package ij.plugin;
import java.awt.*;
import java.awt.event.*;
import java.util.Vector;
import ij.*;
import ij.process.*;
import ij.gui.*;
import ij.util.Tools;
import ij.plugin.frame.Recorder;
import ij.measure.Calibration;

/** This plugin implements the Image/Duplicate command.
   // test script
   img1 = IJ.getImage();
   img2 = new Duplicator().run(img1);
   //img2 = new Duplicator().run(img1,1,10);
   img2.show();

*/
public class Duplicator implements PlugIn, TextListener, ItemListener {
	private static boolean staticDuplicateStack;
	private boolean duplicateStack;
	private int first, last;
	private Checkbox checkbox;
	private TextField titleField, rangeField;
	private TextField[] rangeFields;
	private int firstC, lastC, firstZ, lastZ, firstT, lastT;
	private String defaultTitle;
	private String sliceLabel;
	private ImagePlus imp;
	private boolean legacyMacro;
	private boolean titleChanged;
	private GenericDialog gd;

	public void run(String arg) {
		imp = IJ.getImage();
		Roi roiA = imp.getRoi();
		ImagePlus impA = imp;
		boolean isRotatedRect = (roiA!=null &&  roiA instanceof RotatedRectRoi);
		if (isRotatedRect) {
			Rectangle bounds = imp.getRoi().getBounds();
			imp.setRoi(bounds);
		}
		int stackSize = imp.getStackSize();
		String title = imp.getTitle();
		String newTitle = WindowManager.getUniqueName(title);
		defaultTitle = newTitle;
		duplicateStack = staticDuplicateStack && !IJ.isMacro();
		if (!IJ.altKeyDown()||stackSize>1) {
			if (imp.isHyperStack() || imp.isComposite()) {
				duplicateHyperstack(imp, newTitle);			
				if (isRotatedRect) {
					straightenRotatedRect(impA, roiA, IJ.getImage());	
				}								
				return;
			} else
				newTitle = showDialog(imp, "Duplicate...", "Title: ");
		}
		if (newTitle==null) {
			if (isRotatedRect)
				imp.setRoi(roiA);
			return;
		}
		ImagePlus imp2;
		Roi roi = imp.getRoi();		
			if (duplicateStack && (first>1||last1 && imp2.getStackSize()==stackSize)
			imp2.setSlice(imp.getCurrentSlice());
		if (isRotatedRect)
			straightenRotatedRect(impA, roiA, imp2);		
	}
	
 /** Rotates duplicated part of image
	- impA is original image,
	- roiA is orig rotatedRect
	- impB contains duplicated overlapping bounding rectangle	
	processing steps:
	- increase canvas of impB before rotation
	- rotate impB
	- calculate excentricity
	- translate to compensate excentricity 
	- create orthogonal rectangle in center
	- crop to impC	
	Author: N. Vischer
	*/
	private void straightenRotatedRect(ImagePlus impA, Roi roiA, ImagePlus impB) {
		impB.deleteRoi(); //we have it in roiA
		Color colorBack = Toolbar.getBackgroundColor();	
		IJ.setBackgroundColor(0,0,0);
		String title = impB.getTitle();
		if(impB.getOverlay() != null)
			impB.getOverlay().clear();
		int boundLeft = roiA.getBounds().x;
		int boundTop = roiA.getBounds().y;
		int boundWidth = roiA.getBounds().width;
		int boundHeight = roiA.getBounds().height;

		float[] xx = roiA.getFloatPolygon().xpoints;
		float[] yy = roiA.getFloatPolygon().ypoints;

		double dx1 = xx[1] - xx[0];//calc sides and angle
		double dy1 = yy[1] - yy[0];
		double dx2 = xx[2] - xx[1];
		double dy2 = yy[2] - yy[1];

		double rrWidth = Math.sqrt(dx1 * dx1 + dy1 * dy1);//width of rot rect
		double rrHeight = Math.sqrt(dx2 * dx2 + dy2 * dy2);
		double rrDia = Math.sqrt(rrWidth * rrWidth + rrHeight * rrHeight);

