package ij.plugin.frame;
import java.awt.*;
import java.awt.event.*;
import java.io.*;
import java.util.*;
import java.awt.List;
import java.util.zip.*;
import ij.*;
import ij.process.*;
import ij.gui.*;
import ij.io.*;
import ij.plugin.filter.*;
import ij.plugin.Colors;
import ij.util.*;
import ij.macro.*;
import ij.measure.*;

/** This plugin implements the Analyze/Tools/ROI Manager command. */
public class RoiManager extends PlugInFrame implements ActionListener, ItemListener, MouseListener, MouseWheelListener {
	public static final String LOC_KEY = "manager.loc";
	private static final int BUTTONS = 11;
	private static final int DRAW=0, FILL=1, LABEL=2;
	private static final int SHOW_ALL=0, SHOW_NONE=1, LABELS=2, NO_LABELS=3;
	private static final int MENU=0, COMMAND=1;
	private static int rows = 15;
	private static int lastNonShiftClick = -1;
	private static boolean allowMultipleSelections = true; 
	private static String moreButtonLabel = "More "+'\u00bb';
	private Panel panel;
	private static Frame instance;
	private static int colorIndex = 4;
	private java.awt.List list;
	private Hashtable rois = new Hashtable();
	private boolean canceled;
	private boolean macro;
	private boolean ignoreInterrupts;
	private PopupMenu pm;
	private Button moreButton, colorButton;
	private Checkbox showAllCheckbox = new Checkbox("Show All", false);
	private Checkbox labelsCheckbox = new Checkbox("Edit Mode", false);

	private static boolean measureAll = true;
	private static boolean onePerSlice = true;
	private static boolean restoreCentered;
	private int prevID;
	private boolean noUpdateMode;
	private int defaultLineWidth = 1;
	private Color defaultColor;
	private boolean firstTime = true;
	private int[] selectedIndexes;
	
	public RoiManager() {
		super("ROI Manager");
		if (instance!=null) {
			WindowManager.toFront(instance);
			return;
		}
		instance = this;
		list = new List(rows, allowMultipleSelections);
		showWindow();
	}
	
	public RoiManager(boolean hideWindow) {
		super("ROI Manager");
		list = new List(rows, allowMultipleSelections);
	}

	void showWindow() {
		ImageJ ij = IJ.getInstance();
 		addKeyListener(ij);
 		addMouseListener(this);
		addMouseWheelListener(this);
		WindowManager.addWindow(this);
		//setLayout(new FlowLayout(FlowLayout.CENTER,5,5));
		setLayout(new BorderLayout());
		list.add("012345678901234");
		list.addItemListener(this);
 		list.addKeyListener(ij);
 		list.addMouseListener(this);
 		list.addMouseWheelListener(this);
		if (IJ.isLinux()) list.setBackground(Color.white);
		add("Center", list);
		panel = new Panel();
		int nButtons = BUTTONS;
		panel.setLayout(new GridLayout(nButtons, 1, 5, 0));
		addButton("Add [t]");
		addButton("Update");
		addButton("Delete");
		addButton("Rename...");
		addButton("Measure");
		addButton("Deselect");
		addButton("Properties...");
		addButton("Flatten [F]");
		addButton(moreButtonLabel);
		showAllCheckbox.addItemListener(this);
		panel.add(showAllCheckbox);
		labelsCheckbox.addItemListener(this);
		panel.add(labelsCheckbox);
		add("East", panel);		
		addPopupMenu();
		pack();
		Dimension size = getSize();
		if (size.width>270)
			setSize(size.width-40, size.height);
		list.remove(0);
		Point loc = Prefs.getLocation(LOC_KEY);
		if (loc!=null)
			setLocation(loc);
		else
			GUI.center(this);
		show();
		if (IJ.isMacOSX() && IJ.isJava16()) {
			list.setMultipleMode(false);
			list.setMultipleMode(true);
			//EventQueue.invokeLater(new Runnable() {
			//	public void run() {
			//		list.setMultipleMode(false);
			//		list.setMultipleMode(true);
			//	}
			//});
		}
	}

	void addButton(String label) {
		Button b = new Button(label);
		b.addActionListener(this);
		b.addKeyListener(IJ.getInstance());
 		b.addMouseListener(this);
 		if (label.equals(moreButtonLabel)) moreButton = b;
		panel.add(b);
	}

	void addPopupMenu() {
		pm=new PopupMenu();
		//addPopupItem("Select All");
		addPopupItem("Open...");
		addPopupItem("Save...");
		addPopupItem("Fill");
		addPopupItem("Draw");
		addPopupItem("AND");
		addPopupItem("OR (Combine)");
		addPopupItem("XOR");
		addPopupItem("Split");
		addPopupItem("Add Particles");
		addPopupItem("Multi Measure");
		addPopupItem("Multi Plot");
		addPopupItem("Sort");
		addPopupItem("Specify...");
		addPopupItem("Remove Slice Info");
		addPopupItem("Help");
		addPopupItem("Options...");
		add(pm);
	}

	void addPopupItem(String s) {
		MenuItem mi=new MenuItem(s);
		mi.addActionListener(this);
		pm.add(mi);
	}
	
	public void actionPerformed(ActionEvent e) {
		String label = e.getActionCommand();
		if (label==null)
			return;
		String command = label;
		if (command.equals("Add [t]"))
			runCommand("add");
		else if (command.equals("Update"))
			update(true);
		else if (command.equals("Delete"))
			delete(false);
		else if (command.equals("Rename..."))
			rename(null);
		else if (command.equals("Properties..."))
			setProperties(null, -1, null);
		else if (command.equals("Flatten [F]"))
			flatten();
		else if (command.equals("Measure"))
			measure(MENU);
		else if (command.equals("Open..."))
			open(null);
		else if (command.equals("Save..."))
			save();
		else if (command.equals("Fill"))
			drawOrFill(FILL);
		else if (command.equals("Draw"))
			drawOrFill(DRAW);
		else if (command.equals("Deselect"))
			select(-1);
		else if (command.equals(moreButtonLabel)) {
			Point ploc = panel.getLocation();
			Point bloc = moreButton.getLocation();
			pm.show(this, ploc.x, bloc.y);
		} else if (command.equals("OR (Combine)"))
			combine();
		else if (command.equals("Split"))
			split();
		else if (command.equals("AND"))
			and();
		else if (command.equals("XOR"))
			xor();
		else if (command.equals("Add Particles"))
			addParticles();
		else if (command.equals("Multi Measure"))
			multiMeasure();
		else if (command.equals("Multi Plot"))
			multiPlot();
		else if (command.equals("Sort"))
			sort();
		else if (command.equals("Specify..."))
			specify();
		else if (command.equals("Remove Slice Info"))
			removeSliceInfo();
		else if (command.equals("Help"))
			help();
		else if (command.equals("Options..."))
			options();
		else if (command.equals("\"Show All\" Color..."))
			setShowAllColor();
	}

