org.scijava.vecmath.Color3f Java Examples

public Content addDiscsTo3DViewer(final Image3DUniverse univ, final Color3f c, final ImagePlus colorImage) {
	if (!hasCircles())
		return null;

	final Color3f[] originalColors = Pipe.getPointColors(precise_x_positions, precise_y_positions,
			precise_z_positions, c, colorImage);

	final List<Color3f> meshColors = new ArrayList<>();

	final int edges = 8;
	final List<Point3f> allTriangles = new ArrayList<>(edges * points);
	for (int i = 0; i < points; ++i) {
		final List<Point3f> discMesh = customnode.MeshMaker.createDisc(precise_x_positions[i],
				precise_y_positions[i], precise_z_positions[i], tangents_x[i], tangents_y[i], tangents_z[i],
				radiuses[i], 8);
		final int pointsInDiscMesh = discMesh.size();
		for (int j = 0; j < pointsInDiscMesh; ++j)
			meshColors.add(originalColors[i]);
		allTriangles.addAll(discMesh);
	}
	return univ.addTriangleMesh(allTriangles, meshColors, univ.getSafeContentName("Discs for path " + getName()));
}
 

public Content asContent(final Display3D d3d) {
	double[] wi = widths;
	if (null == widths) {
		wi = new double[vs.getPoints(0).length];
		Arrays.fill(wi, 2.0);
	} else if (widths.length != vs.length()) {
		Utils.log("ERROR: widths.length != VectorString3D.length()");
		return null;
	}
	float transp = 1 - alpha;
	if (transp < 0) transp = 0;
	if (transp > 1) transp = 1;
	if (1 == transp) {
		Utils.log("WARNING: adding a 3D object fully transparent.");
	}
	final List<Point3f> triangles = Pipe.generateTriangles(Pipe.makeTube(vs.getPoints(0), vs.getPoints(1), vs.getPoints(2), wi, 1, 12, null), d3d.scale);
	final Content ct = d3d.universe.createContent(new CustomTriangleMesh(triangles, new Color3f(color), 0), title);
	ct.setTransparency(transp);
	ct.setLocked(true);
	return ct;
}
 

public MeshData generateMesh(final double scale, final int resample) {
	final HashMap<Layer,Area> areas = new HashMap<Layer,Area>();
	synchronized (node_layer_map) {
		for (final Map.Entry<Layer,Set<Node<Area>>> e : node_layer_map.entrySet()) {
			final Area a = new Area();
			for (final AreaNode nd : (Collection<AreaNode>) (Collection) e.getValue()) {
				if (null != nd.aw) a.add(nd.aw.getArea());
			}
			areas.put(e.getKey(), a);
		}
	}
	final List<Point3f> ps = AreaUtils.generateTriangles(this, scale, resample, areas);

	final List<Color3f> colors = new ArrayList<Color3f>();
	// Determine colors by proximity to a node, since there isn't any other way.
	// TODO
	Utils.log("WARNING: AreaTree multicolor 3D mesh is not yet implemented.");
	final Color3f cf = new Color3f(color);
	for (int i=0; i<ps.size(); i++) colors.add(cf);

	return new MeshData(ps, colors);
}
 

@Override
public ImageProcessor render(RenderingState kf) {
	int displayMode    =   (int)kf.getNonChannelProperty(IJ3DRenderingState.DISPLAY_MODE);
	int red            =   (int)kf.getNonChannelProperty(IJ3DRenderingState.COLOR_RED);
	int green          =   (int)kf.getNonChannelProperty(IJ3DRenderingState.COLOR_GREEN);
	int blue           =   (int)kf.getNonChannelProperty(IJ3DRenderingState.COLOR_BLUE);
	float transparency = (float)kf.getNonChannelProperty(IJ3DRenderingState.TRANSPARENCY);
	int threshold      =   (int)kf.getNonChannelProperty(IJ3DRenderingState.THRESHOLD);

	Color3f color = (red < 0 || green < 0 || blue < 0) ? null : new Color3f(red / 255f, green / 255f, blue / 255f);

	content.setThreshold(threshold);
	content.setTransparency(transparency);
	content.setColor(color);
	if(content.getType() != displayMode)
		content.displayAs(displayMode);

	CombinedTransform transform = kf.getFwdTransform();
	float[] translation = transform.getTranslation();
	float[] rotation    = transform.getRotation();
	float scale         = transform.getScale();

	if(Math.abs(scale - 1) > 1e-3)
		throw new RuntimeException("View zooming is now allowed with the 3D Viewer, please move in Z instead.");

	float[] fwd = rotation.clone();
	Transform.applyTranslation(translation[0], translation[1], translation[2], fwd);


