Java Code Examples for ij.gui.Roi#getBounds()

public void moveBlow(int dx, int dy) throws Exception {
	int x = box.width/2 + dx;
	int y = box.height/2 + dy;
	// Keep within bounds
	if (x < 0) x = 0;
	if (y < 0) y = 0;
	if (x > box.width -1) x = box.width -1;
	if (y > box.height -1) y = box.height -1;
	lasso.moveBlow(x, y);
	// extract ROI
	Roi roi = imp.getRoi();
	if (null == roi) Display.getFront().getCanvas().getFakeImagePlus().setRoi(roi); // can't set to null? Java, gimme a break
	else {
		Roi sroi = new ShapeRoi(roi);
		Rectangle b = sroi.getBounds();
		sroi.setLocation(box.x + b.x, box.y + b.y);
		Display.getFront().getCanvas().getFakeImagePlus().setRoi(sroi);
	}
}
 

@Override
public < T> T convert(Object o, Class< T> type) {
Roi r =(Roi)o; 
    Rectangle r1 = r.getBounds();
    opencv_core.Rect2f rect = new opencv_core.Rect2f(r1.x, r1.y, r1.width, r1.height);
    return (T)rect;
}
 

@Override
public < T> T convert(Object o, Class< T> type) {
Roi r =(Roi)o; 
    Rectangle r1 = r.getBounds();
    opencv_core.Rect2d rect = new opencv_core.Rect2d(r1.x, r1.y, r1.width, r1.height);
    return (T)rect;
}
 

@Override
public < T> T convert(Object o, Class< T> type) {
    Roi r =(Roi)o; 
    Rectangle r1 = r.getBounds();
    Rect rect = new Rect(r1.x, r1.y, r1.width, r1.height);
    return (T)rect;
}
 

public void restrictToROIFilter() {
    double mag = new EmptyRendererUI().magnification.getValue();
    IJResultsTable rt = IJResultsTable.getResultsTable();
    ImagePlus preview = rt.getPreviewImage();
    Roi roi2 = null;
    if(preview != null) {
        roi2 = preview.getRoi();
    }
    if(roi2 == null) {
        GUI.showBalloonTip(restrictToROIButton, "There is no ROI in the preview image!");
        return;
    }
    Rectangle2D[] rectangleList;
    if(roi2 instanceof ShapeRoi) {
        ShapeRoi shapeRoi = (ShapeRoi) roi2;
        Roi[] roiList = shapeRoi.getRois();
        rectangleList = new Rectangle2D[roiList.length];
        for(int i = 0; i < roiList.length; i++) {
            rectangleList[i] = roiList[i].getBounds();
        }
    } else {
        rectangleList = new Rectangle2D[]{roi2.getBounds()};
    }
    Units ux = rt.getColumnUnits(LABEL_X);
    Units uy = rt.getColumnUnits(LABEL_Y);
    //
    for(int i = 0; i < rectangleList.length; i++) {
        rectangleList[i] = convertRectangleUnits(rectangleList[i], ux, uy, mag);
    }
    addNewRectanglesFilter(rectangleList);
}
 

/**
 * Returns true if a custom ROI has been selected, i.e if the current ROI does
 * not have the extent of the whole image.
 * 
 * @return true if custom ROI selected, false otherwise
 */
protected boolean hasValidRoi(final ImagePlus imp) {
	final Roi roi = imp.getRoi();
	if (roi == null) return false;

	final Rectangle theROI = roi.getBounds();

	// if the ROI is the same size as the image (default ROI), return false
	return (theROI.height != imp.getHeight() || theROI.width != imp.getWidth());
}
 

/**
 * Creates appropriate data structures from the ROI information
 * passed. If an irregular ROI is found, it will be put into a
 * frame of its bounding box size and put into an {@code Image<T>}.
 *
 * In the end the members ROIs, masks and maskBBs will be
 * filled if ROIs or masks were found. They will be null
 * otherwise.
 */
protected void createMasksAndRois(final Roi[] rois, final int width,
	final int height)
{
	// create empty list
	masks.clear();

	for (final Roi r : rois) {
		final MaskInfo mi = new MaskInfo();
		// add it to the list of masks/ROIs
		masks.add(mi);
		// get the ROIs/masks bounding box
		final Rectangle rect = r.getBounds();
		mi.roi = new BoundingBox(new long[] { rect.x, rect.y }, new long[] {
			rect.width, rect.height });
		final ImageProcessor ipMask = r.getMask();
		// check if we got a regular ROI and return if so
		if (ipMask == null) {
			continue;
		}

		// create a mask processor of the same size as a slice
		final ImageProcessor ipSlice = ipMask.createProcessor(width, height);
		// fill the new slice with black
		ipSlice.setValue(0.0);
		ipSlice.fill();
		// position the mask on the new mask processor
		ipSlice.copyBits(ipMask, (int) mi.roi.offset[0], (int) mi.roi.offset[1],
			Blitter.COPY);
		// create an Image<T> out of it
		final ImagePlus maskImp = new ImagePlus("Mask", ipSlice);
		// and remember it and the masks bounding box
		mi.mask = ImagePlusAdapter.<T> wrap(maskImp);
	}
}
 

