// Script for manual acquisition
// based on manualAcq.bsh, Nenad Amodaj, Feb 2008, Nico Stuurman, April 2008
// Egor Zindy, Dec 2014

import mmcorej.TaggedImage;
import org.micromanager.api.SequenceSettings;
import org.micromanager.api.ImageCache;
import org.micromanager.api.MMTags;
import org.micromanager.utils.ChannelSpec;
import org.micromanager.utils.ImageUtils;
import org.micromanager.acquisition.TaggedImageStorageMultipageTiff;
import java.util.ArrayList;
import ij.process.ImageProcessor;
import ij.gui.NonBlockingGenericDialog;
import ij.gui.WaitForUserDialog;
import org.json.JSONObject;
import org.json.JSONArray;

//A nice big font to display the current Channel.
Font font = new Font("SansSerif", Font.BOLD, 24);

//a method for creating a new directory name.
String[] newDirectory(String rootDirName, String prefixName) {
	File f = new File(rootDirName, prefixName);
	String name = prefixName;
	int i = 1;

	while(f.exists()) {
		name = prefixName + i;
		f = new File(rootDirName, name);
		i = i+1;
	}

	String[] ret = {name, f.getPath()};
	return ret;
}

//a method for creating a new prefix underscore number from prefix + number
String newPrefix(String prefixName, int increment) {
	Long[] iArray = new Long[] {increment};
	String name = prefixName + "_" + String.format("%04d", iArray);
	return name;
}

// file locations
acqName = "manual-acq-multi";
rootDirName = acq.getRootName();
prefixName = "image";
SequenceSettings s = acq.getSequenceSettings();
ArrayList channelList = new ArrayList();
ArrayList imgList = new ArrayList();

// clear previous acqName acquisition
// This doesn't close the windows
gui.clearMessageWindow();

// parameters
numFrames = 1;
numSlices = 1;
numChannels = 0;

//number of active channels
for (int i=0; i<s.channels.size(); i++) {
	ChannelSpec channel = s.channels.get(i);

	if (!channel.useChannel)
		continue;

	channelList.add(channel);
	numChannels += 1;
}

if (numChannels == 0)
{
	WaitForUserDialog dlg = new WaitForUserDialog("Manual Acquisition", "Check the Multi-D Acq. dialog\n\nNo active channels in use!"); 
	dlg.show();
	return false;
}

String prefixCurrent;
String rootCurrent;
String[] ndArray;

//check the prefixName. Change it if a directory already exists.
ndArray = newDirectory(rootDirName, prefixName);
prefixName = ndArray[0];
fullDirName = ndArray[1];

boolean isRunning = true;
int i = 0; // prefix index
int j = 0; // Channel counter. Best place to define it, as we need to set it to numChannels-1 if the directory cannot be created. Hence the reason why the channel loop isn't a for loop.

int currentImageWidth = (int)mmc.getImageWidth();
int currentImageHeight = (int)mmc.getImageHeight();
int currentBytesPerPixel = (int)mmc.getBytesPerPixel();

//this allows to close the window without prompting to save
if (gui.acquisitionExists(acqName)) {
	gui.getAcquisition(acqName).promptToSave(false);
	gui.closeAcquisitionWindow(acqName);
}

//image loop
while(isRunning) {
	//create a working prefix for image i.
	prefixCurrent = newPrefix(prefixName,i);
	File f;

	String channelGroup = (String)mmc.getChannelGroup();
	//channel loop
	while (j<numChannels) {
		ChannelSpec channel = channelList.get(j);
		currentExposure=channel.exposure;
		mmc.setExposure(currentExposure);
		gui.enableLiveMode(true);

		NonBlockingGenericDialog dlg = new NonBlockingGenericDialog("Manual Acquisition ( "+prefixCurrent+" - "+(j+1)+"/"+numChannels+")");
		dlg.addMessage("Set filters for " + channel.config + " ("+(j+1)+"/"+numChannels+")",font,channel.color);
		m = dlg.getMessage();
		m.setAlignment(1);
		dlg.setCancelLabel("Stop!");
		dlg.addNumericField("Exposure time (ms):", currentExposure, 0); 
		dlg.addStringField("Image directory:", rootDirName, 30); 
		dlg.addStringField("Image prefix:", prefixName, 30); 
		dlg.showDialog();

		if (dlg.wasCanceled()) {
			isRunning = false;
			break;
		}

		currentExposure = dlg.getNextNumber(); 

		rootCurrent = dlg.getNextString();
		prefixCurrent = dlg.getNextString();

		//have we changed the prefix? have we changed the root directory?
		if (!prefixName.equals(prefixCurrent) || !rootDirName.equals(rootCurrent)) {
			//it's a new prefix or root. Reset the image counter.
			i = 0;
			if (!rootDirName.equals(rootCurrent)) {
				rootDirName = rootCurrent;
				acq.setRootName(rootDirName);
			}
			//check the prefixName. If alread exists, create a new one.
			ndArray = newDirectory(rootDirName, prefixCurrent);
			prefixName = ndArray[0];
			fullDirName = ndArray[1];

			//Let the user decide if they like the new prefix.
			if (!prefixName.equals(prefixCurrent)) {
				continue;
			}
		}