	Transform.invert(fwd);
	float[] m = new float[16];
	System.arraycopy(fwd, 0, m, 0, 12);
	m[15] = 1;
	animateTF.set(m);
	animateTG.setTransform(animateTF);

	viewer.fireTransformationUpdated();

	return takeSnapshot().getProcessor();
}
 

protected void addSphere(final String name, final double x, final double y, final double z, final Color color,
		final double radius) {
	if (use3DViewer) {
		final List<Point3f> sphere = customnode.MeshMaker.createSphere(x, y, z, radius);
		univ.addTriangleMesh(sphere, new Color3f(color), name);
	}
}
 

static public final void randomizeColors(final Image3DUniverse univ) {
	final ArrayList<Content> cs = new ArrayList<Content>(getOrderedContents(univ));
	for (int i=0; i<cs.size(); ++i) {
		if (i < colors.length) {
			cs.get(i).setColor(new Color3f(colors[i]));
		} else {
			cs.get(i).setColor(new Color3f((float)Math.random(), (float)Math.random(), (float)Math.random()));
		}
	}
	// Update the color bars if something is selected:
	final Content content = univ.getSelected();
	if (null != content) univ.fireContentChanged(content);
}
 

static public Future<Boolean> setColor(final Displayable d, final Color color) {
	final Display3D d3d = getDisplay(d.getLayer().getParent());
	if (null == d3d) return null; // no 3D displays open
	return d3d.executors.submit(new Callable<Boolean>() { @Override
	public Boolean call() {
		Content content = d3d.universe.getContent(makeTitle(d));
		if (null == content) content = getProfileContent(d);
		if (null != content) {
			content.setColor(new Color3f(color));
			return true;
		}
		return false;
	}});
}
 

/** Expects uncalibrated wx,wy,wz, (i.e. pixel values), to be calibrated by @param ls calibration. */
static public final Future<Content> addFatPoint(final String title, final LayerSet ls, final double wx, final double wy, final double wz, final double wr, final Color color) {
	final Display3D d3d = Display3D.get(ls);
	d3d.universe.removeContent(title);
	final Content ct = d3d.universe.createContent(new CustomTriangleMesh(d3d.createFatPoint(wx, wy, wz, wr, ls.getCalibrationCopy()), new Color3f(color), 0), title);
	ct.setLocked(true);
	return d3d.addContent(ct);
}
 

public Content addAsLinesTo3DViewer(final Image3DUniverse univ, final Color c, final ImagePlus colorImage) {
	return addAsLinesTo3DViewer(univ, new Color3f(c), colorImage);
}
 

public Content addAsLinesTo3DViewer(final Image3DUniverse univ, final Color3f c, final ImagePlus colorImage) {
	final String safeName = univ.getSafeContentName(getName() + " as lines");
	return univ.addLineMesh(getPoint3fList(), c, safeName, true);
}
 

public Content addDiscsTo3DViewer(final Image3DUniverse univ, final Color c, final ImagePlus colorImage) {
	return addDiscsTo3DViewer(univ, new Color3f(c), colorImage);
}
 

synchronized public void addTo3DViewer(final Image3DUniverse univ, final Color c, final ImagePlus colorImage) {
	if (c == null)
		throw new RuntimeException("In addTo3DViewer, Color can no longer be null");
	addTo3DViewer(univ, new Color3f(c), colorImage);
}
 

public void showCorrespondencesTo(final File tracesFile, final Color c, final double maxDistance) {

		final PathAndFillManager pafmTraces = new PathAndFillManager(width, height, depth, (float) x_spacing,
				(float) y_spacing, (float) z_spacing, spacing_units);

		/*
		 * FIXME: may well want to odd SWC options here, which isn't done with
		 * the "loadGuessingType" method:
		 */
		if (!pafmTraces.loadGuessingType(tracesFile.getAbsolutePath())) {
			SNT.error("Failed to load traces from: " + tracesFile.getAbsolutePath());
			return;
		}

		final List<Point3f> linePoints = new ArrayList<>();

		// Now find corresponding points from the first one, and draw lines to
		// them:
		final ArrayList<NearPoint> cp = pathAndFillManager.getCorrespondences(pafmTraces, 2.5);
		int done = 0;
		for (final NearPoint np : cp) {
			if (np != null) {
				// SNT.log("Drawing:");
				// SNT.log(np.toString());

				linePoints.add(new Point3f((float) np.nearX, (float) np.nearY, (float) np.nearZ));
				linePoints.add(new Point3f((float) np.closestIntersection.x, (float) np.closestIntersection.y,
						(float) np.closestIntersection.z));

				final String ballName = univ.getSafeContentName("ball " + done);
				final List<Point3f> sphere = customnode.MeshMaker.createSphere(np.nearX, np.nearY, np.nearZ,
						Math.abs(x_spacing / 2));
				univ.addTriangleMesh(sphere, new Color3f(c), ballName);
			}
			++done;
		}
		univ.addLineMesh(linePoints, new Color3f(Color.red), "correspondences", false);

		for (int pi = 0; pi < pafmTraces.size(); ++pi) {
			final Path p = pafmTraces.getPath(pi);
			if (p.getUseFitted())
				continue;
			p.addAsLinesTo3DViewer(univ, c, null);
		}
		// univ.resetView();
	}
 

public void setSelectedColor(final Color newColor) {
	selectedColor = newColor;
	selectedColor3f = new Color3f(newColor);
	repaintAllPanes();
	update3DViewerContents();
}
 

public void setDeselectedColor(final Color newColor) {
	deselectedColor = newColor;
	deselectedColor3f = new Color3f(newColor);
	repaintAllPanes();
	update3DViewerContents();
}
 

public MeshData(final List<Point3f> v, final List<Color3f> c) {
	this.verts = v;
	this.colors = c;
}