Examples with Random gdsc.core.utils.Random used on opensource projects

Example 1 with Random

use of gdsc.core.utils.Random in project GDSC-SMLM by aherbert.

the class PSFEstimator method calculateStatistics.

private boolean calculateStatistics(PeakFit fitter, double[] params, double[] params_dev) {
    debug("  Fitting PSF");
    swapStatistics();
    // Create the fit engine using the PeakFit plugin
    FitConfiguration fitConfig = config.getFitConfiguration();
    fitConfig.setInitialAngle((float) params[0]);
    fitConfig.setInitialPeakStdDev0((float) params[1]);
    fitConfig.setInitialPeakStdDev1((float) params[2]);
    ImageStack stack = imp.getImageStack();
    Rectangle roi = stack.getProcessor(1).getRoi();
    ImageSource source = new IJImageSource(imp);
    // Allow interlaced data by wrapping the image source
    if (interlacedData) {
        source = new InterlacedImageSource(source, dataStart, dataBlock, dataSkip);
    }
    // Allow frame aggregation by wrapping the image source
    if (integrateFrames > 1) {
        source = new AggregatedImageSource(source, integrateFrames);
    }
    fitter.initialiseImage(source, roi, true);
    fitter.addPeakResults(this);
    fitter.initialiseFitting();
    FitEngine engine = fitter.createFitEngine();
    // Use random slices
    int[] slices = new int[stack.getSize()];
    for (int i = 0; i < slices.length; i++) slices[i] = i + 1;
    Random rand = new Random();
    rand.shuffle(slices);
    IJ.showStatus("Fitting ...");
    // Use multi-threaded code for speed
    int i;
    for (i = 0; i < slices.length; i++) {
        int slice = slices[i];
        //debug("  Processing slice = %d\n", slice);
        IJ.showProgress(size(), settings.numberOfPeaks);
        ImageProcessor ip = stack.getProcessor(slice);
        // stack processor does not set the bounds required by ImageConverter
        ip.setRoi(roi);
        FitJob job = new FitJob(slice, ImageConverter.getData(ip), roi);
        engine.run(job);
        if (sampleSizeReached() || Utils.isInterrupted()) {
            break;
        }
    }
    if (Utils.isInterrupted()) {
        IJ.showProgress(1);
        engine.end(true);
        return false;
    }
    // Wait until we have enough results
    while (!sampleSizeReached() && !engine.isQueueEmpty()) {
        IJ.showProgress(size(), settings.numberOfPeaks);
        try {
            Thread.sleep(50);
        } catch (InterruptedException e) {
            break;
        }
    }
    // End now if we have enough samples
    engine.end(sampleSizeReached());
    IJ.showStatus("");
    IJ.showProgress(1);
    // This count will be an over-estimate given that the provider is ahead of the consumer
    // in this multi-threaded system
    debug("  Processed %d/%d slices (%d peaks)", i, slices.length, size());
    setParams(ANGLE, params, params_dev, sampleNew[ANGLE]);
    setParams(X, params, params_dev, sampleNew[X]);
    setParams(Y, params, params_dev, sampleNew[Y]);
    if (settings.showHistograms) {
        int[] idList = new int[NAMES.length];
        int count = 0;
        boolean requireRetile = false;
        for (int ii = 0; ii < 3; ii++) {
            if (sampleNew[ii].getN() == 0)
                continue;
            StoredDataStatistics stats = new StoredDataStatistics(sampleNew[ii].getValues());
            idList[count++] = Utils.showHistogram(TITLE, stats, NAMES[ii], 0, 0, settings.histogramBins, "Mean = " + Utils.rounded(stats.getMean()) + ". Median = " + Utils.rounded(sampleNew[ii].getPercentile(50)));
            requireRetile = requireRetile || Utils.isNewWindow();
        }
        if (requireRetile && count > 0) {
            new WindowOrganiser().tileWindows(Arrays.copyOf(idList, count));
        }
    }
    if (size() < 2) {
        log("ERROR: Insufficient number of fitted peaks, terminating ...");
        return false;
    }
    return true;
}

Example 2 with Random

use of gdsc.core.utils.Random in project GDSC-SMLM by aherbert.

the class TraceManagerTest method canTraceMultiplePulseWithMovingCoords.