		double phi1 = -Math.atan2(dy1, dx1);
		double phi0 = phi1 * 180 / Math.PI;

		double usedL = Math.max(boundLeft, 0); //usedrect is orthogonal rect to be rotated
		double usedR = Math.min(boundLeft + boundWidth, impA.getWidth());
		double usedT = Math.max(boundTop, 0);
		double usedB = Math.min(boundTop + boundHeight, impA.getHeight());
		double usedCX = (usedL + usedR) / 2;
		double usedCY = (usedT + usedB) / 2; //Center of UsedRect

		double boundsCX = boundLeft + boundWidth / 2;//Center of Bound = center of RotRect
		double boundsCY = boundTop + boundHeight / 2;

		double dx3 = boundsCX - usedCX;//calculate excentricity
		double dy3 = boundsCY - usedCY;
		double rad3 = Math.sqrt(dx3 * dx3 + dy3 * dy3);
		double phi3 = Math.atan2(dy3, dx3);
		double phi4 = phi3 + phi1;
		double dx4 = -rad3 * Math.cos(phi4);
		double dy4 = -rad3 * Math.sin(phi4);

		//Increase canvas to a square large enough for rotation
		ImageStack stackOld = impB.getStack();
		int currentSlice = impB.getCurrentSlice();
		double xOff = (rrDia - (usedR - usedL)) / 2;//put img in center
		double yOff = (rrDia - (usedB - usedT)) / 2;

		ImageStack stackNew = (new CanvasResizer()).expandStack(stackOld, (int) rrDia, (int) rrDia, (int) xOff, (int) yOff);
		impB.setStack(stackNew);
		ImageProcessor ip = impB.getProcessor();
		ip.setInterpolationMethod(ImageProcessor.BILINEAR);
		ip.setBackgroundValue(0);

		for (int slc = 0; slc < stackNew.size(); slc++) {
			impB.setSlice(slc+1);
			ip.rotate(phi0); //Rotate
			ip.translate(dx4, dy4); //Translate
		}

		int x = (impB.getWidth() - (int) rrWidth) / 2;
		int y = (impB.getHeight() - (int) rrHeight) / 2;

		impB.setStack(impB.getStack().crop(x, y, 0, (int) rrWidth, (int) rrHeight, impB.getStack().getSize()));//Crop
		impB.setSlice(currentSlice);
		impB.setTitle(title);
		impB.show();
		impB.updateAndDraw();
		impA.setRoi(roiA); //restore rotated rect in source image
		Toolbar.setBackgroundColor(colorBack);
	}	
	                
	/** Returns a copy of the image, stack or hyperstack contained in the specified ImagePlus.
	* @see ij.ImagePlus#duplicate
	*/
	public ImagePlus run(ImagePlus imp) {
		if (imp.getStackSize()==1)
			return crop(imp);
		Rectangle rect = null;
		Roi roi = imp.getRoi();
		Roi roi2 = cropRoi(imp, roi);
		if (roi2!=null && roi2.isArea())
			rect = roi2.getBounds();
		ImageStack stack = imp.getStack();
		boolean virtualStack = stack.isVirtual();
		double min = imp.getDisplayRangeMin();
		double max = imp.getDisplayRangeMax();
		ImageStack stack2 = null;
		int n = stack.getSize();
		for (int i=1; i<=n; i++) {
			if (stack.isVirtual())
				IJ.showStatus("Duplicating: "+i+"/"+n);
			ImageProcessor ip2 = stack.getProcessor(i);
			ip2.setRoi(rect);
			ip2 = ip2.crop();
			if (stack2==null)
				stack2 = new ImageStack(ip2.getWidth(), ip2.getHeight(), imp.getProcessor().getColorModel());
			stack2.addSlice(stack.getSliceLabel(i), ip2);
		}
		ImagePlus imp2 = imp.createImagePlus();
		imp2.setStack("DUP_"+imp.getTitle(), stack2);
		String info = (String)imp.getProperty("Info");
		if (info!=null)
			imp2.setProperty("Info", info);
		int[] dim = imp.getDimensions();
		imp2.setDimensions(dim[2], dim[3], dim[4]);
		if (imp.isComposite()) {
			imp2 = new CompositeImage(imp2, 0);
			((CompositeImage)imp2).copyLuts(imp);
		}
		if (virtualStack)
			imp2.setDisplayRange(min, max);
		if (imp.isHyperStack())
			imp2.setOpenAsHyperStack(true);
		Overlay overlay = imp.getOverlay();
		if (overlay!=null && !imp.getHideOverlay())
			imp2.setOverlay(overlay.crop(rect));
   		if (Recorder.record)
   			Recorder.recordCall("imp2 = imp.duplicate();");
		return imp2;
	}
	