	public void itemStateChanged(ItemEvent e) {
		Object source = e.getSource();
		if (source==showAllCheckbox) {
			if (firstTime)
				labelsCheckbox.setState(true);
			showAll(showAllCheckbox.getState()?SHOW_ALL:SHOW_NONE);
			firstTime = false;
			return;
		}
		if (source==labelsCheckbox) {
			if (firstTime)
				showAllCheckbox.setState(true);
			boolean editState = labelsCheckbox.getState();
			boolean showAllState = showAllCheckbox.getState();
			if (!showAllState && !editState)
				showAll(SHOW_NONE);
			else {
				showAll(editState?LABELS:NO_LABELS);
				if (editState) showAllCheckbox.setState(true);
			}
			firstTime = false;
			return;
		}
		if (e.getStateChange()==ItemEvent.SELECTED && !ignoreInterrupts) {
			int index = 0;
			//IJ.log("item="+e.getItem()+" shift="+IJ.shiftKeyDown()+" ctrl="+IJ. controlKeyDown());
            try {index = Integer.parseInt(e.getItem().toString());}
            catch (NumberFormatException ex) {}
			if (index<0) index = 0;
            if (!IJ.isMacintosh()) {      //handle shift-click, ctrl-click (on Mac, OS takes care of this)
                if (!IJ.shiftKeyDown()) lastNonShiftClick = index;
    			if (!IJ.shiftKeyDown() && !IJ.controlKeyDown()) {  //simple click, deselect everything else
    				int[] indexes = getSelectedIndexes();
    				for (int i=0; i<indexes.length; i++) {
    					if (indexes[i]!=index)
    						list.deselect(indexes[i]);
    				}
    			} else if (IJ.shiftKeyDown() && lastNonShiftClick>=0 && lastNonShiftClick<list.getItemCount()) {
                    int firstIndex = Math.min(index, lastNonShiftClick);
                    int lastIndex = Math.max(index, lastNonShiftClick);
    				int[] indexes = getSelectedIndexes();
    				for (int i=0; i<indexes.length; i++)
    					if (indexes[i]<firstIndex || indexes[i]>lastIndex)
    						list.deselect(indexes[i]);      //deselect everything else
                    for (int i=firstIndex; i<=lastIndex; i++)
                        list.select(i);                     //select range
                }
            }
			if (WindowManager.getCurrentImage()!=null) {
				restore(getImage(), index, true);
				if (record()) {
					if (Recorder.scriptMode())
						Recorder.recordCall("rm.select(imp, "+index+");");
					else
						Recorder.record("roiManager", "Select", index);
				}
			}
		}
	}
	
	void add(boolean shiftKeyDown, boolean altKeyDown) {
		if (shiftKeyDown)
			addAndDraw(altKeyDown);
		else if (altKeyDown)
			addRoi(true);
		else
			addRoi(false);
	}
	
	/** Adds the specified ROI. */
	public void addRoi(Roi roi) {
		addRoi(roi, false, null, -1);
	}
	
	boolean addRoi(boolean promptForName) {
		return addRoi(null, promptForName, null, -1);
	}

	boolean addRoi(Roi roi, boolean promptForName, Color color, int lineWidth) {
		ImagePlus imp = roi==null?getImage():WindowManager.getCurrentImage();
		if (roi==null) {
			if (imp==null)
				return false;
			roi = imp.getRoi();
			if (roi==null) {
				error("The active image does not have a selection.");
				return false;
			}
		}
		if (color==null && roi.getStrokeColor()!=null)
			color = roi.getStrokeColor();
		else if (color==null && defaultColor!=null)
			color = defaultColor;
		if (lineWidth<0) {
			int sw = (int)roi.getStrokeWidth();
			lineWidth = sw>1?sw:defaultLineWidth;
		}
		if (lineWidth>100) lineWidth = 1;
		int n = list.getItemCount();
		if (n>0 && !IJ.isMacro() && imp!=null) {
			// check for duplicate
			String label = list.getItem(n-1);
			Roi roi2 = (Roi)rois.get(label);
			if (roi2!=null) {
				int slice2 = getSliceNumber(roi2, label);
				if (roi.equals(roi2) && (slice2==-1||slice2==imp.getCurrentSlice()) && imp.getID()==prevID && !Interpreter.isBatchMode())
					return false;
			}
		}
		prevID = imp!=null?imp.getID():0;
		String name = roi.getName();
		if (isStandardName(name))
			name = null;
		String label = name!=null?name:getLabel(imp, roi, -1);
		if (promptForName)
			label = promptForName(label);
		else
			label = getUniqueName(label);
		if (label==null) return false;
		list.add(label);
		roi.setName(label);
		Roi roiCopy = (Roi)roi.clone();
		if (lineWidth>1)
			roiCopy.setStrokeWidth(lineWidth);
		if (color!=null)
			roiCopy.setStrokeColor(color);
		rois.put(label, roiCopy);
		updateShowAll();
		if (record())
			recordAdd(defaultColor, defaultLineWidth);
		return true;
	}
	
	void recordAdd(Color color, int lineWidth) {
		if (Recorder.scriptMode())
			Recorder.recordCall("rm.addRoi(imp.getRoi());");
		else if (color!=null && lineWidth==1)
			Recorder.recordString("roiManager(\"Add\", \""+getHex(color)+"\");\n");
		else if (lineWidth>1)
			Recorder.recordString("roiManager(\"Add\", \""+getHex(color)+"\", "+lineWidth+");\n");
		else
			Recorder.record("roiManager", "Add");
	}
	
	String getHex(Color color) {
		if (color==null) color = ImageCanvas.getShowAllColor();
		String hex = Integer.toHexString(color.getRGB());
		if (hex.length()==8) hex = hex.substring(2);
		return hex;
	}
	
	/** Adds the specified ROI to the list. The third argument ('n') will 
		be used to form the first part of the ROI label if it is >= 0. */
	public void add(ImagePlus imp, Roi roi, int n) {
		if (roi==null) return;
		String label = roi.getName();
		if (label==null)
			label = getLabel(imp, roi, n);
		if (label==null) return;
		list.add(label);
		roi.setName(label);
		rois.put(label, (Roi)roi.clone());
	}

	boolean isStandardName(String name) {
		if (name==null) return false;
		boolean isStandard = false;
		int len = name.length();
		if (len>=14 && name.charAt(4)=='-' && name.charAt(9)=='-' )
			isStandard = true;
		else if (len>=17 && name.charAt(5)=='-' && name.charAt(11)=='-' )
			isStandard = true;
		else if (len>=9 && name.charAt(4)=='-')
			isStandard = true;
		else if (len>=11 && name.charAt(5)=='-')
			isStandard = true;
		return isStandard;
	}
	
	String getLabel(ImagePlus imp, Roi roi, int n) {
		Rectangle r = roi.getBounds();
		int xc = r.x + r.width/2;
		int yc = r.y + r.height/2;
		if (n>=0)
			{xc = yc; yc=n;}
		if (xc<0) xc = 0;
		if (yc<0) yc = 0;
		int digits = 4;
		String xs = "" + xc;
		if (xs.length()>digits) digits = xs.length();
		String ys = "" + yc;
		if (ys.length()>digits) digits = ys.length();
		if (digits==4 && imp!=null && imp.getStackSize()>=10000) digits = 5;
		xs = "000000" + xc;
		ys = "000000" + yc;
		String label = ys.substring(ys.length()-digits) + "-" + xs.substring(xs.length()-digits);
		if (imp!=null && imp.getStackSize()>1) {
			int slice = roi.getPosition();
			if (slice==0)
				slice = imp.getCurrentSlice();
			String zs = "000000" + slice;
			label = zs.substring(zs.length()-digits) + "-" + label;
			roi.setPosition(slice);
		}
		return label;
	}

	void addAndDraw(boolean altKeyDown) {
		if (altKeyDown) {
			if (!addRoi(true)) return;
		} else if (!addRoi(false))
			return;
		ImagePlus imp = WindowManager.getCurrentImage();
		if (imp!=null) {
			Undo.setup(Undo.COMPOUND_FILTER, imp);
			IJ.run(imp, "Draw", "slice");
			Undo.setup(Undo.COMPOUND_FILTER_DONE, imp);
		}
		if (record()) Recorder.record("roiManager", "Add & Draw");
	}
	
	boolean delete(boolean replacing) {
		int count = list.getItemCount();
		if (count==0)
			return error("The list is empty.");
		int index[] = getSelectedIndexes();
		if (index.length==0 || (replacing&&count>1)) {
			String msg = "Delete all items on the list?";
			if (replacing)
				msg = "Replace items on the list?";
			canceled = false;
			if (!IJ.isMacro() && !macro) {
				YesNoCancelDialog d = new YesNoCancelDialog(this, "ROI Manager", msg);
				if (d.cancelPressed())
					{canceled = true; return false;}
				if (!d.yesPressed()) return false;
			}
			index = getAllIndexes();
		}
		if (count==index.length && !replacing) {
			rois.clear();
			list.removeAll();
		} else {
			for (int i=count-1; i>=0; i--) {
				boolean delete = false;
				for (int j=0; j<index.length; j++) {
					if (index[j]==i)
						delete = true;
				}
				if (delete) {
					rois.remove(list.getItem(i));
					list.remove(i);
				}
			}
		}
		ImagePlus imp = WindowManager.getCurrentImage();
		if (count>1 && index.length==1 && imp!=null)
			imp.killRoi();
		updateShowAll();
		if (record()) Recorder.record("roiManager", "Delete");
		return true;
	}
	
