package ij.plugin;
import ij.*;
import ij.macro.Interpreter;
import ij.process.*; 
import ij.gui.*;
import java.awt.*;
import ij.measure.*;
import ij.plugin.filter.*;
import ij.plugin.frame.Recorder;
import java.awt.event.*;
import java.util.*;
import java.lang.*;
import java.awt.image.ColorModel;

/** This plugin, which concatenates two or more images or stacks,
 *	implements the Image/Stacks/Tools/Concatenate command.
 *	Has the option of viewing the concatenated stack as a 4D image.
 *	@author Jon Jackson j.jackson # ucl.ac.uk
 */
public class Concatenator implements PlugIn, ItemListener{
	public String pluginName =	"Concatenator";
	public int maxEntries = 18;	 // limit number of entries to fit on screen
	private static boolean all_option = false;
	private boolean keep = false;
	private static boolean keep_option = false;
	private boolean batch = false;
	private boolean macro = false;
	private boolean im4D = true;
	private static boolean im4D_option = true;
	private String[] imageTitles;
	private ImagePlus[] images;
	private Vector choices;
	private Checkbox allWindows;
	private final String none = "-- None --";
	private String newtitle = "Untitled";
	private ImagePlus newImp;
	private int stackSize;
	private double min = 0, max = Float.MAX_VALUE;
	private int maxWidth, maxHeight;
	private boolean showingDialog;

	
	/** Optional string argument sets the name dialog boxes if called from another plugin. */
	public void run(String arg) {
		macro = !arg.equals("");
		if (!showDialog())
			return;
		newImp = concatenate(images, keep);
		if (newImp!=null)
			newImp.show();
	}
	
	/** Displays a dialog requiring user to choose images and
		returns ImagePlus of concatenated images. */
	public ImagePlus run() {
		if (!showDialog())
			return null;
		newImp = createHypervol();
		return newImp;
	}
	
	/** Concatenates two images, stacks or hyperstacks. */
	public static ImagePlus run(ImagePlus img1, ImagePlus img2) {
		ImagePlus[] images = new ImagePlus[2];
		images[0]=img1; images[1]=img2;
		return (new Concatenator()).concatenate(images, false);
	}

	/** Concatenates three images, stacks or hyperstacks. */
	public static ImagePlus run(ImagePlus img1, ImagePlus img2, ImagePlus img3) {
		ImagePlus[] images = new ImagePlus[3];
		images[0]=img1; images[1]=img2;  images[2]=img3;
		return (new Concatenator()).concatenate(images, false);
	}

	/** Concatenates four images, stacks or hyperstacks. */
	public static ImagePlus run(ImagePlus img1, ImagePlus img2, ImagePlus img3, ImagePlus img4) {
		ImagePlus[] images = new ImagePlus[4];
		images[0]=img1; images[1]=img2;  images[2]=img3; images[2]=img4;
		return (new Concatenator()).concatenate(images, false);
	}

	/** Concatenates five images, stacks or hyperstacks. */
	public static ImagePlus run(ImagePlus img1, ImagePlus img2, ImagePlus img3, ImagePlus img4, ImagePlus img5) {
		ImagePlus[] images = new ImagePlus[5];
		images[0]=img1; images[1]=img2;  images[2]=img3; images[2]=img4; images[5]=img5;
		return (new Concatenator()).concatenate(images, false);
	}

	/** Concatenates two or more images, stacks or hyperstacks.
	 * @param images Array of source images
	 * @return Returns the concatenated images as an ImagePlus
	*/
	public static ImagePlus run(ImagePlus[] images) {
		return  (new Concatenator()).concatenate(images, false);
	}

	/*
	// Why does this not work with Java 6?
	public static ImagePlus run(ImagePlus... args) {
		return (new Concatenator()).concatenate(args, false);
	}
	*/

	/** Concatenates two or more images or stacks. */
	public ImagePlus concatenate(ImagePlus[] ims, boolean keepIms) {
		images = ims;
		imageTitles = new String[ims.length];
		for (int i = 0; i < ims.length; i++) {
			if (ims[i] != null) {
				imageTitles[i] = ims[i].getTitle();
			} else {
				IJ.error(pluginName, "Null ImagePlus passed to concatenate(...) method");
				return null;
			}
		}
		keep = keepIms;
		batch = true;
		ImagePlus imp0 = images[0];
		if (imp0.isComposite() || imp0.getNChannels()>1)
			newImp = concatenateHyperstacks(images, newtitle, keep);
		else
			newImp = createHypervol();
		if (Recorder.scriptMode()) {
			String args = "imp1";
			for (int i=1; i<images.length; i++)
				args += ", imp"+(i+1);
			Recorder.recordCall("imp"+(images.length+1)+" = Concatenator.run("+args+");");
		}
		return newImp;
	}
	
