// expects as input two Z series named as follows:
// r is magenta
// g is green


//==================================================================
macro "Make Fixed Size Box [F5]" {
   makeRectangle(10, 10, 100, 100);
}



//==================================================================
macro "simple merge and rotate [q]" {

  selectWindow("r");
  setMinAndMax(4096, 29000);
  run("8-bit");

  selectWindow("g");
  setMinAndMax(17414, 40070);
  run("8-bit");
  run("Median...", "radius=1 stack");

  run("Merge Channels...", "c1=r c2=g c3=r");
  run("3D Project...", "projection=[Brightest Point] axis=Y-Axis slice=0.30 initial=0 total=360 rotation=10 lower=1 upper=255 opacity=0 surface=100 interior=50 interpolate");
  run("In [+]");
  run("In [+]");
}

/==================================================================
macro "Get Title and Print it to insert into other macro" {
   print(getTitle());
   selectWindow("Log");
}


/==================================================================
macro "pull all Z series from two windows, merge, and 3D" {
  clipsize = 100;
  redWindow = "C2-effectord4Cl132z8lamincopy M.tif";
  greenWindow = "C1-effectord4Cl132z8lamincopy G.tif";
  // blueWindow= 

  for (i=0;  i<roiManager("count");  i++){
      selectWindow(redWindow);
      s = nSlices();
      roiManager("select", i);
      run("Measure");
      xc = getResult("X", nResults-1);
      yc = getResult("Y", nResults-1);
      toUnscaled(xc, yc);
      selectWindow(redWindow);
      makeRectangle(xc-(clipsize/2), yc-(clipsize/2), clipsize, clipsize);
      run("Duplicate...", "title=[r] duplicate range=1-"+s+"");
      selectWindow(redWindow);    // get the selection for the restore command
      selectWindow(greenWindow); 
      run("Restore Selection");
      run("Duplicate...", "title=[g] duplicate range=1-"+s+"");

      selectWindow("r");
      setMinAndMax(4096, 29000);
      run("8-bit");

      selectWindow("g");
      setMinAndMax(17414, 40070);
      run("8-bit");
      run("Median...", "radius=1 stack");

      run("Merge Channels...", "c1=r c2=g c3=r"); 
      run("3D Project...", "projection=[Brightest Point] axis=Y-Axis slice=0.30 initial=0 total=360 rotation=10 lower=1 upper=255 opacity=0 surface=100 interior=50 interpolate");
      rename("Proj_" + i);
      selectWindow("RGB");
      run("Close");
   } // for i
} // end