Java Code Examples for java.awt.geom.Area#createTransformedArea()

@Override
   synchronized public boolean apply(final Layer la, final Area roi, final mpicbg.models.CoordinateTransform ict) throws Exception {
	double[] fp = null;
	mpicbg.models.CoordinateTransform chain = null;
	Area localroi = null;
	AffineTransform inverse = null;
	for (int i=0; i<n_points; i++) {
		if (p_layer[i] == la.getId()) {
			if (null == localroi) {
				inverse = this.at.createInverse();
				localroi = roi.createTransformedArea(inverse);
			}
			if (localroi.contains(p[0][i], p[1][i])) {
				if (null == chain) {
					chain = M.wrap(this.at, ict, inverse);
					fp = new double[2];
				}
				M.apply(chain, p, i, fp);
			}
		}
	}
	if (null != chain) calculateBoundingBox(true, la); // may be called way too many times, but avoids lots of headaches.
	return true;
}
 

@Override
public boolean apply(final Layer la, final Area roi, final mpicbg.models.CoordinateTransform ict) throws Exception {
	mpicbg.models.CoordinateTransform chain = null;
	synchronized (node_layer_map) {
		if (null == root) return true;
		final Set<Node<T>> nodes = node_layer_map.get(la);
		if (null == nodes || nodes.isEmpty()) return true;
		final AffineTransform inverse = this.at.createInverse();
		final Area localroi = roi.createTransformedArea(inverse);
		for (final Node<T> nd : nodes) {
			if (nd.intersects(localroi)) {
				if (null == chain) {
					chain = M.wrap(this.at, ict, inverse);
				}
			}
			nd.apply(chain, roi);
		}
	}
	if (null != chain) calculateBoundingBox(la);
	return true;
}
 

/** Subtracts the given ROI, and then creates a new AreaList with identical properties and the content of the subtracted part. Returns null if there is no intersection between sroi and the Area for layer_id. */
public AreaList part(final long layer_id, final ShapeRoi sroi) throws NoninvertibleTransformException {
	// The Area to subtract, in world coordinates:
	final Area sub = M.getArea(sroi);
	// The area to subtract from:
	final Area a = getArea(layer_id);
	if (null == a || M.isEmpty(a)) return null;
	// The intersection:
	final Area inter = a.createTransformedArea(this.at);
	inter.intersect(sub);
	if (M.isEmpty(inter)) return null;

	// Subtract from this:
	this.subtract(layer_id, sroi);

	// Create new AreaList with the intersection area, and add it to the same LayerSet as this:
	final AreaList ali = new AreaList(this.project, this.title, 0, 0);
	ali.color = new Color(color.getRed(), color.getGreen(), color.getBlue());
	ali.visible = this.visible;
	ali.alpha = this.alpha;
	ali.addArea(layer_id, inter);
	this.layer_set.add(ali); // needed to call updateBucket
	ali.calculateBoundingBox(null != layer_set ? layer_set.getLayer(layer_id) : null);

	return ali;
}
 

/** For each area that ali contains, add it to the corresponding area here.*/
private void add(final AreaList ali) {
	for (final Map.Entry<Long,Area> entry : ali.ht_areas.entrySet()) {
		Area ob_area = entry.getValue();
		final long lid = entry.getKey();
		if (UNLOADED == ob_area) ob_area = ali.loadLayer(lid);
		Area area = (Area)ob_area;
		area = area.createTransformedArea(ali.at);
		// now need to inverse transform it by this.at
		try {
			area = area.createTransformedArea(this.at.createInverse());
		} catch (final NoninvertibleTransformException nte) {
			IJError.print(nte);
			// do what?
		}
		Object this_area = this.ht_areas.get(entry.getKey());
		if (UNLOADED == this_area) { this_area = loadLayer(lid); }
		if (null == this_area) this.ht_areas.put(entry.getKey(), (Area)area.clone());
		else ((Area)this_area).add(area);
		updateInDatabase("points=" + ((Long)entry.getKey()).intValue());
	}
}
 