	/** Returns a copy the current stack image, cropped if there is a selection.
	* @see ij.ImagePlus#crop
	*/
	public ImagePlus crop(ImagePlus imp) {
		ImageProcessor ip = imp.getProcessor();
		ImageProcessor ip2 = ip.crop();
		ImagePlus imp2 = imp.createImagePlus();
		imp2.setProcessor("DUP_"+imp.getTitle(), ip2);
		String info = (String)imp.getProperty("Info");
		if (info!=null)
			imp2.setProperty("Info", info);
		if (imp.isStack()) {
			ImageStack stack = imp.getStack();
			String label = stack.getSliceLabel(imp.getCurrentSlice());
			if (label!=null) {
				if (label.length()>250 && label.indexOf('\n')>0 && label.contains("0002,"))
					imp2.setProperty("Info", label); // DICOM metadata
				else
					imp2.setProperty("Label", label);					
			}
			if (imp.isComposite()) {
				LUT lut = ((CompositeImage)imp).getChannelLut();
				imp2.getProcessor().setColorModel(lut);
			}
		} else {
			String label = (String)imp.getProperty("Label");
			if (label!=null)
				imp2.setProperty("Label", label);
		}
		Overlay overlay = imp.getOverlay();
		if (overlay!=null && !imp.getHideOverlay()) {
			Overlay overlay2 = overlay.crop(ip.getRoi());
 			if (imp.getStackSize()>1)
 				overlay2.crop(imp.getCurrentSlice(), imp.getCurrentSlice());
 			imp2.setOverlay(overlay2);
 		}
   		if (Recorder.record) {
   			if (imp.getStackSize()==1)
   				Recorder.recordCall("imp2 = imp.duplicate();");
   			else
   				Recorder.recordCall("imp2 = imp.crop();");
   		}
		return imp2;
	}
	
	/** Returns a new stack containing a subrange of the specified stack. */
	public ImagePlus run(ImagePlus imp, int firstSlice, int lastSlice) {
		Rectangle rect = null;
		Roi roi = imp.getRoi();
		if (roi!=null && roi.isArea())
			rect = roi.getBounds();
		ImageStack stack = imp.getStack();
		boolean virtualStack = stack.isVirtual();
		double min = imp.getDisplayRangeMin();
		double max = imp.getDisplayRangeMax();
		ImageStack stack2 = null;
		for (int i=firstSlice; i<=lastSlice; i++) {
			if (stack.isVirtual())
				IJ.showStatus("Duplicating: "+i+"/"+lastSlice);
			ImageProcessor ip2 = stack.getProcessor(i);
			ip2.setRoi(rect);
			ip2 = ip2.crop();
			if (stack2==null)
				stack2 = new ImageStack(ip2.getWidth(), ip2.getHeight(), imp.getProcessor().getColorModel());
			stack2.addSlice(stack.getSliceLabel(i), ip2);
		}
		ImagePlus imp2 = imp.createImagePlus();
		imp2.setStack("DUP_"+imp.getTitle(), stack2);
		String info = (String)imp.getProperty("Info");
		if (info!=null)
			imp2.setProperty("Info", info);
		int size = stack2.getSize();
		boolean tseries = imp.getNFrames()==imp.getStackSize();
		if (tseries)
			imp2.setDimensions(1, 1, size);
		else
			imp2.setDimensions(1, size, 1);
		if (virtualStack)
			imp2.setDisplayRange(min, max);
		Overlay overlay = imp.getOverlay();
		if (overlay!=null && !imp.getHideOverlay()) {
			Overlay overlay2 = overlay.crop(rect);
			overlay2.crop(firstSlice, lastSlice);
			imp2.setOverlay(overlay2);
		}
   		if (Recorder.record)
   			Recorder.recordCall("imp2 = new Duplicator().run(imp, "+firstSlice+", "+lastSlice+");");
		return imp2;
	}