	/** Concatenate two images or stacks. */
	public ImagePlus concatenate(ImagePlus imp1, ImagePlus imp2, boolean keep) {
		images = new ImagePlus[2];
		images[0] = imp1;
		images[1] = imp2;
		return concatenate(images, keep);
	}
	
	private ImagePlus createHypervol() {
		boolean firstImage = true;
		boolean duplicated;
		Properties[] propertyArr = new Properties[images.length];
		ImagePlus currentImp = null;
		ImageStack concat_Stack = null;
		stackSize = 0;
		int dataType = 0, width= 0, height = 0;
		Calibration cal = null;
		int count = 0;
		findMaxDimensions(images);
		for (int i = 0; i < images.length; i++) {
			if (images[i] != null) { // Should only find null imp if user has closed an image after starting plugin (unlikely...)
				currentImp = images[i];
				if (firstImage) { // Initialise based on first image
					//concat_Imp = images[i];
					cal = currentImp.getCalibration();
					width = currentImp.getWidth();
					height = currentImp.getHeight();
					stackSize = currentImp.getNSlices();
					dataType = currentImp.getType();
					ColorModel cm = currentImp.getProcessor().getColorModel();
					concat_Stack = new ImageStack(maxWidth, maxHeight, cm);
					min = currentImp.getProcessor().getMin();
					max = currentImp.getProcessor().getMax();
					firstImage = false;
				}
				
				// Safety Checks
				boolean unequalSizes = currentImp.getNSlices()!=stackSize;
				if (unequalSizes)
					im4D = false;
				if (currentImp.getType() != dataType) {
					IJ.log("Omitting " + imageTitles[i] + " - image type not matched");
					continue;
				}

			   // concatenate
				duplicated = isDuplicated(currentImp, i);
				concat(concat_Stack, currentImp.getStack(), (keep || duplicated));
				propertyArr[count] = currentImp.getProperties();
				imageTitles[count] = currentImp.getTitle();
				if (! (keep || duplicated)) {
					currentImp.changes = false;
					currentImp.hide();
				}
				count++;
			}
		}
		
		// Copy across info fields
		ImagePlus imp = new ImagePlus(newtitle, concat_Stack);
		imp.setCalibration(cal);
		imp.setProperty("Number of Stacks", new Integer(count));
		imp.setProperty("Stacks Properties", propertyArr);
		imp.setProperty("Image Titles", imageTitles);
		imp.getProcessor().setMinAndMax(min, max);
		if (im4D) {
			imp.setDimensions(1, stackSize, imp.getStackSize()/stackSize);
			imp.setOpenAsHyperStack(true);
		}
		return imp;
	}
	
	// taken from WSR's Concatenator_.java
	private void concat(ImageStack stack3, ImageStack stack1, boolean dup) {
		int slice = 1;
		int size = stack1.getSize();
		for (int i = 1; i <= size; i++) {
			ImageProcessor ip = stack1.getProcessor(slice);
			String label = stack1.getSliceLabel(slice);
			if (dup) {
				ip = ip.duplicate();
				slice++;
			} else
				stack1.deleteSlice(slice);
			ImageProcessor ip2 = ip;
			if (ip.getWidth()!=maxWidth || ip.getHeight()!=maxHeight) {
				ip2 = ip.createProcessor(maxWidth, maxHeight);
				ip2.insert(ip, (maxWidth-ip.getWidth())/2, (maxHeight-ip.getHeight())/2);
			}
			stack3.addSlice(label, ip2);
		}
	} 
	
	/** Obsolete, replaced by concatenate(images,keep) and Concatenator.run(images). */
	public ImagePlus concatenateHyperstacks(ImagePlus[] images, String newTitle, boolean keep) {
		int n = images.length;
		int width = images[0].getWidth();
		int height = images[0].getHeight();
		int bitDepth = images[0].getBitDepth();
		int channels = images[0].getNChannels();
		int slices =  images[0].getNSlices();
		int frames = images[0].getNFrames();
		boolean concatSlices = slices>1 && frames==1;
		boolean keepCalibration = true;
		Calibration cal = images[0].getCalibration();
		maxWidth = width;
		maxHeight = height;
		
