/*
  * Script to acquire Z-stack at very high speeds using the ASI piezo stage and Arduino control
  * This will only work with the newest ASI firmware (as of October 2008)
  * The camera should be able to generate a TTL pulse.  
  * Hook up the camera TTL out to the ARduino 
  * Set up the numbers below and run the script
  * Make sure that the ASI Pieze Z-drive is the Core-Focus device
  */

// file locations
acqName = "test-ASI-Z";
rootDirName = "C:/acquisitionData";

// number of slices
nrSlices = 10;
// distance in um between slices
distance = 0.25;
// number of channels (should be two or less)
nrChannels = 2;
// Number of timepoints
nrFrames = 3;
// Time between timePoints (in Ms);
intervalMs = 2000;

// The following two arrays must have size nrChannels
String [] channelName = new String [] {"Cy3", "FITC"};
Color [] channelColor = new Color [] {Color.RED, Color.GREEN};

//Arduino digital patters (MUST have size of 2 * nrChannels)
// Odd patterns are triggered on exposure start, even patterns on exposure stop
int [] dPattern = new int [] {1,0,32,2};

// Port for communication with ASI stage controller
port = "COM4";


// DO NOT EDIT BELOW THIS LINE
// Remember original channel group
channelPreset = mmc.getCurrentConfig("Channel");
mmc.setConfig("Channel", "DAC-Open");

int nrPatterns = nrChannels * 2;
// Set up Arduino: 
for (int i = 0; i < nrPatterns; i++) { 
   mmc.setProperty("Arduino-Switch", "State", new Integer (dPattern[i]).toString());
   mmc.setProperty("Arduino-Switch", "SetPattern", " " + new Integer(i).toString());
}
mmc.setProperty("Arduino-Switch", "Nr. Patterns Used", new Integer(nrPatterns).toString());

// switch off autoshutter but remember its state so that it can be restored
boolean autoShutter = false;
if (mmc.getAutoShutter()) {
   autoShutter = true;
   mmc.setAutoShutter(false);
}

// clear all previous acquisitions
gui.closeAllAcquisitions();
gui.clearMessageWindow();
gui.openAcquisition(acqName, rootDirName, nrFrames, nrChannels, nrSlices);
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();


// Use TTL mode 2 (repeat last MOVREL command).  

// Store current Z position as a reference to retrun to after acquiring the stack
zPos = mmc.getPosition(mmc.getFocusDevice());
gui.message("Position: "  + zPos);

// Move down so that the current position will be in the middle of the stack
//mmc.setRelativePosition(mmc.getFocusDevice(), -distance * (nrSlices / 2));
double basePos = zPos - (distance * (nrSlices / 2));
mmc.setPosition(mmc.getFocusDevice(), basePos);


// First give it the correct MOVREL by going down and then back up
command = "R Z=" +  -10*distance;
mmc.setSerialPortCommand(port, command, "\r");
answer = mmc.getSerialPortAnswer(port, "\r\n");
gui.message(answer);

command = "R Z=" + 10*distance;
mmc.setSerialPortCommand(port, command, "\r");
answer = mmc.getSerialPortAnswer(port, "\r\n");
gui.message(answer);
// Set controller in TTL Mode 2
command ="TTL X=2";
mmc.setSerialPortCommand(port, command, "\r");
answer = mmc.getSerialPortAnswer(port, "\r\n");
gui.message(answer);


mmc.setProperty("Arduino-Switch", "TriggerMode", "Start");

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

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

// There is an extra image to deal with if the exposure is more than 35 ms
int extra = 1;
if (binning.equals("1")) {
   if (exposure > 35.0)
      extra = 2;
} else if (binning.equals("2")) {
   if (exposure > 20.0)
      extra = 2;
} else if (binning.equals("4")) {
   if (exposure > 11.5) 
      extra = 2;
}
gui.message ("Extra: " + extra);

for (frame=0; frame < nrFrames; frame++) {

   // 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((nrChannels * nrSlices) + extra, 0, false);

   now = System.currentTimeMillis();
   int slice = 0;
   int channel = 0;
   int counter = 0;
   while (mmc.getRemainingImageCount() > 0 || mmc.deviceBusy(mmc.getCameraDevice())) {
      if (mmc.getRemainingImageCount() > 0) {
         img = mmc.popNextImage();
         if (counter > 0 && (slice < nrSlices)) {
            gui.addImage(acqName, img, frame, channel, slice);
            gui.setImageProperty(acqName, frame, channel, slice, "ZPositionUm", Double.toString(basePos + (slice * distance)));
            gui.setImageProperty(acqName, frame, channel, slice, "Exposure", Double.toString(mmc.getExposure()));
            if (channel == (nrChannels - 1)) {
               if (slice == (nrSlices /2) + 1)
                  gui.setContrastBasedOnFrame(acqName, frame, slice -1);
               slice++;
               channel = 0;
            } else
               channel++;        
         }
         counter++;
      } 
   }
   mmc.setPosition(mmc.getFocusDevice(), basePos);
   itTook = System.currentTimeMillis() - now;
   if ((intervalMs - itTook) > 0)
      gui.sleep(intervalMs - itTook);

}

mmc.stopSequenceAcquisition();

// Reset Arduino
mmc.setProperty("Arduino-Switch", "TriggerMode", "Stop");

// Reset ASI controller TTL behavior
command ="TTL X=0";
mmc.setSerialPortCommand(port, command, "\r");
answer = mmc.getSerialPortAnswer(port, "\r\n");
gui.message(answer);

// Return to original position
mmc.setPosition(mmc.getFocusDevice(), zPos);

// Restore original Channel
mmc.setConfig("Channel", channelPreset);

// restore autoShutter status
if (autoShutter)
   mmc.setAutoShutter(true);