@Override
   synchronized public boolean apply(final Layer la, final Area roi, final mpicbg.models.CoordinateTransform ict) throws Exception {
	if (this.layer != la) return true;
	double[] fp = null;
	mpicbg.models.CoordinateTransform chain = null;
	Area localroi = null;
	AffineTransform inverse = null;
	for (int i=0; i<n_points; i++) {
		if (null == localroi) {
			inverse = this.at.createInverse();
			localroi = roi.createTransformedArea(inverse);
		}
		if (localroi.contains(p[0][i], p[1][i])) {
			if (null == chain) {
				chain = M.wrap(this.at, ict, inverse);
				fp = new double[2];
			}
			// The point and its two associated control points:
			M.apply(chain, p, i, fp);
			M.apply(chain, p_l, i, fp);
			M.apply(chain, p_r, i, fp);
		}
	}
	if (null != chain) {
		generateInterpolatedPoints(0.05);
		calculateBoundingBox(true);
	}
	return true;
}
 

/** Returns the approximated area of the given Area object; Loader can be null; if not, it's used to secure memory space. */
static public final double measureArea(Area area, final Loader loader) {
	double sum = 0;
	try {
		Rectangle bounds = area.getBounds();
		double scale = 1;
		if (bounds.width > 2048 || bounds.height > 2048) { // TODO value 2048 should be reconsidered as a project property
			scale = 2048.0 / bounds.width;
		}
		if (0 == scale) {
			Utils.log("Can't measure: area too large, out of scale range for approximation.");
			return sum;
		}
		final AffineTransform at = new AffineTransform();
		at.translate(-bounds.x, -bounds.y);
		at.scale(scale, scale);
		area = area.createTransformedArea(at);
		bounds = area.getBounds();
		if (0 == bounds.width || 0 == bounds.height) {
			Utils.log("Can't measure: area too large, approximates zero.");
			return sum;
		}
		if (null != loader) loader.releaseToFit(bounds.width * bounds.height * 3);
		final BufferedImage bi = new BufferedImage(bounds.width, bounds.height, BufferedImage.TYPE_BYTE_INDEXED);
		final Graphics2D g = bi.createGraphics();
		g.setColor(Color.white);
		g.fill(area);
		final byte[] pixels = ((DataBufferByte)bi.getRaster().getDataBuffer()).getData(); // buffer.getData();
		for (int i=pixels.length-1; i>-1; i--) {
			//if (255 == (pixels[i]&0xff)) sum++;
			if (0 != pixels[i]) sum++;
		}
		bi.flush();
		g.dispose();
		if (1 != scale) sum = sum / (scale * scale);
	} catch (final Throwable e) {
		IJError.print(e);
	}
	return sum;
}
 

@Override
public boolean apply(final Layer la, final Area roi, final mpicbg.models.CoordinateTransform ict) throws Exception {
	double[] fp = null;
	mpicbg.models.CoordinateTransform chain = null;
	Area localroi = null;
	AffineTransform inverse = null;
	for (final Item item : al_items) {
		final long[] p_layer = item.p_layer;
		final double[][] p = item.p;
		for (int i=0; i<item.n_points; i++) {
			if (p_layer[i] == la.getId()) {
				if (null == localroi) {
					inverse = this.at.createInverse();
					localroi = roi.createTransformedArea(inverse);
				}
				if (localroi.contains(p[0][i], p[1][i])) {
					if (null == chain) {
						chain = M.wrap(this.at, ict, inverse);
						fp = new double[2];
					}
					// Transform the point
					M.apply(chain, p, i, fp);
				}
			}
		}
	}
	if (null != chain) calculateBoundingBox(la);
	return true;
}
 

@Override
public boolean intersects(final Area area, final double z_first, final double z_last) {
	Area ai;
	try {
		ai = area.createTransformedArea(this.at.createInverse());
	} catch (final NoninvertibleTransformException nite) {
		nite.printStackTrace();
		return false;
	}
	for (final Item item : al_items) {
		if (item.intersects(ai, z_first, z_last)) return true;
	}
	return false;
}
 

/** In world coordinates, a copy of the area at {@code layer}. May be null. */
@Override
public Area getAreaAt(final Layer layer) {
	final Area a = getArea(layer);
	if (null == a) return null;
	return a.createTransformedArea(this.at);
}
 

/** Returns whether the point x,y is contained in this object at the given Layer. */
@Override
public boolean contains(final Layer layer, final double x, final double y) {
	Object ob = ht_areas.get(new Long(layer.getId()));
	if (null == ob) return false;
	if (AreaList.UNLOADED == ob) {
		ob = loadLayer(layer.getId());
		if (null == ob) return false;
	}
	Area area = (Area)ob;
	if (!this.at.isIdentity()) area = area.createTransformedArea(this.at);
	return area.contains(x, y);
}
 

