoordinates[1]-yCoordinates[0] , xCoordinates[1]-xCoordinates[0]);
alpha2 = atan2(height-1 , width-1);
alpha = alpha1-alpha2;

//print (alpha1, alpha2);
ddxx = (xCoordinates[1]-xCoordinates[0]);
ddyy = (yCoordinates[1]-yCoordinates[0]);
d = sqrt(ddxx*ddxx+ddyy*ddyy);
dx = d*cos(alpha2)/(width-1);
dy = d*sin(alpha2)/(height-1);
//print(alpha1*180/3.1412,alpha2*180/3.1412,alpha*180/3.1412);

  
diam = diam/pxlsz;

for  (ix = 1; ix<= height; ix = ix+1){
	for  (iy = 1; iy<= width; iy = iy+1){
		label = Block + iy + substring(xCoordNames, ix-1,ix);
		//print(label);
		posx = xCoordinates[0] - (ix-1)*dx*sin(alpha)+(iy-1)*dy*cos(alpha) - diam/2;
		posy = yCoordinates[0] + (ix-1)*dx*cos(alpha)+(iy-1)*dy*sin(alpha) - diam/2;
		makeOval(posx, posy, diam, diam);
		current = roiManager("count");//iy + (ix-1)*height-1;
		roiManager("Add");
		//print(current);
		roiManager("Select", current);
		roiManager("Rename", label);
	}
	
}