	boolean update(boolean clone) {
		ImagePlus imp = getImage();
		if (imp==null) return false;
		ImageCanvas ic = imp.getCanvas();
		boolean showingAll = ic!=null &&  ic.getShowAllROIs();
		Roi roi = imp.getRoi();
		if (roi==null) {
			error("The active image does not have a selection.");
			return false;
		}
		int index = list.getSelectedIndex();
		if (index<0 && !showingAll)
			return error("Exactly one item in the list must be selected.");
		if (index>=0) {
			String name = list.getItem(index);
			rois.remove(name);
			if (clone) {
				Roi roi2 = (Roi)roi.clone();
				int position = roi.getPosition();
				if (imp.getStackSize()>1)
					roi2.setPosition(imp.getCurrentSlice());
				roi.setName(name);
				roi2.setName(name);
				rois.put(name, roi2);
			} else
				rois.put(name, roi);
		}
		if (record()) Recorder.record("roiManager", "Update");
		if (showingAll) imp.draw();
		return true;
	}

	boolean rename(String name2) {
		int index = list.getSelectedIndex();
		if (index<0)
			return error("Exactly one item in the list must be selected.");
		String name = list.getItem(index);
		if (name2==null) name2 = promptForName(name);
		if (name2==null) return false;
		Roi roi = (Roi)rois.get(name);
		rois.remove(name);
		roi.setName(name2);
		rois.put(name2, roi);
		list.replaceItem(name2, index);
		list.select(index);
		if (Prefs.useNamesAsLabels && labelsCheckbox.getState()) {
			ImagePlus imp = WindowManager.getCurrentImage();
			if (imp!=null) imp.draw();
		}
		if (record())
			Recorder.record("roiManager", "Rename", name2);
		return true;
	}
	
	String promptForName(String name) {
		GenericDialog gd = new GenericDialog("ROI Manager");
		gd.addStringField("Rename As:", name, 20);
		gd.showDialog();
		if (gd.wasCanceled())
			return null;
		String name2 = gd.getNextString();
		name2 = getUniqueName(name2);
		return name2;
	}

	boolean restore(ImagePlus imp, int index, boolean setSlice) {
		String label = list.getItem(index);
		Roi roi = (Roi)rois.get(label);
		if (imp==null || roi==null)
			return false;
        if (setSlice) {
            int n = getSliceNumber(roi, label);
            if (n>=1 && n<=imp.getStackSize()) {
            	if (imp.isHyperStack()||imp.isComposite())
                	imp.setPosition(n);
                else
                	imp.setSlice(n);
            }
        }
        Roi roi2 = (Roi)roi.clone();
		Calibration cal = imp.getCalibration();
		Rectangle r = roi2.getBounds();
		int width= imp.getWidth(), height=imp.getHeight();
		if (restoreCentered) {
			ImageCanvas ic = imp.getCanvas();
			if (ic!=null) {
				Rectangle r1 = ic.getSrcRect();
				Rectangle r2 = roi2.getBounds();
				roi2.setLocation(r1.x+r1.width/2-r2.width/2, r1.y+r1.height/2-r2.height/2);
			}
		}
		if (r.x>=width || r.y>=height || (r.x+r.width)<=0 || (r.y+r.height)<=0)
			roi2.setLocation((width-r.width)/2, (height-r.height)/2);
		if (noUpdateMode) {
			imp.setRoi(roi2, false);
			noUpdateMode = false;
		} else
			imp.setRoi(roi2, true);
		return true;
	}
	
	boolean restoreWithoutUpdate(int index) {
		noUpdateMode = true;
		return restore(getImage(), index, false);
	}
	
	/** Returns the slice number associated with the specified name,
		or -1 if the name does not include a slice number. */
	public int getSliceNumber(String label) {
		int slice = -1;
		if (label.length()>=14 && label.charAt(4)=='-' && label.charAt(9)=='-')
			slice = (int)Tools.parseDouble(label.substring(0,4),-1);
		else if (label.length()>=17 && label.charAt(5)=='-' && label.charAt(11)=='-')
			slice = (int)Tools.parseDouble(label.substring(0,5),-1);
		else if (label.length()>=20 && label.charAt(6)=='-' && label.charAt(13)=='-')
			slice = (int)Tools.parseDouble(label.substring(0,6),-1);
		return slice;
	}
	
	/** Returns the slice number associated with the specified ROI or name,
		or -1 if the ROI or name does not include a slice number. */
	int getSliceNumber(Roi roi, String label) {
		int slice = roi!=null?roi.getPosition():-1;
		if (slice==0)
			slice=-1;
		if (slice==-1)
			slice = getSliceNumber(label);
		return slice;
	}

	void open(String path) {
		Macro.setOptions(null);
		String name = null;
		if (path==null || path.equals("")) {
			OpenDialog od = new OpenDialog("Open Selection(s)...", "");
			String directory = od.getDirectory();
			name = od.getFileName();
			if (name==null)
				return;
			path = directory + name;
		}
		if (Recorder.record && !Recorder.scriptMode())
			Recorder.record("roiManager", "Open", path);
		if (path.endsWith(".zip")) {
			openZip(path);
			return;
		}
		Opener o = new Opener();
		if (name==null) name = o.getName(path);
		Roi roi = o.openRoi(path);
		if (roi!=null) {
			if (name.endsWith(".roi"))
				name = name.substring(0, name.length()-4);
			name = getUniqueName(name);
			list.add(name);
			rois.put(name, roi);
		}		
		updateShowAll();
	}
	
	// Modified on 2005/11/15 by Ulrik Stervbo to only read .roi files and to not empty the current list
	void openZip(String path) { 
		ZipInputStream in = null; 
		ByteArrayOutputStream out; 
		int nRois = 0; 
		try { 
			in = new ZipInputStream(new FileInputStream(path)); 
			byte[] buf = new byte[1024]; 
			int len; 
			ZipEntry entry = in.getNextEntry(); 
			while (entry!=null) { 
				String name = entry.getName();
				if (name.endsWith(".roi")) { 
					out = new ByteArrayOutputStream(); 
					while ((len = in.read(buf)) > 0) 
						out.write(buf, 0, len); 
					out.close(); 
					byte[] bytes = out.toByteArray(); 
					RoiDecoder rd = new RoiDecoder(bytes, name); 
					Roi roi = rd.getRoi(); 
					if (roi!=null) { 
						name = name.substring(0, name.length()-4); 
						name = getUniqueName(name); 
						list.add(name); 
						rois.put(name, roi); 
						nRois++;
					} 
				} 
				entry = in.getNextEntry(); 
			} 
			in.close(); 
		} catch (IOException e) {error(e.toString());} 
		if(nRois==0)
				error("This ZIP archive does not appear to contain \".roi\" files");
		updateShowAll();
	} 