		for (int i=1; i<n; i++) {
			if (images[i].getNFrames()>1)
				concatSlices = false;
			if (images[i].getBitDepth()!=bitDepth
			|| images[i].getNChannels()!=channels
			|| (!concatSlices && images[i].getNSlices()!=slices)) {
				IJ.error(pluginName, "Images do not all have the same dimensions or type");
				return null;
			}
			Calibration cal2 = images[i].getCalibration();
			if (cal2.pixelWidth!=cal.pixelWidth 
			|| cal2.pixelHeight!=cal.pixelHeight 
			|| cal2.pixelDepth != cal.pixelDepth)
				keepCalibration = false;
			if (images[i].getWidth()>maxWidth)
				maxWidth = images[i].getWidth();
			if (images[i].getHeight()>maxHeight)
				maxHeight = images[i].getHeight();
		}
		ImageStack stack2 = new ImageStack(maxWidth, maxHeight);
		int slices2=0, frames2=0;
		for (int i=0;i<n;i++) {
			ImageStack stack = images[i].getStack();
			slices = images[i].getNSlices();
			if (concatSlices) {
				slices = images[i].getNSlices();
				slices2 += slices;
				frames2 = frames;
			} else {
				frames = images[i].getNFrames();
				frames2 += frames;
				slices2 = slices;
			}
			for (int f=1; f<=frames; f++) {
				for (int s=1; s<=slices; s++) {
					for (int c=1; c<=channels; c++) {
						int index = (f-1)*channels*slices + (s-1)*channels + c;
						ImageProcessor ip = stack.getProcessor(index);
						if (keep)
							ip = ip.duplicate();
						String label = stack.getSliceLabel(index);
						ImageProcessor ip2 = ip;
						if (ip.getWidth()!=maxWidth || ip.getHeight()!=maxHeight) {
							ip2 = ip.createProcessor(maxWidth, maxHeight);
							ip2.insert(ip, (maxWidth-ip.getWidth())/2, (maxHeight-ip.getHeight())/2);
						}
						stack2.addSlice(label, ip2);
					}
				}
			}
		}
		ImagePlus imp2 = new ImagePlus(newTitle, stack2);
		imp2.setDimensions(channels, slices2, frames2);
		if (channels>1) {
			int mode = 0;
			if (images[0].isComposite())
				mode = ((CompositeImage)images[0]).getMode();
			imp2 = new CompositeImage(imp2, mode);
			((CompositeImage)imp2).copyLuts(images[0]);
		}
		if (channels>1 && frames2>1)
			imp2.setOpenAsHyperStack(true);
		if (keepCalibration)
			imp2.setCalibration(cal);
		if (!keep) {
			for (int i=0; i<n; i++) {
				images[i].changes = false;
				images[i].close();
			}
		}
		return imp2;
	}	
	
	private boolean showDialog() {
		boolean all_windows = false;
		batch = Interpreter.isBatchMode();
		macro = macro || (IJ.isMacro()&&Macro.getOptions()!=null);
		if (Menus.commandInUse("Stack to Image5D") && !batch)
			im4D = true;
		showingDialog = Macro.getOptions()==null;
		if (macro) {
			String options = Macro.getOptions();
			if (options.contains("stack1")&&options.contains("stack2"))
				Macro.setOptions(options.replaceAll("stack", "image"));
			int macroImageCount = 0;
			options = Macro.getOptions();
			while (true) {
				if (options.contains("image"+(macroImageCount+1)))
					macroImageCount++;
				else
					break;
			}
			maxEntries = macroImageCount;
		}
		
		// Checks
		int[] wList = WindowManager.getIDList();
		if (wList==null) {
			IJ.error("No windows are open.");
			return false;
		} else if (wList.length < 2) {
			IJ.error("Two or more windows must be open");
			return false;
		}
		int nImages = wList.length;
		
		String[] titles = new String[nImages];
		String[] titles_none = new String[nImages + 1];
		for (int i=0; i<nImages; i++) {
			ImagePlus imp = WindowManager.getImage(wList[i]);
			if (imp!=null) {
				titles[i] = imp.getTitle();
				titles_none[i] = imp.getTitle();
			} else {
				titles[i] = "";
				titles_none[i] = "";
			}
		}
		titles_none[nImages] = none;
		
