Java Code Examples for ij.measure.Calibration#setUnit()

public RenderingThread(Renderer3D raycaster) {
	this.raycaster = raycaster;
	final ExtendedRenderingState rs = raycaster.getRenderingState();
	rs.setNonChannelProperty(ExtendedRenderingState.TIMEPOINT, raycaster.getImage().getT() - 1);
	this.event = new Event(rs);
	out = new ImagePlus("3D Animation", raycaster.render(rs));
	// TODO
	Calibration cal = out.getCalibration();
	cal.setUnit(raycaster.getImage().getCalibration().getUnit());
	rs.getFwdTransform().adjustOutputCalibration(cal);
	out.show();

	thread = new Thread("3D-Animation rendering thread") {
		@Override
		public void run() {
			loop(rs);
		}
	};
	thread.start();
}
 

protected AbstractRendering(AbstractBuilder builder) {
    this.xmin = builder.xmin;
    this.xmax = builder.xmax;
    this.ymin = builder.ymin;
    this.ymax = builder.ymax;
    this.resolution = builder.resolution;
    this.imSizeX = builder.imSizeX;
    this.imSizeY = builder.imSizeY;
    this.forceDefaultDX = builder.forceDefaultDX;
    this.forceDefaultDZ = builder.forceDefaultDZ;
    this.defaultDX = builder.defaultDX;
    this.defaultDZ = builder.defaultDZ;
    this.zFrom = builder.zFrom;
    this.zSlices = builder.zSlices;
    this.zStep = builder.zStep;
    this.zTo = builder.zTo;
    this.threeDimensions = builder.threeDimensions;
    this.colorize = builder.colorize;
    this.colorizationLut = builder.colorizationLut;
    slices = new ImageProcessor[zSlices];
    stack = new ImageStack(imSizeX, imSizeY);
    for(int i = 0; i < zSlices; i++) {
        slices[i] = new FloatProcessor(imSizeX, imSizeY);
        stack.addSlice((i * zStep + zFrom) + " to " + ((i + 1) * zStep + zFrom), slices[i]);
    }
    image = new ImagePlus(getRendererName(), stack);
    Calibration calibration = new Calibration();
    double pixelSize = resolution * CameraSetupPlugIn.getPixelSize() / 1000;
    calibration.pixelHeight = pixelSize;
    calibration.pixelWidth = pixelSize;
    if(threeDimensions) {
        calibration.pixelDepth = zStep / 1000;
    }
    calibration.setUnit("um");
    image.setCalibration(calibration);
    if(colorize) {
        image.setDimensions(zSlices, 1, 1);
        CompositeImage image2 = new CompositeImage(image);
        image = image2;
        setupLuts();
    }
}
 

private void runGenerator() throws InterruptedException {
    IJ.showStatus("ThunderSTORM is generating your image sequence...");
    IJ.showProgress(0.0);
    //
    IJGroundTruthTable gt = IJGroundTruthTable.getGroundTruthTable();
    gt.reset();
    ImageStack stack = new ImageStack(width, height);
    //FloatProcessor bkg = new DataGenerator().generateBackground(width, height, drift);
    //
    int numThreads = Math.min(Prefs.getThreads(), frames);
    GeneratorWorker[] generators = new GeneratorWorker[numThreads];
    Thread[] threads = new Thread[numThreads];
    processing_frame = 0;
    // prepare the workers and allocate resources for all the threads
    for(int c = 0, f_start = 0, f_end, f_inc = frames / numThreads; c < numThreads; c++) {
        if((c + 1) < numThreads) {
            f_end = f_start + f_inc - 1;
        } else {
            f_end = frames - 1;
        }
        generators[c] = new GeneratorWorker(f_start, f_end/*, bkg*/);
        threads[c] = new Thread(generators[c]);
        f_start = f_end + 1;
    }
    // start all the workers
    for(int c = 0; c < numThreads; c++) {
        threads[c].start();
    }
    // wait for all the workers to finish
    int wait = 1000 / numThreads;    // max 1s
    boolean finished = false;
    while(!finished) {
        finished = true;
        for(int c = 0; c < numThreads; c++) {
            threads[c].join(wait);
            finished &= !threads[c].isAlive();   // all threads must not be alive to finish!
        }
        if(IJ.escapePressed()) {    // abort?
            // stop the workers
            for(int ci = 0; ci < numThreads; ci++) {
                threads[ci].interrupt();
            }
            // wait so the message below is not overwritten by any of the threads
            for(int ci = 0; ci < numThreads; ci++) {
                threads[ci].join();
            }
            // show info and exit the plugin
            IJ.showProgress(1.0);
            IJ.showStatus("Operation has been aborted by user!");
            return;
        }
    }
    processing_frame = 0;
    gt.setOriginalState();
    for(int c = 0; c < numThreads; c++) {
        generators[c].fillResults(stack, gt);   // and generate stack and table of ground-truth data
    }
    gt.insertIdColumn();
    gt.copyOriginalToActual();
    gt.setActualState();
    gt.convertAllColumnsToAnalogUnits();
    //
    ImagePlus imp = IJ.createImage("Artificial dataset", "16-bit", width, height, frames);
    imp.setStack(stack);
    Calibration cal = new Calibration();
    cal.setUnit("um");
    cal.pixelWidth = cal.pixelHeight = Units.NANOMETER.convertTo(Units.MICROMETER, CameraSetupPlugIn.getPixelSize());
    imp.setCalibration(cal);
    imp.show();
    gt.show();
    //
    IJ.showProgress(1.0);
    IJ.showStatus("ThunderSTORM has finished generating your image sequence.");
}