// Acquisition script for Long Cai
// Nico Stuurman, Dec. 2010

import org.micromanager.api.AcquisitionOptions;
import org.micromanager.navigation.PositionList;
import org.micromanager.navigation.MultiStagePosition;
import org.micromanager.navigation.StagePosition;
import java.lang.System;

// clear all previous acquisitions
gui.closeAllAcquisitions();
gui.clearMessageWindow();

// file locations
acqName = "test-acq-col";
rootDirName = "C:/acquisitionData";

// parameters
numRepetitions = 2;
numFrames = 3;
String[] channels = {"Cy5", "FITC"};
Color[] colors = {Color.WHITE, Color.GREEN};
int[] exposures = {100, 30};
numSlices = 1;
intervalFrame = 100;
intervalRep = 5000;
channelGroup = "Channel";


PositionList pl = gui.getPositionList();
String[] acqs = new String[pl.getNumberOfPositions()];
for (int l=0; l < pl.getNumberOfPositions(); l++) {
	acqs[l] = pl.getPosition(l).getLabel();
	MultiStagePosition.goToPosition(pl.getPosition(l), mmc);


	// create acquisition and set options
	gui.openAcquisition(acqs[l], rootDirName, numFrames * numRepetitions,
	channels.length, numSlices);
	for (int i=0; i<colors.length; i++)
 		gui.setChannelColor(acqs[l], i, colors[i]);
	for (int i=0; i<channels.length; i++)
  	gui.setChannelName(acqs[l]	, i, channels[i]);

	for (int k=0; k< numRepetitions; k++)  {
		reStart = System.currentTimeMillis();
		for (int j=0; j<channels.length; j++) {
   		mmc.setExposure(exposures[j]);
   		mmc.setConfig(channelGroup, channels[j]);
   		mmc.waitForConfig(channelGroup, channels[j]);
			for (int i=0; i<numFrames; i++) {
   			now = System.currentTimeMillis();
   			gui.message("Acquiring frame " + i + ", channel " + channels[j] +
".");
	 			gui.snapAndAddImage(acqs[l], (k*numFrames) + i, j, 0);
				itTook = System.currentTimeMillis() - now;
				if (itTook < intervalFrame)
 				gui.sleep(intervalFrame - itTook);
			}
 		// set channel contrast based on the first frame
 		if (i==0 && k==0) {
    		gui.setContrastBasedOnFrame(acqs[l], i, 0);
 		}
		}
		itTook = System.currentTimeMillis() - reStart;
		if (itTook < intervalRep)
 			gui.sleep(intervalRep - itTook);
	}
}