	String getUniqueName(String name) {
			String name2 = name;
			int n = 1;
			Roi roi2 = (Roi)rois.get(name2);
			while (roi2!=null) {
				roi2 = (Roi)rois.get(name2);
				if (roi2!=null) {
					int lastDash = name2.lastIndexOf("-");
					if (lastDash!=-1 && name2.length()-lastDash<5)
						name2 = name2.substring(0, lastDash);
					name2 = name2+"-"+n;
					n++;
				}
				roi2 = (Roi)rois.get(name2);
			}
			return name2;
	}
	
	boolean save() {
		if (list.getItemCount()==0)
			return error("The selection list is empty.");
		int[] indexes = getSelectedIndexes();
		if (indexes.length==0)
			indexes = getAllIndexes();
		if (indexes.length>1)
			return saveMultiple(indexes, null);
		String name = list.getItem(indexes[0]);
		Macro.setOptions(null);
		SaveDialog sd = new SaveDialog("Save Selection...", name, ".roi");
		String name2 = sd.getFileName();
		if (name2 == null)
			return false;
		String dir = sd.getDirectory();
		Roi roi = (Roi)rois.get(name);
		rois.remove(name);
		if (!name2.endsWith(".roi")) name2 = name2+".roi";
		String newName = name2.substring(0, name2.length()-4);
		rois.put(newName, roi);
		roi.setName(newName);
		list.replaceItem(newName, indexes[0]);
		RoiEncoder re = new RoiEncoder(dir+name2);
		try {
			re.write(roi);
		} catch (IOException e) {
			IJ.error("ROI Manager", e.getMessage());
		}
		return true;
	}

	boolean saveMultiple(int[] indexes, String path) {
		Macro.setOptions(null);
		if (path==null) {
			SaveDialog sd = new SaveDialog("Save ROIs...", "RoiSet", ".zip");
			String name = sd.getFileName();
			if (name == null)
				return false;
			if (!(name.endsWith(".zip") || name.endsWith(".ZIP")))
				name = name + ".zip";
			String dir = sd.getDirectory();
			path = dir+name;
		}
		try {
			ZipOutputStream zos = new ZipOutputStream(new FileOutputStream(path));
			DataOutputStream out = new DataOutputStream(new BufferedOutputStream(zos));
			RoiEncoder re = new RoiEncoder(out);
			for (int i=0; i<indexes.length; i++) {
				String label = list.getItem(indexes[i]);
				Roi roi = (Roi)rois.get(label);
				if (!label.endsWith(".roi")) label += ".roi";
        		zos.putNextEntry(new ZipEntry(label));
				re.write(roi);
				out.flush();
			}
			out.close();
		}
		catch (IOException e) {
			error(""+e);
			return false;
		}
		if (record()) Recorder.record("roiManager", "Save", path);
		return true;
	}
		
	boolean measure(int mode) {
		ImagePlus imp = getImage();
		if (imp==null)
			return false;
		int[] indexes = getSelectedIndexes();
		if (indexes.length==0)
			indexes = getAllIndexes();
        if (indexes.length==0) return false;
		boolean allSliceOne = true;
		for (int i=0; i<indexes.length; i++) {
			String label = list.getItem(indexes[i]);
			Roi roi = (Roi)rois.get(label);
			if (getSliceNumber(roi,label)>1) allSliceOne = false;
		}
		int measurements = Analyzer.getMeasurements();
		if (imp.getStackSize()>1)
			Analyzer.setMeasurements(measurements|Measurements.SLICE);
		int currentSlice = imp.getCurrentSlice();
		for (int i=0; i<indexes.length; i++) {
			if (restore(getImage(), indexes[i], !allSliceOne))
				IJ.run("Measure");
			else
				break;
		}
		imp.setSlice(currentSlice);
		Analyzer.setMeasurements(measurements);
		if (indexes.length>1)
			IJ.run("Select None");
		if (record()) Recorder.record("roiManager", "Measure");
		return true;
	}	
	
	/*
	void showIndexes(int[] indexes) {
		for (int i=0; i<indexes.length; i++) {
			String label = list.getItem(indexes[i]);
			Roi roi = (Roi)rois.get(label);
			IJ.log(i+" "+roi.getName());
		}
	}
	*/

	/* This method performs measurements for several ROI's in a stack
		and arranges the results with one line per slice.  By constast, the 
		measure() method produces several lines per slice.  The results 
		from multiMeasure() may be easier to import into a spreadsheet 
		program for plotting or additional analysis. Based on the multi() 
		method in Bob Dougherty's Multi_Measure plugin
		(http://www.optinav.com/Multi-Measure.htm).
	*/
 	boolean multiMeasure() {
		ImagePlus imp = getImage();
		if (imp==null) return false;
		int[] indexes = getSelectedIndexes();
		if (indexes.length==0)
			indexes = getAllIndexes();
        if (indexes.length==0) return false;
		int measurements = Analyzer.getMeasurements();

		int nSlices = imp.getStackSize();
		if (IJ.isMacro()) {
			if (nSlices>1) measureAll = true;
			onePerSlice = true;
		} else {
			GenericDialog gd = new GenericDialog("Multi Measure");
			if (nSlices>1)
				gd.addCheckbox("Measure All "+nSlices+" Slices", measureAll);
			gd.addCheckbox("One Row Per Slice", onePerSlice);
			int columns = getColumnCount(imp, measurements)*indexes.length;
			String str = nSlices==1?"this option":"both options";
			gd.setInsets(10, 25, 0);
			gd.addMessage(
				"Enabling "+str+" will result\n"+
				"in a table with "+columns+" columns."
			);
			gd.showDialog();
			if (gd.wasCanceled()) return false;
			if (nSlices>1)
				measureAll = gd.getNextBoolean();
			onePerSlice = gd.getNextBoolean();
		}
		if (!measureAll) nSlices = 1;
		int currentSlice = imp.getCurrentSlice();
		
		if (!onePerSlice) {
			int measurements2 = nSlices>1?measurements|Measurements.SLICE:measurements;
			ResultsTable rt = new ResultsTable();
			Analyzer analyzer = new Analyzer(imp, measurements2, rt);
			for (int slice=1; slice<=nSlices; slice++) {
				if (nSlices>1) imp.setSliceWithoutUpdate(slice);
				for (int i=0; i<indexes.length; i++) {
					if (restoreWithoutUpdate(indexes[i]))
						analyzer.measure();
					else
						break;
				}
			}
			rt.show("Results");
			if (nSlices>1) imp.setSlice(currentSlice);
			return true;
		}

		Analyzer aSys = new Analyzer(imp); //System Analyzer
		ResultsTable rtSys = Analyzer.getResultsTable();
		ResultsTable rtMulti = new ResultsTable();
		Analyzer aMulti = new Analyzer(imp, measurements, rtMulti); //Private Analyzer

		for (int slice=1; slice<=nSlices; slice++) {
			int sliceUse = slice;
			if(nSlices == 1)sliceUse = currentSlice;
			imp.setSliceWithoutUpdate(sliceUse);
			rtMulti.incrementCounter();
			int roiIndex = 0;
			for (int i=0; i<indexes.length; i++) {
				if (restoreWithoutUpdate(indexes[i])) {
					roiIndex++;
					aSys.measure();
					for (int j=0; j<=rtSys.getLastColumn(); j++){
						float[] col = rtSys.getColumn(j);
						String head = rtSys.getColumnHeading(j);
						String suffix = ""+roiIndex;
						Roi roi = imp.getRoi();
						if (roi!=null) {
							String name = roi.getName();
							if (name!=null && name.length()>0 && (name.length()<9||!Character.isDigit(name.charAt(0))))
								suffix = "("+name+")";
						}
						if (head!=null && col!=null && !head.equals("Slice"))
							rtMulti.addValue(head+suffix,rtSys.getValue(j,rtSys.getCounter()-1));
					}
				} else
					break;
			}
			//aMulti.displayResults();
			//aMulti.updateHeadings();
		}
		rtMulti.show("Results");

		imp.setSlice(currentSlice);
		if (indexes.length>1)
			IJ.run("Select None");
		if (record()) Recorder.record("roiManager", "Multi Measure");
		return true;
	}
	
	int getColumnCount(ImagePlus imp, int measurements) {
		ImageStatistics stats = imp.getStatistics(measurements);
		ResultsTable rt = new ResultsTable();
		Analyzer analyzer = new Analyzer(imp, measurements, rt);
		analyzer.saveResults(stats, null);
		int count = 0;
		for (int i=0; i<=rt.getLastColumn(); i++) {
			float[] col = rt.getColumn(i);
			String head = rt.getColumnHeading(i);
			if (head!=null && col!=null)
				count++;
		}
		return count;
	}
	