public ImageStatistics getStatistics(int mOptions, int nBins, double histMin, double histMax) {
	Displayable active = display.getActive();
	if (null == active || !(active instanceof Patch)) {
		Utils.log("No patch selected.");
		return super.getStatistics(mOptions, nBins, histMin, histMax); // TODO can't return null, but something should be done about it.
	}
	ImagePlus imp = active.getProject().getLoader().fetchImagePlus((Patch)active);
	ImageProcessor ip = imp.getProcessor(); // don't create a new onw every time // ((Patch)active).getProcessor();
	Roi roi = super.getRoi();
	if (null != roi) {
		// translate ROI to be meaningful for the Patch
		int patch_x = (int)active.getX();
		int patch_y = (int)active.getY();
		Rectangle r = roi.getBounds();
		roi.setLocation(patch_x - r.x, patch_y - r.y);
	}
	ip.setRoi(roi); // even if null, to reset
	ip.setHistogramSize(nBins);
	Calibration cal = getCalibration();
	if (getType()==GRAY16&& !(histMin==0.0&&histMax==0.0))
		{histMin=cal.getRawValue(histMin); histMax=cal.getRawValue(histMax);}
	ip.setHistogramRange(histMin, histMax);
	ImageStatistics stats = ImageStatistics.getStatistics(ip, mOptions, cal);
	ip.setHistogramSize(256);
	ip.setHistogramRange(0.0, 0.0);
	return stats;
}
 

private static Rectangle getRoi( final LayerSet layerset )
{
	final Roi roi;
	final Display front = Display.getFront();
	if ( front == null )
		roi = null;
	else
		roi = front.getRoi();
	if ( roi == null )
		return new Rectangle( 0, 0, ( int ) layerset.getLayerWidth(), ( int ) layerset.getLayerHeight() );
	else
		return roi.getBounds();
}
 

public int showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr) {
	if (filterType == DESPECKLE) {
		filterType = MEDIAN;
		radius = 1.0;
	} else {
		GenericDialog gd = new GenericDialog(command+"...");
		radius = lastRadius[filterType]<=0 ? 2 :  lastRadius[filterType];
		gd.addNumericField("Radius", radius, 1, 6, "pixels");
		int digits = imp.getType() == ImagePlus.GRAY32 ? 2 : 0;
		if (filterType==OUTLIERS) {
			gd.addNumericField("Threshold", lastThreshold, digits);
			gd.addChoice("Which outliers", outlierStrings, outlierStrings[lastWhichOutliers]);
			gd.addHelp(IJ.URL+"/docs/menus/process.html#outliers");
		} else if (filterType==REMOVE_NAN)
			gd.addHelp(IJ.URL+"/docs/menus/process.html#nans");
		gd.addPreviewCheckbox(pfr);		//passing pfr makes the filter ready for preview
		gd.addDialogListener(this);		//the DialogItemChanged method will be called on user input
		gd.showDialog();				//display the dialog; preview runs in the  now
		if (gd.wasCanceled()) return DONE;
		IJ.register(this.getClass());	//protect static class variables (filter parameters) from garbage collection
		if (Macro.getOptions() == null) { //interactive only: remember parameters entered
			lastRadius[filterType] = radius;
			if (filterType == OUTLIERS) {
				lastThreshold = threshold;
				lastWhichOutliers = whichOutliers;
			}
		}
	}
	this.pfr = pfr;
	flags = IJ.setupDialog(imp, flags); //ask whether to process all slices of stack (if a stack)
	if ((flags&DOES_STACKS)!=0) {
		int size = imp.getWidth() * imp.getHeight();
		Roi roi = imp.getRoi();
		if (roi != null) {
			Rectangle roiRect = roi.getBounds();
			size = roiRect.width * roiRect.height;
		}
		double workToDo = size*(double)radius;	//estimate computing time (arb. units)
		if (filterType==MEAN || filterType==VARIANCE) workToDo *= 0.5;
		else if (filterType==MEDIAN) workToDo *= radius*0.5;
		if (workToDo < 1e6 && imp.getImageStackSize()>=numThreads) {
			numThreads = 1;				//for fast operations, avoid overhead of multi-threading in each image
			flags |= PARALLELIZE_STACKS;
		}
	}
	return flags;
}
 

/**
 * return an {@code Image<T>} as input for the PhaseCorrelation.
 * 
 * @param imp - the {@link ImagePlus}
 * @param imgFactory - the {@link ImageFactory} defining wher to put it into
 * @param channel - which channel (if channel=0 means average all channels)
 * @param timepoint - which timepoint
 * 
 * @return - the {@link Image} or null if it was not an ImagePlus.GRAY8, ImagePlus.GRAY16 or ImagePlus.GRAY32
 */
public static < T extends RealType<T> > Image<T> getImage( final ImagePlus imp, Roi roi, final ImageFactory<T> imgFactory, final int channel, final int timepoint )
{
	// first test the roi
	roi = getOnlyRectangularRoi( roi );
	
	// how many dimensions?
	final int numDimensions;		
	if ( imp.getNSlices() > 1 )
		numDimensions = 3;
	else
		numDimensions = 2;
	
	// the size of the image
	final int[] size = new int[ numDimensions ];
	final int[] offset = new int[ numDimensions ];
	
	if ( roi == null )
	{
		size[ 0 ] = imp.getWidth();
		size[ 1 ] = imp.getHeight();
		
		if ( numDimensions == 3 )
			size[ 2 ] = imp.getNSlices();
	}
	else
	{
		size[ 0 ] = roi.getBounds().width;
		size[ 1 ] = roi.getBounds().height;

		offset[ 0 ] = roi.getBounds().x;
		offset[ 1 ] = roi.getBounds().y;
		
		if ( numDimensions == 3 )
			size[ 2 ] = imp.getNSlices();
	}
	
	// create the Image
	final Image<T> img = imgFactory.createImage( size );
	final boolean success;
	
	// copy the content
	if ( channel == 0 )
	{
		// we need to average all channels
		success = averageAllChannels( img, offset, imp, timepoint );
	}
	else
	{
		// otherwise only copy one channel
		success = fillInChannel( img, offset, imp, channel, timepoint );
	}
	
	if ( success )
	{
		return img;
	}
	img.close();
	return null;
}