	/** Returns a new hyperstack containing a possibly reduced version of the input image. */
	public ImagePlus run(ImagePlus imp, int firstC, int lastC, int firstZ, int lastZ, int firstT, int lastT) {
		Rectangle rect = null;
		Roi roi = imp.getRoi();
		Roi roi2 = cropRoi(imp, roi);
		if (roi2!=null && roi2.isArea())
			rect = roi2.getBounds();
		ImageStack stack = imp.getStack();
		ImageStack stack2 = null;
		for (int t=firstT; t<=lastT; t++) {
			for (int z=firstZ; z<=lastZ; z++) {
				for (int c=firstC; c<=lastC; c++) {
					int n1 = imp.getStackIndex(c, z, t);
					ImageProcessor ip = stack.getProcessor(n1);
					String label = stack.getSliceLabel(n1);
					ip.setRoi(rect);
					ip = ip.crop();
					if (stack2==null)
						stack2 = new ImageStack(ip.getWidth(), ip.getHeight(), null);
					stack2.addSlice(label, ip);
				}
			}
		}
		ImagePlus imp2 = imp.createImagePlus();
		imp2.setStack("DUP_"+imp.getTitle(), stack2);
		imp2.setDimensions(lastC-firstC+1, lastZ-firstZ+1, lastT-firstT+1);
		if (imp.isComposite()) {
			int mode = ((CompositeImage)imp).getMode();
			if (lastC>firstC) {
				imp2 = new CompositeImage(imp2, mode);
				int i2 = 1;
				for (int i=firstC; i<=lastC; i++) {
					LUT lut = ((CompositeImage)imp).getChannelLut(i);
					((CompositeImage)imp2).setChannelLut(lut, i2++);
				}
			} else if (firstC==lastC) {
				LUT lut = ((CompositeImage)imp).getChannelLut(firstC);
				imp2.getProcessor().setColorModel(lut);
				imp2.setDisplayRange(lut.min, lut.max);
			}
        }
		imp2.setOpenAsHyperStack(true);
		Calibration cal = imp2.getCalibration();
		if (roi!=null && (cal.xOrigin!=0.0||cal.yOrigin!=0.0)) {
			cal.xOrigin -= roi.getBounds().x;
			cal.yOrigin -= roi.getBounds().y;
		}
		Overlay overlay = imp.getOverlay();
		if (overlay!=null && !imp.getHideOverlay()) {
			Overlay overlay2 = overlay.crop(roi2!=null?roi2.getBounds():null);
			overlay2.crop(firstC, lastC, firstZ, lastZ, firstT, lastT);
			imp2.setOverlay(overlay2);
		}
   		if (Recorder.record)
   			Recorder.recordCall("imp2 = new Duplicator().run(imp, "+firstC+", "+lastC+", "+firstZ+", "+lastZ+", "+firstT+", "+lastT+");");
		return imp2;
	}