		//check that the acquisition settings are current. If not, close the acquisition window and reset the image prefix / counter.
		if (gui.acquisitionExists(acqName)) {
			mmAcq = gui.getAcquisition(acqName);
			currentImageWidth = (int)mmc.getImageWidth();
			currentImageHeight = (int)mmc.getImageHeight();
			currentBytesPerPixel = (int)mmc.getBytesPerPixel();
			if ((mmAcq.getWidth() != currentImageWidth)
					|| (mmAcq.getHeight() != currentImageHeight)
					|| (mmAcq.getByteDepth() != currentBytesPerPixel)) {

				gui.getAcquisition(acqName).promptToSave(false);
				gui.closeAcquisitionWindow(acqName);

				//reset the image and channel counters
				i = 0;
				j = 0;

				//new prefix
				ndArray = newDirectory(rootDirName, prefixCurrent);
				prefixName = ndArray[0];
				fullDirName = ndArray[1];
				continue;
			}
		} 
		gui.enableLiveMode(false);

		prefixCurrent = newPrefix(prefixName,i);
		gui.message("Acquiring " + prefixCurrent + ", " + channel.config + " channel ("+currentExposure+"ms).");
		mmc.setExposure(currentExposure);
		mmc.setConfig(channelGroup, channel.config);
		mmc.waitForConfig(channelGroup, channel.config);
		mmc.snapImage();

		//Create a tagged image and add the necessary tags
		TaggedImage img = mmc.getTaggedImage();
		img.tags.put(MMTags.Image.FRAME, 0);
		img.tags.put(MMTags.Image.FRAME_INDEX, 0);
		img.tags.put(MMTags.Image.SLICE, 0);
		img.tags.put(MMTags.Image.SLICE_INDEX, 0);
		img.tags.put(MMTags.Image.CHANNEL_INDEX, j);
		img.tags.put(MMTags.Image.CHANNEL_NAME, channel.config);
		img.tags.put(MMTags.Image.CHANNEL, channel.config);

		//check that we have an acquisition window. If not, create it.
		if (!gui.acquisitionExists(acqName)) {
			gui.openAcquisition(acqName, rootDirName, numFrames, numChannels, numSlices, true);
			try {
				//need to check the syntax on this one... string + 3 ints or string + 4 ints?
				gui.initializeAcquisition(acqName, (int)mmc.getImageWidth(), (int)mmc.getImageHeight(), (int)mmc.getBytesPerPixel(), 0);
			} catch ( e ) {
				gui.message("Acquisition will initialize later...");
			}

			for (int k=0;k<numChannels;k++) {
				ChannelSpec channel = channelList.get(k);
				gui.setChannelColor(acqName, k, channel.color);
				gui.setChannelName(acqName, k, channel.config);
			}
		}

		//Add the image to the acquisition window
		gui.addImage(acqName, img, true, true);

		//Empty list to begin with, need to be careful here.
		int imgListSize = imgList.size();
		if (j < imgListSize) {
			imgList.set(j,img);

			//this is where we blank all the other images.
			if (j ==0) {
				for (int k=1;k<imgListSize;k++) {
					ImageProcessor ip = ImageUtils.makeProcessor(imgList.get(k));
					ip.set(0);
				}
			}
		}
		else
			imgList.add(img);

		// set channel contrast based on the frame (frame 0, slice 0)
		gui.setContrastBasedOnFrame(acqName, 0, 0);

		//lets the user re-acquire the image until exposure is OK
		if (currentExposure != channel.exposure) {
			channel.exposure = currentExposure;
			continue;
		}

		j = j+1;
	}

	//for now, don't save partial stacks.
	if (!isRunning)
		break;

	//saving the image
	mmAcq = gui.getAcquisition(acqName);
	ImageCache cache = mmAcq.getImageCache();

	//Building a summary for the image stack
	JSONArray chMins = new JSONArray();
	JSONArray chMaxs = new JSONArray();
	JSONObject summary = mmAcq.getSummaryMetadata();
	summary.put(MMTags.Summary.PREFIX, prefixCurrent);	

	//checking that we can actually save in fullDirName
	f = new File(fullDirName);
	boolean error = false;
	if (!f.exists()) {
		try {
			error = !f.mkdirs();
		} catch ( e ) {
			error = true;
		}
	} else if (f.exists() && !f.isDirectory()) {
		error = true;
	}

	//directory creation failed or there is a file with that name, but isn't a directory
	if (error) {
		WaitForUserDialog dlg = new WaitForUserDialog("Manual Acquisition", "Cannot save!\nCheck your directory name / prefix combo"); 
		dlg.show();
		j = numChannels-1;
		continue;
	}

	//Create a multi-tiff image and store the channel images.
	TaggedImageStorageMultipageTiff storage = new TaggedImageStorageMultipageTiff(fullDirName,true,summary); 
	for (j=0;j<numChannels;j++) {
		TaggedImage img = imgList.get(j);
		//min and max contrast value for each channel (taken from the mmAcq)
		int min = cache.getChannelMin(j);
		int max = cache.getChannelMax(j);
		chMins.put(min);
		chMaxs.put(max);
		storage.putImage(img);
	}

	summary.put(MMTags.Summary.CHANNEL_MINS, chMins);
	summary.put(MMTags.Summary.CHANNEL_MAXES, chMaxs);
	summary.put("ChContrastMin", chMins);
	summary.put("ChContrastMax", chMaxs);

	storage.finished();
	storage.close();

	//saved! No need to prompt when closing the acqName window.
	//putting this here rather than in the channel loop prompt the user to save an incomplete image before closing (one last chance!)
	mmAcq.promptToSave(false);

	//for the next image. Increment the image counter, reset the channel counter.
	i = i+1;
	j = 0;
}

//all done.
gui.enableLiveMode(false);

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