/****
 * Script that measures several aspects of the camera:
 * 1. Averaged background image
 * 2. Calculates read-noise and elctron conversion factor from multiple images of the same object/
 */

import java.lang.Thread;


// file locations
acqName = "cameraTest";
rootDirName = "C:/acquisitionData";


// number of channels (should be two or less)
nrChannels = 1;
// The following two arrays must have size nrChannels
String [] channelName = new String [] {"Dark",};
Color [] channelColor = new Color [] {Color.WHITE};

// Number of timepoints
nrFrames = 25;


// clear all previous acquisitions
gui.closeAllAcquisitions();
gui.clearMessageWindow();
gui.openAcquisition(acqName, rootDirName, nrFrames, 1, 1);
for (int i=0; i< nrChannels; i++) {
   gui.setChannelColor(acqName, i, channelColor[i]);
   gui.setChannelName(acqName, i, channelName[i]);
}
long width = mmc.getImageWidth();
long height = mmc.getImageHeight();
long depth = mmc.getBytesPerPixel();

gui.initializeAcquisition(acqName, (int) width, (int) height, (int) depth);

exposure = mmc.getExposure();
binning = mmc.getProperty(mmc.getCameraDevice(), "Binning");

   // first image is blank.  Skip
   // There is something weird going on depending on exposure time
   // longer exposures need an extra image at the end, shorter ones (< 31 ms) do not...
   // this code adds an extra image at the end
mmc.startSequenceAcquisition(nrFrames, 0, false);

Double exp = mmc.getExposure();

now = System.currentTimeMillis();
int frame = 0;
int slice = 0;
int channel = 0;
int counter = 0;
while (mmc.getRemainingImageCount() > 0 || mmc.isSequenceRunning() ) {
   if (mmc.getRemainingImageCount() > 0) {
      img = mmc.popNextImage();
      if (counter > -1) {
         gui.addImage(acqName, img, frame, channel, slice);
         gui.setImageProperty(acqName, frame, channel, slice, "Exposure", exp.toString());
         gui.setContrastBasedOnFrame(acqName, frame, slice);

			frame++;    
      }
      counter++;
   } 
	Thread.sleep(exp.longValue());
}
itTook = System.currentTimeMillis() - now;