package ij.gui;
import java.awt.*;
import java.util.Vector;
import java.awt.geom.Rectangle2D;
import ij.*;
import ij.process.ImageProcessor;
import ij.plugin.filter.Analyzer;
import ij.measure.ResultsTable;

/** An Overlay is a list of ROIs that can be drawn non-destructively on an Image. */
public class Overlay {
	private Vector list;
    private boolean label;
    private boolean drawNames;
    private boolean drawBackgrounds;
    private Color labelColor;
    private Font labelFont;
    private boolean scalableLabels;
    private boolean isCalibrationBar;
    private boolean selectable = true;
    
    /** Constructs an empty Overlay. */
    public Overlay() {
    	list = new Vector();
    }
    
    /** Constructs an Overlay and adds the specified ROI. */
    public Overlay(Roi roi) {
    	list = new Vector();
    	if (roi!=null)
    		list.add(roi);
    }

    /** Adds an ROI to this Overlay. */
    public void add(Roi roi) {
    	if (roi!=null)
    		list.add(roi);
    }
        
    /** Adds an ROI to this Overlay using the specified name. */
	public void add(Roi roi, String name) {
		roi.setName(name);
		add(roi);
	}

    /** Adds an ROI to this Overlay. */
    public void addElement(Roi roi) {
    	if (roi!=null)
    		list.add(roi);
    }

    /** Replaces the ROI at the specified index. */
    public void set(Roi roi, int index) {
    	if (index<0 || index>=list.size())
    		throw new IllegalArgumentException("set: index out of range");
    	if (roi!=null)
    		list.set(index, roi);
    }

    /** Removes the ROI with the specified index from this Overlay. */
    public void remove(int index) {
    	list.remove(index);
    }
    
    /** Removes the specified ROI from this Overlay. */
    public void remove(Roi roi) {
    	list.remove(roi);
    }

    /** Removes all ROIs that have the specified name. */
	public void remove(String name) {
		if (name==null) return;
		for (int i=size()-1; i>=0; i--) {
			if (name.equals(get(i).getName()))
				remove(i);
		}
	}

   /** Removes all the ROIs in this Overlay. */
    public void clear() {
    	list.clear();
    }

    /** Returns the ROI with the specified index or null if the index is invalid. */
    public Roi get(int index) {
    	try {
    		return (Roi)list.get(index);
    	} catch(Exception e) {
    		return null;
    	}
    }
    
    /** Returns the index of the ROI with the specified name, or -1 if not found. */
    public int getIndex(String name) {
    	if (name==null) return -1;
    	Roi[] rois = toArray();
		for (int i=rois.length-1; i>=0; i--) {
			if (name.equals(rois[i].getName()))
				return i;
		}
		return -1;
    }
    
    /** Returns 'true' if this Overlay contains the specified ROI. */
    public boolean contains(Roi roi) {
    	return list.contains(roi);
    }

    /** Returns the number of ROIs in this Overlay. */
    public int size() {
    	return list.size();
    }
    
    /** Returns on array containing the ROIs in this Overlay. */
    public Roi[] toArray() {
    	Roi[] array = new Roi[list.size()];
    	return (Roi[])list.toArray(array);
    }
    
    /** Sets the stroke color of all the ROIs in this overlay. */
    public void setStrokeColor(Color color) {
		Roi[] rois = toArray();
		for (int i=0; i0?bounds.x:0;
		int dy = bounds.y>0?bounds.y:0;
		if (dx>0 || dy>0)
			overlay2.translate(-dx, -dy);
		return overlay2;
	}

	/** Removes ROIs having positions outside of the  
	* interval defined by firstSlice and lastSlice.
	* Marcel Boeglin, September 2013
	*/
	public void crop(int firstSlice, int lastSlice) {
		for (int i=size()-1; i>=0; i--) {
			Roi roi = get(i);
			int position = roi.getPosition();
			if (position>0) {
				if (positionlastSlice)
					remove(i);
				else
					roi.setPosition(position-firstSlice+1);
			}
		}
	}

	/** Removes ROIs having a C, Z or T coordinate outside the volume
	* defined by firstC, lastC, firstZ, lastZ, firstT and lastT.
	* Marcel Boeglin, September 2013
	*/
	public void crop(int firstC, int lastC, int firstZ, int lastZ, int firstT, int lastT) {
		int nc = lastC-firstC+1, nz = lastZ-firstZ+1, nt = lastT-firstT+1;
		boolean toCStack = nz==1 && nt==1;
		boolean toZStack = nt==1 && nc==1;
		boolean toTStack = nc==1 && nz==1;
		Roi roi;
		int c, z, t, c2, z2, t2;
		for (int i=size()-1; i>=0; i--) {
			roi = get(i);
			c = roi.getCPosition();
			z = roi.getZPosition();
			t = roi.getTPosition();
			c2 = c-firstC+1;
			z2 = z-firstZ+1;
			t2 = t-firstT+1;
			if (toCStack)
				roi.setPosition(c2);
			else if (toZStack)
				roi.setPosition(z2);
			else if (toTStack)
				roi.setPosition(t2);
			else
				roi.setPosition(c2, z2, t2);
			if ((c2<1||c2>nc) && c>0 || (z2<1||z2>nz) && z>0 || (t2<1||t2>nt) && t>0)
				remove(i);
		}
	}

    /** Returns the bounds of this overlay. */
    /*
    public Rectangle getBounds() {
    	if (size()==0)
    		return new Rectangle(0,0,0,0);
    	int xmin = Integer.MAX_VALUE;
    	int xmax = -Integer.MAX_VALUE;
    	int ymin = Integer.MAX_VALUE;
    	int ymax = -Integer.MAX_VALUE;
		Roi[] rois = toArray();
		for (int i=0; ixmax) xmax = r.x+r.width;
			if (r.y+r.height>ymax) ymax = r.y+r.height;
		}
		return new Rectangle(xmin, ymin, xmax-xmin, ymax-ymin);
	}
	*/

	/** Returns a new Overlay that has the same properties as this one. */
	public Overlay create() {
		Overlay overlay2 = new Overlay();
		overlay2.drawLabels(label);
		overlay2.drawNames(drawNames);
		overlay2.drawBackgrounds(drawBackgrounds);
		overlay2.setLabelColor(labelColor);
		overlay2.setLabelFont(labelFont);
		return overlay2;
	}
	
	/** Returns a clone of this Overlay. */
	public Overlay duplicate() {
		Roi[] rois = toArray();
		Overlay overlay2 = create();
		for (int i=0; i