@Override
public Collection<Displayable> findLinkTargets(final AffineTransform aff) {
	if (null == aw) return super.findLinkTargets(aff);
	Area a = aw.getArea();
	if (!aff.isIdentity()) {
		a = a.createTransformedArea(aff);
	}
	return this.la.getDisplayables(Patch.class, a, true);
}
 

@Override
   synchronized public boolean apply(final Layer la, final Area roi, final mpicbg.models.CoordinateTransform ict) throws Exception {
	double[] fp = new double[2];
	mpicbg.models.CoordinateTransform chain = null;
	Area localroi = null;
	AffineTransform inverse = null;
	for (int i=0; i<n_points; i++) {
		if (p_layer[i] == la.getId()) {
			if (null == localroi) {
				inverse = this.at.createInverse();
				localroi = roi.createTransformedArea(inverse);
			}
			if (localroi.contains(p[0][i], p[1][i])) {
				if (null == chain) {
					chain = M.wrap(this.at, ict, inverse);
					fp = new double[2];
				}
				// Keep point copy
				final double ox = p[0][i],
				       oy = p[1][i];
				// Transform the point
				M.apply(chain, p, i, fp);
				// For radius, assume it's a point to the right of the center point
				fp[0] = ox + p_width[i];
				fp[1] = oy;
				chain.applyInPlace(fp);
				p_width[i] = Math.abs(fp[0] - p[0][i]);
				// The two associated control points:
				M.apply(chain, p_l, i, fp);
				M.apply(chain, p_r, i, fp);
			}
		}
	}
	if (null != chain) {
		generateInterpolatedPoints(0.05);
		calculateBoundingBox(true, la);
	}
	return true;
}
 

/** This method could get tones of improvement, which should be pumped upstream into ImageJ's RoiBrush class which is creating it at every while(true) {} iteration!!!
 * The returned area has its coordinates centered around 0,0
 */
static public Area makeBrush(int diameter, double mag) {
	if (diameter < 1) return null;
	if (mag >= 1) return new Area(new OvalRoi(-diameter/2, -diameter/2, diameter, diameter).getPolygon());
	// else, create a smaller brush and transform it up, i.e. less precise, less points to store -but precision matches what the eye sees, and allows for much better storage -less points.
	int screen_diameter = (int)(diameter * mag);
	if (0 == screen_diameter) return null; // can't paint at this mag with this diameter

	Area brush = new Area(new OvalRoi(-screen_diameter/2, -screen_diameter/2, screen_diameter, screen_diameter).getPolygon());
	// scale to world coordinates
	AffineTransform at = new AffineTransform();
	at.scale(1/mag, 1/mag);
	return brush.createTransformedArea(at);


	// smooth out edges
	/*
	Polygon pol = new OvalRoi(-diameter/2, -diameter/2, diameter, diameter).getPolygon();
	Polygon pol2 = new Polygon();
	// cheap and fast: skip every other point, since all will be square angles
	for (int i=0; i<pol.npoints; i+=2) {
		pol2.addPoint(pol.xpoints[i], pol.ypoints[i]);
	}
	return new Area(pol2);
	// the above works nice, but then the fill and fill-remove don't work properly (there are traces in the edges)
	// Needs a workround: before adding/substracting, enlarge the polygon to have square edges
	*/
}
 

static public Area makeMouseBrush(int diameter, double mag) {
	Display front = Display.getFront();
	Area brush = makeBrush(diameter, mag);
	if (null == front) return brush;
	Point p = front.getCanvas().getCursorLoc();
	return brush.createTransformedArea(new AffineTransform(1, 0, 0, 1, p.x, p.y));
}
 

@Override
   synchronized public boolean apply(final Layer la, final Area roi, final mpicbg.models.CoordinateTransform ict) throws Exception {
	double[] fp = null;
	mpicbg.models.CoordinateTransform chain = null;
	Area localroi = null;
	AffineTransform inverse = null;
	for (int i=0; i<n_points; i++) {
		if (p_layer[i] == la.getId()) {
			if (null == localroi) {
				inverse = this.at.createInverse();
				localroi = roi.createTransformedArea(inverse);
			}
			if (localroi.contains(p[0][i], p[1][i])) {
				if (null == chain) {
					chain = M.wrap(this.at, ict, inverse);
					fp = new double[2];
				}
				// Keep point copy
				final double ox = p[0][i],
				       oy = p[1][i];
				// Transform the point
				M.apply(chain, p, i, fp);
				// For radius, assume it's a point to the right of the center point
				fp[0] = (float)(ox + p_width[i]);
				fp[1] = (float)oy;
				chain.applyInPlace(fp);
				p_width[i] = Math.abs(fp[0] - p[0][i]);
			}
		}
	}
	if (null != chain) calculateBoundingBox(true, la); // may be called way too many times, but avoids lots of headaches.
	return true;
}
 

