import org.json.JSONObject;
import org.micromanager.utils.MDUtils;
import org.micromanager.utils.NumberUtils;

String c1 = "Andor-Left";
String c2 = "Andor-Back";
String acq = "2-Color-Grid-PositionsYXC";
int nrXPositions_ = 3;
int nrYPositions_ = 3;
double stepSize_ = 0.12;
xyStageDevice_ = "MCL NanoDrive XY Stage";
xOrigin_ = mmc.getXPosition(xyStageDevice_);
yOrigin_ = mmc.getYPosition(xyStageDevice_);

gui.closeAllAcquisitions();
gui.openAcquisition(acq, "Z:/Images/20101214/", 1, 2, 1, nrXPositions_ * nrYPositions_, true, true);
gui.setChannelColor(acq, 0, Color.RED);
gui.setChannelColor(acq, 1, Color.GREEN);
gui.setChannelName(acq, 0, c1);
gui.setChannelName(acq, 1, c2);
int w = mmc.getImageWidth();
int h = mmc.getImageHeight();
int d = mmc.getBytesPerPixel();
int [] frameNr  = new int [] {0, 0};
gui.initializeAcquisition(acq, w, h, d);

for (int x = 0; x < nrXPositions_; x++) {
	for (int y = 0; y < nrYPositions_; y++) {	
		mmc.setXYPosition(xyStageDevice_, x * stepSize_ + xOrigin_, y * stepSize_ + yOrigin_);

		// delete previous content of circular buffer
		mmc.initializeCircularBuffer();
		//mmc.prepareSequenceAcquisition(c1);
		//mmc.prepareSequenceAcquisition(c2);
		mmc.startSequenceAcquisition(c1, 1, 0, false);
		mmc.startSequenceAcquisition(c2, 1, 0, false);
		while (mmc.isSequenceRunning() || mmc.getRemainingImageCount() > 0) {
			if (mmc.getRemainingImageCount() > 0) {
				img = mmc.popNextTaggedImage();
				JSONObject md = img.tags;

				MDUtils.setFrameIndex(md, 0);
				MDUtils.setSliceIndex(md, 0);
				//int posIndex = (x % nrXPositions_) + (y * nrXPositions_);
				int posIndex = (y % nrYPositions_) + (x * nrYPositions_);
				MDUtils.setPositionIndex(md, posIndex);
				// TODO: use MDUtils.setPositionName instead
				md.put ("PositionName", "Pos" + posIndex);
				cName = md.get("Camera");
				if (c1.equals(cName))
					MDUtils.setChannelIndex(md, 0);
				else
					MDUtils.setChannelIndex(md, 1);
				gui.addImage(acq, img);
			}
		}
	}
}

// Return stage to original positions
mmc.setXYPosition(xyStageDevice_, xOrigin_, yOrigin_);