	void multiPlot() {
		ImagePlus imp = getImage();
		if (imp==null) return;
		int[] indexes = getSelectedIndexes();
		if (indexes.length==0) indexes = getAllIndexes();
		int n = indexes.length;
        if (n==0) return;
		Color[] colors = {Color.blue, Color.green, Color.magenta, Color.red, Color.cyan, Color.yellow};
		if (n>colors.length) {
			colors = new Color[n];
			double c = 0;
			double inc =150.0/n;
			for (int i=0; i<n; i++) {
				colors[i] = new Color((int)c, (int)c, (int)c);
				c += inc;
			}
		}
		int currentSlice = imp.getCurrentSlice();
		double[][] x = new double[n][];
		double[][] y = new double[n][];
		double minY = Double.MAX_VALUE;
		double maxY = -Double.MAX_VALUE;
		double fixedMin = ProfilePlot.getFixedMin();
		double fixedMax = ProfilePlot.getFixedMax();	
		boolean freeYScale = fixedMin==0.0 && fixedMax==0.0;
		if (!freeYScale) {
			minY = fixedMin;
			maxY = fixedMax;
		}
		int maxX = 0;
		Calibration cal = imp.getCalibration();
		double xinc = cal.pixelWidth;
		for (int i=0; i<indexes.length; i++) {
			if (!restore(getImage(), indexes[i], true)) break;
			Roi roi = imp.getRoi();
			if (roi==null) break;
			if (roi.isArea() && roi.getType()!=Roi.RECTANGLE)
				IJ.run(imp, "Area to Line", "");
			ProfilePlot pp = new ProfilePlot(imp, IJ.altKeyDown());
			y[i] = pp.getProfile();
			if (y[i]==null) break;
			if (y[i].length>maxX) maxX = y[i].length;
			if (freeYScale) {
				double[] a = Tools.getMinMax(y[i]);
				if (a[0]<minY) minY=a[0];
				if (a[1]>maxY) maxY = a[1];
			}
			double[] xx = new double[y[i].length];
			for (int j=0; j<xx.length; j++)
				xx[j] = j*xinc;
			x[i] = xx;
		}
		String xlabel = "Distance ("+cal.getUnits()+")";
		Plot plot = new Plot("Profiles",xlabel, "Value", x[0], y[0]);
		plot.setLimits(0, maxX*xinc, minY, maxY);
		for (int i=1; i<indexes.length; i++) {
			plot.setColor(colors[i]);
			if (x[i]!=null)
				plot.addPoints(x[i], y[i], Plot.LINE);
		}
		plot.setColor(colors[0]);
		if (x[0]!=null)
			plot.show();
		imp.setSlice(currentSlice);
		if (indexes.length>1)
			IJ.run("Select None");
		if (record()) Recorder.record("roiManager", "Multi Plot");
	}	

	boolean drawOrFill(int mode) {
		int[] indexes = getSelectedIndexes();
		if (indexes.length==0)
			indexes = getAllIndexes();
		ImagePlus imp = WindowManager.getCurrentImage();
		imp.killRoi();
		ImageProcessor ip = imp.getProcessor();
		ip.setColor(Toolbar.getForegroundColor());
		ip.snapshot();
		Undo.setup(Undo.FILTER, imp);
		Filler filler = mode==LABEL?new Filler():null;
		int slice = imp.getCurrentSlice();
		for (int i=0; i<indexes.length; i++) {
			String name = list.getItem(indexes[i]);
			Roi roi = (Roi)rois.get(name);
			int type = roi.getType();
			if (roi==null) continue;
			if (mode==FILL&&(type==Roi.POLYLINE||type==Roi.FREELINE||type==Roi.ANGLE))
				mode = DRAW;
            int slice2 = getSliceNumber(roi, name);
            if (slice2>=1 && slice2<=imp.getStackSize()) {
                imp.setSlice(slice2);
				ip = imp.getProcessor();
				ip.setColor(Toolbar.getForegroundColor());
				if (slice2!=slice) Undo.reset();
            }
 			switch (mode) {
				case DRAW: roi.drawPixels(ip); break;
				case FILL: ip.fill(roi); break;
				case LABEL:
					roi.drawPixels(ip);
					filler.drawLabel(imp, ip, i+1, roi.getBounds());
					break;
			}
		}
		ImageCanvas ic = imp.getCanvas();
		if (ic!=null) ic.setShowAllROIs(false);
		imp.updateAndDraw();
		return true;
	}

	void setProperties(Color color, int lineWidth, Color fillColor) {
		boolean showDialog = color==null && lineWidth==-1 && fillColor==null;
		int[] indexes = getSelectedIndexes();
		if (indexes.length==0)
			indexes = getAllIndexes();
		int n = indexes.length;
        if (n==0) return;
		Roi rpRoi = null;
		String rpName = null;
		Font font = null;
		int justification = TextRoi.LEFT;
		double opacity = -1;
        if (showDialog) {
			String label = list.getItem(indexes[0]);
			rpRoi = (Roi)rois.get(label);
			if (n==1) {
				fillColor =  rpRoi.getFillColor();
				rpName = rpRoi.getName();
			}
			if (rpRoi.getStrokeColor()==null)
				rpRoi.setStrokeColor(ImageCanvas.getShowAllColor());
			rpRoi = (Roi) rpRoi.clone();
			if (n>1)
				rpRoi.setName("range: "+(indexes[0]+1)+"-"+(indexes[n-1]+1));
			rpRoi.setFillColor(fillColor);
			RoiProperties rp = new RoiProperties("Properties", rpRoi);
			if (!rp.showDialog())
				return;
			lineWidth =  (int)rpRoi.getStrokeWidth();
			defaultLineWidth = lineWidth;
			color =  rpRoi.getStrokeColor();
			fillColor =  rpRoi.getFillColor();
			defaultColor = color;
			if (rpRoi instanceof TextRoi) {
				font = ((TextRoi)rpRoi).getCurrentFont();
				justification = ((TextRoi)rpRoi).getJustification();
			}
			if (rpRoi instanceof ImageRoi)
				opacity = ((ImageRoi)rpRoi).getOpacity();
		}
		ImagePlus imp = WindowManager.getCurrentImage();
		if (n==list.getItemCount() && n>1 && !IJ.isMacro()) {
			GenericDialog gd = new GenericDialog("ROI Manager");
			gd.addMessage("Apply changes to all "+n+" selections?");
			gd.showDialog();
			if (gd.wasCanceled()) return;
		}
		for (int i=0; i<n; i++) {
			String label = list.getItem(indexes[i]);
			Roi roi = (Roi)rois.get(label);
			//IJ.log("set "+color+"  "+lineWidth+"  "+fillColor);
			if (color!=null) roi.setStrokeColor(color);
			if (lineWidth>=0) roi.setStrokeWidth(lineWidth);
			roi.setFillColor(fillColor);
			if (roi!=null && (roi instanceof TextRoi)) {
				roi.setImage(imp);
				if (font!=null)
					((TextRoi)roi).setCurrentFont(font);
				((TextRoi)roi).setJustification(justification);
				roi.setImage(null);
			}
			if (roi!=null && (roi instanceof ImageRoi) && opacity!=-1)
				((ImageRoi)roi).setOpacity(opacity);
		}
		if (rpRoi!=null && rpName!=null && !rpRoi.getName().equals(rpName))
			rename(rpRoi.getName());
		ImageCanvas ic = imp!=null?imp.getCanvas():null;
		Roi roi = imp!=null?imp.getRoi():null;
		boolean showingAll = ic!=null &&  ic.getShowAllROIs();
		if (roi!=null && (n==1||!showingAll)) {
			if (lineWidth>=0) roi.setStrokeWidth(lineWidth);
			if (color!=null) roi.setStrokeColor(color);
			if (fillColor!=null) roi.setFillColor(fillColor);
			if (roi!=null && (roi instanceof TextRoi)) {
				((TextRoi)roi).setCurrentFont(font);
				((TextRoi)roi).setJustification(justification);
			}
			if (roi!=null && (roi instanceof ImageRoi) && opacity!=-1)
				((ImageRoi)roi).setOpacity(opacity);
		}
		if (lineWidth>1 && !showingAll && roi==null) {
			showAll(SHOW_ALL);
			showingAll = true;
		}
		if (imp!=null) imp.draw();
		if (record()) {
			if (fillColor!=null)
				Recorder.record("roiManager", "Set Fill Color", Colors.colorToString(fillColor));
			else {
				Recorder.record("roiManager", "Set Color", Colors.colorToString(color!=null?color:Color.red));
				Recorder.record("roiManager", "Set Line Width", lineWidth);
			}
		}
	}
	