	String showDialog(ImagePlus imp, String dialogTitle, String prompt) {
		int stackSize = imp.getStackSize();
		String options = Macro.getOptions();
		boolean isMacro = options!=null;
		duplicateStack = stackSize>1 && duplicateStack && !isMacro;
		legacyMacro = options!=null && (options.contains("duplicate")||!options.contains("use"));
		String title = getNewTitle();
		if (title==null) title=defaultTitle;
		GenericDialog gd = new GenericDialog(dialogTitle);
		this.gd = gd;
		gd.addStringField(prompt, title, 15);
		if (stackSize>1) {
			gd.addCheckbox("Duplicate stack", duplicateStack);
			gd.setInsets(2, 30, 3);
			gd.addStringField("Range:", "1-"+stackSize);
			if (!isMacro) {
				checkbox = (Checkbox)(gd.getCheckboxes().elementAt(0));
				checkbox.addItemListener(this);
				Vector v = gd.getStringFields();
				titleField = (TextField)v.elementAt(0);
				rangeField = (TextField)v.elementAt(1);
				titleField.addTextListener(this);
				rangeField.addTextListener(this);
			}
		}
		gd.setSmartRecording(true);
		gd.showDialog();
		if (gd.wasCanceled())
			return null;
		title = gd.getNextString();
		if (stackSize>1) {
			duplicateStack = gd.getNextBoolean();
			if (duplicateStack) {
				String[] range = Tools.split(gd.getNextString(), " -");
				double d1 = gd.parseDouble(range[0]);
				double d2 = range.length==2?gd.parseDouble(range[1]):Double.NaN;
				first = Double.isNaN(d1)?1:(int)d1;
				last = Double.isNaN(d2)?stackSize:(int)d2;
				if (first<1) first = 1;
				if (last>stackSize) last = stackSize;
				if (first>last) {first=1; last=stackSize;}
			} else {
				first = 1;
				last = stackSize;
			}
		}
		if (!isMacro)
			staticDuplicateStack = duplicateStack;
		if (Recorder.record && titleField!=null && titleField.getText().equals(sliceLabel))
			Recorder.recordOption("use");
		return title;
	}
	
	private String getNewTitle() {
		if (titleChanged)
			return null;
		String title = defaultTitle;
		if (imp.getStackSize()>1 && !duplicateStack && !legacyMacro && (checkbox==null||!checkbox.getState())) {
			ImageStack stack = imp.getStack();
			String label = stack.getShortSliceLabel(imp.getCurrentSlice());
			if (label!=null && label.length()==0)
				label = null;
			if (label!=null) {
				title = label;
				sliceLabel = label;
			}
		}
		return title;
	}
	
	void duplicateHyperstack(ImagePlus imp, String newTitle) {
		newTitle = showHSDialog(imp, newTitle);
		if (newTitle==null)
			return;
		ImagePlus imp2 = null;
		Roi roi = imp.getRoi();
		if (!duplicateStack) {
			int nChannels = imp.getNChannels();
			boolean singleComposite = imp.isComposite() && nChannels==imp.getStackSize();
			if (!singleComposite && nChannels>1 && imp.isComposite() && ((CompositeImage)imp).getMode()==IJ.COMPOSITE) {
				firstC = 1;
				lastC = nChannels;
			} else
				firstC = lastC = imp.getChannel();
			firstZ = lastZ = imp.getSlice();
			firstT = lastT = imp.getFrame();
		}
		imp2 = run(imp, firstC, lastC, firstZ, lastZ, firstT, lastT);
		if (imp2==null) return;
		imp2.setTitle(newTitle);
		if (imp2.getWidth()==0 || imp2.getHeight()==0) {
			IJ.error("Duplicator", "Selection is outside the image");
			return;
		}
		if (roi!=null && roi.isArea() && roi.getType()!=Roi.RECTANGLE) {
			Roi roi2 = (Roi)cropRoi(imp, roi).clone();
			roi2.setLocation(0, 0);
			imp2.setRoi(roi2);
		}
		imp2.show();
		imp2.setPosition(imp.getC(), imp.getZ(), imp.getT());
		if (IJ.isMacro()&&imp2.getWindow()!=null)
			IJ.wait(50);
	}