		GenericDialog gd = new GenericDialog(pluginName);
		gd.addCheckbox("All_open windows", all_option);
		gd.addChoice("Image1:", titles, titles[0]);
		gd.addChoice("Image2:", titles, titles[1]);
		for (int i = 2; i < ((nImages+1)<maxEntries?(nImages+1):maxEntries); i++)
			gd.addChoice("Image" + (i+1)+":", titles_none, titles_none[i]);
		gd.addStringField("Title:", newtitle, 16);
		gd.addCheckbox("Keep original images", keep_option);
		gd.addCheckbox("Open as 4D_image", im4D_option);
		if (!macro) { // Monitor user selections
			choices = gd.getChoices();
			for (Enumeration e = choices.elements() ; e.hasMoreElements() ;)
				((Choice)e.nextElement()).addItemListener(this);
			Vector v = gd.getCheckboxes();
			allWindows = (Checkbox)v.firstElement();
			allWindows.addItemListener(this);
			if (all_option) itemStateChanged(new ItemEvent(allWindows, ItemEvent.ITEM_STATE_CHANGED, null, ItemEvent.SELECTED));
		}
		gd.showDialog();
		
		if (gd.wasCanceled())
			return false;
		all_windows = gd.getNextBoolean();
		all_option = all_windows;
		gd.setSmartRecording(true);
		newtitle = gd.getNextString();
		gd.setSmartRecording(false);
		keep = gd.getNextBoolean();
		keep_option = keep;
		im4D = gd.getNextBoolean();
		im4D_option = im4D;
		ImagePlus[] tmpImpArr = new ImagePlus[nImages+1];
		String[] tmpStrArr = new String[nImages+1];
		int index=0, count = 0;
		for (int i=0; i<=nImages; i++) { // compile a list of images to concatenate from user selection
			if (all_windows) { // Useful to not have to specify images in batch mode
				index = i;
			} else {
				if (i == ((nImages+1)<maxEntries?(nImages+1):maxEntries) ) break;
				gd.setSmartRecording(i==nImages);
				index = gd.getNextChoiceIndex();
			}
			if (index >= nImages) break; // reached the 'none' string or handled all images (in case of all_windows)
			if (! titles[index].equals("")) {
				tmpStrArr[count] = titles[index];
				tmpImpArr[count] = WindowManager.getImage(wList[index]);
				count++;
			}
		}
		if (count<2) {
			IJ.error(pluginName, "Please select at least 2 images");
			return false;
		}
		
		imageTitles = new String[count];
		images = new ImagePlus[count];
		System.arraycopy(tmpStrArr, 0, imageTitles, 0, count);
		System.arraycopy(tmpImpArr, 0, images, 0, count);
		return true;
	}
	
	// test if this imageplus appears again in the list
	boolean isDuplicated(ImagePlus imp, int index) {
		int length = images.length;
		if (index >= length - 1) return false;
		for (int i = index + 1; i < length; i++) {
			if (imp == images[i]) return true;
		}
		return false;
	}
	
	public void itemStateChanged(ItemEvent ie) {
		Choice c;
		if (ie.getSource() == allWindows) { // User selected / unselected 'all windows' button
			int count = 0;
			if (allWindows.getState()) {
				for (Enumeration e = choices.elements() ; e.hasMoreElements() ;) {
					c = (Choice)e.nextElement();
					c.select(count++);
					c.setEnabled(false);
				}
			} else {
				for (Enumeration e = choices.elements() ; e.hasMoreElements() ;) {
					c = (Choice)e.nextElement();
					c.setEnabled(true);
				}
			}
		} else { // User image selection triggered event
			boolean foundNone = false;
			// All image choices after an occurance of 'none' are reset to 'none'
			for (Enumeration e = choices.elements() ; e.hasMoreElements() ;) {
				c = (Choice)e.nextElement();
				if (! foundNone) {
					c.setEnabled(true);
					if (c.getSelectedItem().equals(none)) foundNone = true;
				} else { // a previous choice was 'none'
					c.select(none);
					c.setEnabled(false);
				}
			}
		}
	}
	
	public void setIm5D(boolean bool) {
		im4D_option = bool;
		im4D = bool;
	}
	
	private void findMaxDimensions(ImagePlus[] images) {
		boolean first = true;
		ImagePlus currentImp = null;
		int dataType = 0;
		maxWidth = maxHeight = 0;
		for (int i = 0; i < images.length; i++) {
			if (images[i] != null) {
				currentImp = images[i];
				if (first) {
					dataType = currentImp.getType();
					first = false;
				}
				if (currentImp.getType() != dataType)
					continue;
				if (currentImp.getWidth()>maxWidth)
					maxWidth = currentImp.getWidth();
				if (currentImp.getHeight()>maxHeight)
					maxHeight = currentImp.getHeight();
			}
		}
	}
	
}