	void flatten() {
		ImagePlus imp = WindowManager.getCurrentImage();
		if (imp==null)
			{IJ.noImage(); return;}
		ImageCanvas ic = imp.getCanvas();
		if (!ic.getShowAllROIs() && ic.getDisplayList()==null && imp.getRoi()==null)
			error("Image does not have an overlay or ROI");
		else
			IJ.doCommand("Flatten"); // run Image>Flatten in separate thread
	}
			
	public boolean getDrawLabels() {
		return labelsCheckbox.getState();
	}

	void combine() {
		ImagePlus imp = getImage();
		if (imp==null) return;
		int[] indexes = getSelectedIndexes();
		if (indexes.length==1) {
			error("More than one item must be selected, or none");
			return;
		}
		if (indexes.length==0)
			indexes = getAllIndexes();
		int nPointRois = 0;
		for (int i=0; i<indexes.length; i++) {
			Roi roi = (Roi)rois.get(list.getItem(indexes[i]));
			if (roi.getType()==Roi.POINT)
				nPointRois++;
			else
				break;
		}
		if (nPointRois==indexes.length)
			combinePoints(imp, indexes);
		else
			combineRois(imp, indexes);
		if (record()) Recorder.record("roiManager", "Combine");
	}
	
	void combineRois(ImagePlus imp, int[] indexes) {
		ShapeRoi s1=null, s2=null;
		for (int i=0; i<indexes.length; i++) {
			Roi roi = (Roi)rois.get(list.getItem(indexes[i]));
			if (roi.isLine() || roi.getType()==Roi.POINT)
				continue;
			if (s1==null) {
				if (roi instanceof ShapeRoi)
					s1 = (ShapeRoi)roi;
				else
					s1 = new ShapeRoi(roi);
				if (s1==null) return;
			} else {
				if (roi instanceof ShapeRoi)
					s2 = (ShapeRoi)roi;
				else
					s2 = new ShapeRoi(roi);
				if (s2==null) continue;
				if (roi.isArea())
					s1.or(s2);
			}
		}
		if (s1!=null)
			imp.setRoi(s1);
	}

	void combinePoints(ImagePlus imp, int[] indexes) {
		int n = indexes.length;
		Polygon[] p = new Polygon[n];
		int points = 0;
		for (int i=0; i<n; i++) {
			Roi roi = (Roi)rois.get(list.getItem(indexes[i]));
			p[i] = roi.getPolygon();
			points += p[i].npoints;
		}
		if (points==0) return;
		int[] xpoints = new int[points];
		int[] ypoints = new int[points];
		int index = 0;
		for (int i=0; i<p.length; i++) {
			for (int j=0; j<p[i].npoints; j++) {
				xpoints[index] = p[i].xpoints[j];
				ypoints[index] = p[i].ypoints[j];
				index++;
			}	
		}
		imp.setRoi(new PointRoi(xpoints, ypoints, xpoints.length));
	}

	void and() {
		ImagePlus imp = getImage();
		if (imp==null) return;
		int[] indexes = getSelectedIndexes();
		if (indexes.length==1) {
			error("More than one item must be selected, or none");
			return;
		}
		if (indexes.length==0)
			indexes = getAllIndexes();
		ShapeRoi s1=null, s2=null;
		for (int i=0; i<indexes.length; i++) {
			Roi roi = (Roi)rois.get(list.getItem(indexes[i]));
			if (!roi.isArea()) continue;
			if (s1==null) {
				if (roi instanceof ShapeRoi)
					s1 = (ShapeRoi)roi.clone();
				else
					s1 = new ShapeRoi(roi);
				if (s1==null) return;
			} else {
				if (roi instanceof ShapeRoi)
					s2 = (ShapeRoi)roi.clone();
				else
					s2 = new ShapeRoi(roi);
				if (s2==null) continue;
				s1.and(s2);
			}
		}
		if (s1!=null) imp.setRoi(s1);
		if (record()) Recorder.record("roiManager", "AND");
	}

	void xor() {
		ImagePlus imp = getImage();
		if (imp==null) return;
		int[] indexes = getSelectedIndexes();
		if (indexes.length==1) {
			error("More than one item must be selected, or none");
			return;
		}
		if (indexes.length==0)
			indexes = getAllIndexes();
		ShapeRoi s1=null, s2=null;
		for (int i=0; i<indexes.length; i++) {
			Roi roi = (Roi)rois.get(list.getItem(indexes[i]));
			if (!roi.isArea()) continue;
			if (s1==null) {
				if (roi instanceof ShapeRoi)
					s1 = (ShapeRoi)roi.clone();
				else
					s1 = new ShapeRoi(roi);
				if (s1==null) return;
			} else {
				if (roi instanceof ShapeRoi)
					s2 = (ShapeRoi)roi.clone();
				else
					s2 = new ShapeRoi(roi);
				if (s2==null) continue;
				s1.xor(s2);
			}
		}
		if (s1!=null) imp.setRoi(s1);
		if (record()) Recorder.record("roiManager", "XOR");
	}

	void addParticles() {
		String err = IJ.runMacroFile("ij.jar:AddParticles", null);
		if (err!=null && err.length()>0)
			error(err);
	}

	void sort() {
		int n = rois.size();
		if (n==0) return;
		String[] labels = new String[n];
		int index = 0;
		for (Enumeration en=rois.keys(); en.hasMoreElements();)
			labels[index++] = (String)en.nextElement();
		list.removeAll();
		StringSorter.sort(labels);
		for (int i=0; i<labels.length; i++)
			list.add(labels[i]);
		if (record()) Recorder.record("roiManager", "Sort");
	}
	
	void specify() {
		try {IJ.run("Specify...");}
		catch (Exception e) {return;}
		runCommand("add");
	}
	
	void removeSliceInfo() {
		int[] indexes = getSelectedIndexes();
		if (indexes.length==0)
			indexes = getAllIndexes();
		for (int i=0; i<indexes.length; i++) {
			int index = indexes[i];
			String name = list.getItem(index);
			int n = getSliceNumber(name);
			if (n==-1) continue;
			String name2 = name.substring(5, name.length());
			name2 = getUniqueName(name2);
			Roi roi = (Roi)rois.get(name);
			rois.remove(name);
			roi.setName(name2);
			roi.setPosition(0);
			rois.put(name2, roi);
			list.replaceItem(name2, index);
		}
		if (record()) Recorder.record("roiManager", "Remove Slice Info");
	}

	void help() {
		String macro = "run('URL...', 'url="+IJ.URL+"/docs/menus/analyze.html#manager');";
		new MacroRunner(macro);
	}

	void options() {
		Color c = ImageCanvas.getShowAllColor();
		GenericDialog gd = new GenericDialog("Options");
		gd.addPanel(makeButtonPanel(gd), GridBagConstraints.CENTER, new Insets(5, 0, 0, 0));
		gd.addCheckbox("Associate \"Show All\" ROIs with slices", Prefs.showAllSliceOnly);
		gd.addCheckbox("Restore ROIs centered", restoreCentered);
		gd.addCheckbox("Use ROI names as labels", Prefs.useNamesAsLabels);
		gd.showDialog();
		if (gd.wasCanceled()) {
			if (c!=ImageCanvas.getShowAllColor())
				ImageCanvas.setShowAllColor(c);
			return;
		}
		Prefs.showAllSliceOnly = gd.getNextBoolean();
		restoreCentered = gd.getNextBoolean();
		Prefs.useNamesAsLabels = gd.getNextBoolean();
		ImagePlus imp = WindowManager.getCurrentImage();
		if (imp!=null) imp.draw();
		if (record()) {
			Recorder.record("roiManager", "Associate", Prefs.showAllSliceOnly?"true":"false");
			Recorder.record("roiManager", "Centered", restoreCentered?"true":"false");
			Recorder.record("roiManager", "UseNames", Prefs.useNamesAsLabels?"true":"false");
		}
	}