	String showHSDialog(ImagePlus imp, String newTitle) {
		int nChannels = imp.getNChannels();
		int nSlices = imp.getNSlices();
		int nFrames = imp.getNFrames();
		boolean composite = imp.isComposite() && nChannels==imp.getStackSize();
		String options = Macro.getOptions();
		boolean isMacro = options!=null;
		GenericDialog gd = new GenericDialog("Duplicate");
		gd.addStringField("Title:", newTitle, 15);
		gd.setInsets(12, 20, 8);
		gd.addCheckbox("Duplicate hyperstack", (duplicateStack&&!isMacro)||composite);
		int nRangeFields = 0;
		if (nChannels>1) {
			gd.setInsets(2, 30, 3);
			gd.addStringField("Channels (c):", "1-"+nChannels);
			nRangeFields++;
		}
		if (nSlices>1) {
			gd.setInsets(2, 30, 3);
			gd.addStringField("Slices (z):", "1-"+nSlices);
			nRangeFields++;
		}
		if (nFrames>1) {
			gd.setInsets(2, 30, 3);
			gd.addStringField("Frames (t):", "1-"+nFrames);
			nRangeFields++;
		}
		if (!isMacro) {
			checkbox = (Checkbox)(gd.getCheckboxes().elementAt(0));
			checkbox.addItemListener(this);
			Vector v = gd.getStringFields();
			rangeFields = new TextField[3];
			for (int i=0; i1) {
			String[] range = Tools.split(gd.getNextString(), " -");
			double c1 = gd.parseDouble(range[0]);
			double c2 = range.length==2?gd.parseDouble(range[1]):Double.NaN;
			firstC = Double.isNaN(c1)?1:(int)c1;
			lastC = Double.isNaN(c2)?firstC:(int)c2;
			if (firstC<1) firstC = 1;
			if (lastC>nChannels) lastC = nChannels;
			if (firstC>lastC) {firstC=1; lastC=nChannels;}
		} else
			firstC = lastC = 1;
		if (nSlices>1) {
			String[] range = Tools.split(gd.getNextString(), " -");
			double z1 = gd.parseDouble(range[0]);
			double z2 = range.length==2?gd.parseDouble(range[1]):Double.NaN;
			firstZ = Double.isNaN(z1)?1:(int)z1;
			lastZ = Double.isNaN(z2)?firstZ:(int)z2;
			if (firstZ<1) firstZ = 1;
			if (lastZ>nSlices) lastZ = nSlices;
			if (firstZ>lastZ) {firstZ=1; lastZ=nSlices;}
		} else
			firstZ = lastZ = 1;
		if (nFrames>1) {
			String[] range = Tools.split(gd.getNextString(), " -");
			double t1 = gd.parseDouble(range[0]);
			double t2 = range.length==2?gd.parseDouble(range[1]):Double.NaN;
			firstT= Double.isNaN(t1)?1:(int)t1;
			lastT = Double.isNaN(t2)?firstT:(int)t2;
			if (firstT<1) firstT = 1;
			if (lastT>nFrames) lastT = nFrames;
			if (firstT>lastT) {firstT=1; lastT=nFrames;}
		} else
			firstT = lastT = 1;
		if (!isMacro)
			staticDuplicateStack = duplicateStack;
		return newTitle;
	}
	
	/*
	* Returns the part of 'roi' overlaping 'imp'
	* Author Marcel Boeglin 2013.12.15
	*/
	Roi cropRoi(ImagePlus imp, Roi roi) {
		if (roi==null)
			return null;
		if (imp==null)
			return roi;
		Rectangle b = roi.getBounds();
		int w = imp.getWidth();
		int h = imp.getHeight();
		if (b.x<0 || b.y<0 || b.x+b.width>w || b.y+b.height>h) {
			ShapeRoi shape1 = new ShapeRoi(roi);
			ShapeRoi shape2 = new ShapeRoi(new Roi(0, 0, w, h));
			roi = shape2.and(shape1);
		}
		if (roi.getBounds().width==0 || roi.getBounds().height==0)
			throw new IllegalArgumentException("Selection is outside the image");
		return roi;
	}

	public static Overlay cropOverlay(Overlay overlay, Rectangle bounds) {
		return overlay.crop(bounds);
	}

	public void textValueChanged(TextEvent e) {
		if (IJ.debugMode) IJ.log("Duplicator.textValueChanged: "+e);
		if (e.getSource()==titleField) {
			if (!titleField.getText().equals(getNewTitle()))
				titleChanged = true;
		} else
			checkbox.setState(true);
	}
	
	public void itemStateChanged(ItemEvent e) {
		duplicateStack = checkbox.getState();
		if (titleField!=null) {
			String title = getNewTitle();
			if (title!=null && !title.equals(titleField.getText())) {
				titleField.setText(title);
				if (gd!=null) gd.setDefaultString(0, title);
			}
		}
	}

	
}