/*
 * This script takes a 'pre-Burst' image using the specified preChannel and preExposure
 * It then starts a burst imaging with the specified channel and exposure
 * All other paramters can be set in the GUI.
 * Written by Nenad Amodaj for Julia Kardon, November 2007
 */

import ij.process.*;
import ij.ImagePlus;
import ij.io.FileSaver;

//set-up parameterers
preExposure = 40.0;
burstExposure = 30.0;
preChannel = "DAPI";
burstChannel = "FITC";
prePath = "image-1.tif";

// acquire pre-frame
mmc.setExposure(preExposure);
mmc.setConfig("Channel", preChannel);
mmc.waitForSystem();
mmc.snapImage();
img = mmc.getImage();

// save pre-frame to TIF
width = mmc.getImageWidth();
height = mmc.getImageHeight();
byteDepth = mmc.getBytesPerPixel();
if (byteDepth == 1) {
   ip = new ByteProcessor((int)width, (int)height);
   ip.setPixels(img);
} else if (byteDepth==16) {
   ip = new ShortProcessor((int)width, (int)height);
   ip.setPixels(img);
} else {
   console.message("Unknown byte depth.");
   return;
}
ImagePlus imp = new ImagePlus(prePath, ip);
FileSaver fs = new FileSaver(imp);
fs.saveAsTiff(prePath);
gui.message("Pre-acquisition image saved!");

//start burst
mmc.setExposure(burstExposure);
mmc.setConfig("Channel", burstChannel);
mmc.waitForSystem();
gui.startBurstAcquisition();
gui.message("Burst acquisition started!");