	Panel makeButtonPanel(GenericDialog gd) {
		Panel panel = new Panel();
    	//buttons.setLayout(new FlowLayout(FlowLayout.CENTER, 5, 0));
		colorButton = new Button("\"Show All\" Color...");
		colorButton.addActionListener(this);
		panel.add(colorButton);
		return panel;
	}
	
	void setShowAllColor() {
            ColorChooser cc = new ColorChooser("\"Show All\" Color", ImageCanvas.getShowAllColor(),  false);
            ImageCanvas.setShowAllColor(cc.getColor());
	}

	void split() {
		ImagePlus imp = getImage();
		if (imp==null) return;
		Roi roi = imp.getRoi();
		if (roi==null || roi.getType()!=Roi.COMPOSITE) {
			error("Image with composite selection required");
			return;
		}
		boolean record = Recorder.record;
		Recorder.record = false;
		Roi[] rois = ((ShapeRoi)roi).getRois();
		for (int i=0; i<rois.length; i++) {
			imp.setRoi(rois[i]);
			addRoi(false);
		}
		Recorder.record = record;
		if (record()) Recorder.record("roiManager", "Split");
	}
	
	void showAll(int mode) {
		ImagePlus imp = WindowManager.getCurrentImage();
		if (imp==null)
			{error("There are no images open."); return;}
		ImageCanvas ic = imp.getCanvas();
		if (ic==null) return;
		boolean showAll = mode==SHOW_ALL;
		if (mode==LABELS) {
			showAll = true;
			if (record())
				Recorder.record("roiManager", "Show All with labels");
		} else if (mode==NO_LABELS) {
			showAll = true;
			if (record())
				Recorder.record("roiManager", "Show All without labels");
		}
		if (showAll) imp.killRoi();
		ic.setShowAllROIs(showAll);
		if (record())
			Recorder.record("roiManager", showAll?"Show All":"Show None");
		imp.draw();
	}

	void updateShowAll() {
		ImagePlus imp = WindowManager.getCurrentImage();
		if (imp==null) return;
		ImageCanvas ic = imp.getCanvas();
		if (ic!=null && ic.getShowAllROIs())
			imp.draw();
	}

	int[] getAllIndexes() {
		int count = list.getItemCount();
		int[] indexes = new int[count];
		for (int i=0; i<count; i++)
			indexes[i] = i;
		return indexes;
	}
		
	ImagePlus getImage() {
		ImagePlus imp = WindowManager.getCurrentImage();
		if (imp==null) {
			error("There are no images open.");
			return null;
		} else
			return imp;
	}

	boolean error(String msg) {
		new MessageDialog(this, "ROI Manager", msg);
		Macro.abort();
		return false;
	}
	
	public void processWindowEvent(WindowEvent e) {
		super.processWindowEvent(e);
		if (e.getID()==WindowEvent.WINDOW_CLOSING) {
			instance = null;	
		}
		if (!IJ.isMacro())
			ignoreInterrupts = false;
	}
	
	/** Returns a reference to the ROI Manager
		or null if it is not open. */
	public static RoiManager getInstance() {
		return (RoiManager)instance;
	}
	
	/** Returns a reference to the ROI Manager window or to the
		macro batch mode RoiManager, or null if neither exists. */
	public static RoiManager getInstance2() {
		RoiManager rm = getInstance();
		if (rm==null && IJ.isMacro())
			rm = Interpreter.getBatchModeRoiManager();
		return rm;
	}



	/**	Returns the ROI Hashtable.
		@see getCount
		@see getRoisAsArray
	*/
	public Hashtable getROIs() {
		return rois;
	}

	/** Returns the selection list.
		@see getCount
		@see getRoisAsArray
	*/
	public List getList() {
		return list;
	}
	
	/** Returns the ROI count. */
	public int getCount() {
		return list.getItemCount();
	}

	/** Returns the ROIs as an array. */
	public Roi[] getRoisAsArray() {
		int n = list.getItemCount();
		Roi[] array = new Roi[n];
		for (int i=0; i<n; i++) {
			String label = list.getItem(i);
			array[i] = (Roi)rois.get(label);
		}
		return array;
	}
	
	/** Returns the selected ROIs as an array, or
		all the ROIs if none are selected. */
	public Roi[] getSelectedRoisAsArray() {
		int[] indexes = getSelectedIndexes();
		if (indexes.length==0)
			indexes = getAllIndexes();
		int n = indexes.length;
		Roi[] array = new Roi[n];
		for (int i=0; i<n; i++) {
			String label = list.getItem(indexes[i]);
			array[i] = (Roi)rois.get(label);
		}
		return array;
	}
			
	/** Returns the name of the ROI with the specified index,
		or null if the index is out of range. */
	public String getName(int index) {
		if (index>=0 && index<list.getItemCount())
       	 	return  list.getItem(index);
		else
			return null;
	}

	/** Returns the name of the ROI with the specified index.
		Can be called from a macro using
		<pre>call("ij.plugin.frame.RoiManager.getName", index)</pre>
		Returns "null" if the Roi Manager is not open or index is
		out of range.
	*/
	public static String getName(String index) {
		int i = (int)Tools.parseDouble(index, -1);
		RoiManager instance = getInstance();
		if (instance!=null && i>=0 && i<instance.list.getItemCount())
       	 	return  instance.list.getItem(i);
		else
			return "null";
	}

	/** Executes the ROI Manager "Add", "Add & Draw", "Update", "Delete", "Measure", "Draw",
		"Show All", Show None", "Fill", "Deselect", "Select All", "Combine", "AND", "XOR", "Split",
		"Sort" or "Multi Measure" command.  Returns false if <code>cmd</code>
		is not one of these strings. */
	public boolean runCommand(String cmd) {
		cmd = cmd.toLowerCase();
		macro = true;
		boolean ok = true;
		if (cmd.equals("add")) {
			boolean shift = IJ.shiftKeyDown();
			boolean alt = IJ.altKeyDown();
			if (Interpreter.isBatchMode()) {
				shift = false;
				alt = false;
			}
			ImagePlus imp = WindowManager.getCurrentImage();
			Roi roi = imp!=null?imp.getRoi():null;
			if (roi!=null) roi.setPosition(0);
			add(shift, alt);
		} else if (cmd.equals("add & draw"))
			addAndDraw(false);
		else if (cmd.equals("update"))
			update(true);
		else if (cmd.equals("update2"))
			update(false);
		else if (cmd.equals("delete"))
			delete(false);
		else if (cmd.equals("measure"))
			measure(COMMAND);
		else if (cmd.equals("draw"))
			drawOrFill(DRAW);
		else if (cmd.equals("fill"))
			drawOrFill(FILL);
		else if (cmd.equals("label"))
			drawOrFill(LABEL);
		else if (cmd.equals("and"))
			and();
		else if (cmd.equals("or") || cmd.equals("combine"))
			combine();
		else if (cmd.equals("xor"))
			xor();
		else if (cmd.equals("split"))
			split();
		else if (cmd.equals("sort"))
			sort();
		else if (cmd.equals("multi measure"))
			multiMeasure();
		else if (cmd.equals("multi plot"))
			multiPlot();
		else if (cmd.equals("show all")) {
			if (WindowManager.getCurrentImage()!=null) {
				showAll(SHOW_ALL);
				showAllCheckbox.setState(true);
			}
		} else if (cmd.equals("show none")) {
			if (WindowManager.getCurrentImage()!=null) {
				showAll(SHOW_NONE);
				showAllCheckbox.setState(false);
			}
		} else if (cmd.equals("show all with labels")) {
			labelsCheckbox.setState(true);
			showAll(LABELS);
			if (Interpreter.isBatchMode()) IJ.wait(250);
		} else if (cmd.equals("show all without labels")) {
			labelsCheckbox.setState(false);
			showAll(NO_LABELS);
			if (Interpreter.isBatchMode()) IJ.wait(250);
		} else if (cmd.equals("deselect")||cmd.indexOf("all")!=-1) {
			if (IJ.isMacOSX()) ignoreInterrupts = true;
			select(-1);
			IJ.wait(50);
		} else if (cmd.equals("reset")) {
			if (IJ.isMacOSX() && IJ.isMacro())
				ignoreInterrupts = true;
			list.removeAll();
			rois.clear();
			updateShowAll();
		} else if (cmd.equals("debug")) {
			//IJ.log("Debug: "+debugCount);
			//for (int i=0; i<debugCount; i++)
    		//	IJ.log(debug[i]);
		} else if (cmd.equals("enable interrupts")) {
			ignoreInterrupts = false;
		} else if (cmd.equals("remove slice info")) {
			removeSliceInfo();
		} else
			ok = false;
		macro = false;
		return ok;
	}