/** Find the nearest parent with a non-null, non-empty Area, and interpolate from {@code nd} to it.
 *
 * @param nd The node to start interpolating from, towards its nearest parent with an area.
 * @param node_centric If true, consider areas relative to the node coordinates. If false, relative to the overall AreaTree.
 *
 * @throws Exception */
public boolean interpolateTowardsParent(final Node<Area> nd, final boolean node_centric, final boolean always_use_distance_map) throws Exception {
	if (null == nd || null == nd.parent) return false;
	Area first = nd.getData();
	if (null == first || first.isEmpty()) {
		return false;
	}
	final LinkedList<Node<Area>> chain = new LinkedList<Node<Area>>();
	Node<Area> p = nd.parent;
	while (null != p && (null == p.getData() || p.getData().isEmpty())) {
		chain.add(p);
		p = p.parent;
	}
	if (p == nd.parent) {
		// Nothing to interpolate
		return false;
	}

	Area last = p.getData();

	int minx = 0, miny = 0;
	if (node_centric) {
		// Make areas relative to the nodes:
		first = first.createTransformedArea(new AffineTransform(1, 0, 0, 1, -nd.x, -nd.y));
		last = last.createTransformedArea(new AffineTransform(1, 0, 0, 1, -p.x, -p.y));
		// Remove translations
		final Rectangle bfirst = first.getBounds();
		final Rectangle blast = last.getBounds();
		minx = Math.min(bfirst.x, blast.x);
		miny = Math.min(bfirst.y, blast.y);
		final AffineTransform rmtrans = new AffineTransform(1, 0, 0, 1, -minx, -miny);
		first = first.createTransformedArea(rmtrans);
		last = last.createTransformedArea(rmtrans);
	}
	// Interpolate
	final Area[] as;
	if (!always_use_distance_map && first.isSingular() && last.isSingular()) {
		as = AreaUtils.singularInterpolation(first, last, chain.size());
	} else {
		as = AreaUtils.manyToManyInterpolation(first, last, chain.size());
	}
	// Assign each area
	for (final Area interpolated : as) {
		final Node<Area> target = chain.removeFirst();
		if (node_centric) {
			interpolated.transform(new AffineTransform(1, 0, 0, 1, minx + target.x, miny + target.y));
		}
		target.setData(interpolated);
	}

	return true;
}
 

/** Returns a stack of images representing the pixel data of this LayerSet inside this AreaList. */
public ImagePlus getStack(final int type, final double scale) {
	final ImageProcessor ref_ip = Utils.createProcessor(type, 2, 2);
	if (null == ref_ip) {
		Utils.log("AreaList.getStack: Unknown type " + type);
		return null;
	}
	final Rectangle b = getBoundingBox();
	final int w = (int)(0.5 + b.width * scale);
	final int h = (int)(0.5 + b.height * scale);
	final ImageStack stack = new ImageStack(w, h);
	for (final Layer la : getLayerRange()) {
		final Area area = getArea(la);
		final double z = layer.getZ();
		project.getLoader().releaseToFit(w * h * 10);
		final ImageProcessor ip = ref_ip.createProcessor(w, h);
		if (null == area) {
			stack.addSlice(Double.toString(z), ip);
			continue;
		}
		// Create a ROI from the area at Layer la:
		final AffineTransform aff = getAffineTransformCopy();
		aff.translate(-b.x, -b.y);
		aff.scale(scale, scale);
		final ShapeRoi roi = new ShapeRoi(area.createTransformedArea(aff));
		// Create a cropped snapshot of the images at Layer la under the area:
		final ImageProcessor flat = Patch.makeFlatImage(type, la, b, scale, la.getAll(Patch.class), Color.black);
		flat.setRoi(roi);
		final Rectangle rb = roi.getBounds();
		ip.insert(flat.crop(), rb.x, rb.y);
		// Clear the outside
		final ImagePlus bimp = new ImagePlus("", ip);
		bimp.setRoi(roi);
		ip.setValue(0);
		ip.setBackgroundValue(0);
		IJ.run(bimp, "Clear Outside", "");

		stack.addSlice(Double.toString(z), ip);
	}

	final ImagePlus imp = new ImagePlus("AreaList stack for " + this, stack);
	imp.setCalibration(layer_set.getCalibrationCopy());
	return imp;
}