	/** Executes the ROI Manager "Open", "Save" or "Rename" command. Returns false if 
	<code>cmd</code> is not "Open", "Save" or "Rename", or if an error occurs. */
	public boolean runCommand(String cmd, String name) {
		cmd = cmd.toLowerCase();
		macro = true;
		if (cmd.equals("open")) {
			open(name);
			macro = false;
			return true;
		} else if (cmd.equals("save")) {
			if (!name.endsWith(".zip") && !name.equals(""))
				return error("Name must end with '.zip'");
			if (list.getItemCount()==0)
				return error("The selection list is empty.");
			int[] indexes = getAllIndexes();
			boolean ok = false;
			if (name.equals(""))
				ok = saveMultiple(indexes, null);
			else
				ok = saveMultiple(indexes, name);
			macro = false;
			return ok;
		} else if (cmd.equals("rename")) {
			rename(name);
			macro = false;
			return true;
		} else if (cmd.equals("set color")) {
			Color color = Colors.decode(name, Color.cyan);
			setProperties(color, -1, null);
			macro = false;
			return true;
		} else if (cmd.equals("set fill color")) {
			Color fillColor = Colors.decode(name, Color.cyan);
			setProperties(null, -1, fillColor);
			macro = false;
			return true;
		} else if (cmd.equals("set line width")) {
			int lineWidth = (int)Tools.parseDouble(name, 0);
			if (lineWidth>=0)
				setProperties(null, lineWidth, null);
			macro = false;
			return true;
		} else if (cmd.equals("associate")) {
			Prefs.showAllSliceOnly = name.equals("true")?true:false;
			macro = false;
			return true;
		} else if (cmd.equals("centered")) {
			restoreCentered = name.equals("true")?true:false;
			macro = false;
			return true;
		} else if (cmd.equals("usenames")) {
			Prefs.useNamesAsLabels = name.equals("true")?true:false;
			macro = false;
			if (labelsCheckbox.getState()) {
				ImagePlus imp = WindowManager.getCurrentImage();
				if (imp!=null) imp.draw();
			}
			return true;
		}
		return false;
	}
	
	/** Adds the current selection to the ROI Manager, using the
		specified color (a 6 digit hex string) and line width. */
	public boolean runCommand(String cmd, String hexColor, double lineWidth) {
		ImagePlus imp = WindowManager.getCurrentImage();
		Roi roi = imp!=null?imp.getRoi():null;
		if (roi!=null) roi.setPosition(0);
		if (hexColor==null && lineWidth==1.0 && (IJ.altKeyDown()&&!Interpreter.isBatchMode()))
			addRoi(true);
		else {
			Color color = hexColor!=null?Colors.decode(hexColor, Color.cyan):null;
			addRoi(null, false, color, (int)Math.round(lineWidth));
		}
		return true;	
	}
	
	/** Assigns the ROI at the specified index to the current image. */
	public void select(int index) {
		select(null, index);
	}
	
	/** Assigns the ROI at the specified index to 'imp'. */
	public void select(ImagePlus imp, int index) {
		selectedIndexes = null;
		int n = list.getItemCount();
		if (index<0) {
			for (int i=0; i<n; i++)
				list.deselect(i);
			if (record()) Recorder.record("roiManager", "Deselect");
			return;
		}
		if (index>=n) return;
		boolean mm = list.isMultipleMode();
		if (mm) list.setMultipleMode(false);
		int delay = 1;
		long start = System.currentTimeMillis();
		while (true) {
			list.select(index);
			if (delay>1) IJ.wait(delay);
			if (list.isIndexSelected(index))
				break;
			for (int i=0; i<n; i++)
				if (list.isSelected(i)) list.deselect(i);
			IJ.wait(delay);
			delay *= 2; if (delay>32) delay=32;
			if ((System.currentTimeMillis()-start)>1000L)
				error("Failed to select ROI "+index);
		}
		if (imp==null) imp=getImage();
		restore(imp, index, true);	
		if (mm) list.setMultipleMode(true);
	}
	
	public void select(int index, boolean shiftKeyDown, boolean altKeyDown) {
		if (!(shiftKeyDown||altKeyDown))
			select(index);
		ImagePlus imp = IJ.getImage();
		if (imp==null) return;
		Roi previousRoi = imp.getRoi();
		if (previousRoi==null)
			{select(index); return;}
		Roi.previousRoi = (Roi)previousRoi.clone();
		String label = list.getItem(index);
		Roi roi = (Roi)rois.get(label);
		if (roi!=null) {
			roi.setImage(imp);
			roi.update(shiftKeyDown, altKeyDown);
		}
	}
	
	public void setEditMode(ImagePlus imp, boolean editMode) {
		ImageCanvas ic = imp.getCanvas();
		boolean showAll = false;
		if (ic!=null) {
			showAll = ic.getShowAllROIs() | editMode;
			ic.setShowAllROIs(showAll);
			imp.draw();
		}
		showAllCheckbox.setState(showAll);
		labelsCheckbox.setState(editMode);
	}
	
	/*
	void selectAll() {
		boolean allSelected = true;
		int count = list.getItemCount();
		for (int i=0; i<count; i++) {
			if (!list.isIndexSelected(i))
				allSelected = false;
		}
		if (allSelected)
			select(-1);
		else {
			for (int i=0; i<count; i++)
				if (!list.isSelected(i)) list.select(i);
		}
	}
	*/

    /** Overrides PlugInFrame.close(). */
    public void close() {
    	super.close();
    	instance = null;
		Prefs.saveLocation(LOC_KEY, getLocation());
    }
    
    public void mousePressed (MouseEvent e) {
		int x=e.getX(), y=e.getY();
		if (e.isPopupTrigger() || e.isMetaDown())
			pm.show(e.getComponent(),x,y);
	}

	public void mouseWheelMoved(MouseWheelEvent event) {
		synchronized(this) {
			int index = list.getSelectedIndex();
			int rot = event.getWheelRotation();
			if (rot<-1) rot = -1;
			if (rot>1) rot = 1;
			index += rot;
			if (index<0) index = 0;
			if (index>=list.getItemCount()) index = list.getItemCount();
			//IJ.log(index+"  "+rot);
			select(index);
			if (IJ.isWindows())
				list.requestFocusInWindow();
		}
	}
	
	/** Temporarily selects multiple ROIs, where 'indexes' is an array of integers, 
		each greater than or equal to 0 and less than the value returned by getCount().
		The selected ROIs are not highlighted in the ROI Manager list and are no 
		longer selected after the next ROI Manager command is executed.
	*/
	public void setSelectedIndexes(int[] indexes) {
		int count = getCount();
		if (count==0) return;
		for (int i=0; i<indexes.length; i++) {
			if (indexes[i]<0) indexes[i]=0;
			if (indexes[i]>=count) indexes[i]=count-1;
		}
		selectedIndexes = indexes;
	}
	
	private int[] getSelectedIndexes() {
		if (selectedIndexes!=null) {
			int[] indexes = selectedIndexes;
			selectedIndexes = null;
			return indexes;
		} else
			return list.getSelectedIndexes();
	}

	private boolean record() {
		return Recorder.record && !IJ.isMacro();
	}

 	public void mouseReleased (MouseEvent e) {}
	public void mouseClicked (MouseEvent e) {}
	public void mouseEntered (MouseEvent e) {}
	public void mouseExited (MouseEvent e) {}

}