@Test
public void canTraceMultiplePulseWithMovingCoords() {
    Random rand = new Random(30051977);
    float distance = 0.5f;
    int maxOffTime = 5;
    float[] params = createParams(rand);
    Trace trace = new Trace();
    for (int i = 0; i < 5; i++) {
        move(rand, params, distance);
        trace.add(new PeakResult(i, 0, 0, 0, 0, 0, params, null));
    }
    for (int i = 0; i < 5; i++) {
        move(rand, params, distance);
        trace.add(new PeakResult(i + maxOffTime, 0, 0, 0, 0, 0, params, null));
    }
    runTracing(distance, maxOffTime + 1, trace);
}

Example 3 with Random

use of gdsc.core.utils.Random in project GDSC-SMLM by aherbert.

the class TraceManagerTest method canTraceSinglePulseWithMovingCoords.

@Test
public void canTraceSinglePulseWithMovingCoords() {
    Random rand = new Random(30051977);
    float distance = 0.5f;
    float[] params = createParams(rand);
    Trace trace = new Trace();
    for (int i = 0; i < 5; i++) {
        move(rand, params, distance);
        trace.add(new PeakResult(i, 0, 0, 0, 0, 0, params, null));
    }
    runTracing(distance, 1, trace);
}

Example 4 with Random

use of gdsc.core.utils.Random in project GDSC-SMLM by aherbert.

the class ImageSourceTest method interlacedImageSourceCanReturnDataWithGet.

@Test
public void interlacedImageSourceCanReturnDataWithGet() {
    int w = 5;
    int h = 3;
    float[][] data = createData(w, h, 15);
    int start = 4;
    int size = 2;
    int skip = 1;
    ImageSource source = new InterlacedImageSource(new MemoryImageSource(w, h, data), start, size, skip);
    int[] frames = new int[data.length];
    for (int i = 0; i < data.length; i++) frames[i] = i + 1;
    Random rand = new Random();
    rand.shuffle(frames);
    int[] expected = new int[] { 4, 5, 7, 8, 10, 11, 13, 14 };
    Assert.assertTrue(source.open());
    for (int i = 0; i < data.length; i++) {
        int frame = frames[i];
        Assert.assertTrue(source.isValid(frame));
        float[] d = source.get(frame);
        if (isExpected(frame, expected))
            Assert.assertArrayEquals(data[frame - 1], d, 0);
        else
            Assert.assertNull(d);
    }
    Assert.assertFalse(source.isValid(0));
    Assert.assertFalse(source.isValid(data.length + 1));
}

Example 5 with Random

use of gdsc.core.utils.Random in project GDSC-SMLM by aherbert.

the class ImageSourceTest method aggregatedInterlacedImageSourceCanReturnDataWithGet.

@Test
public void aggregatedInterlacedImageSourceCanReturnDataWithGet() {
    int w = 5;
    int h = 3;
    int n = 15;
    float[][] data = createData(w, h, n);
    int aggregate = 3;
    int start = 4;
    int size = 2;
    int skip = 1;
    ImageSource source = new AggregatedImageSource(new InterlacedImageSource(new MemoryImageSource(w, h, data), start, size, skip), aggregate);
    // Set the expected frames returned by the interlacing
    int[] expected = new int[] { 4, 5, 7, 8, 10, 11, 13, 14 };
    // Randomly pick points from the positions used by next()
    int[] frames = new int[source.getFrames()];
    for (int i = 0, ii = 0; ii < expected.length; i++, ii += 3) frames[i] = ii;
    Random rand = new Random();
    rand.shuffle(frames);
    Assert.assertTrue(source.open());
    for (int i = 0; i < frames.length; i++) {
        // Get the range for the data
        int e = frames[i];
        int endE = FastMath.min(e + 2, expected.length - 1);
        int startFrame = expected[e];
        int endFrame = expected[endE];
        // Get the data
        float[] d = source.get(startFrame);
        // Check the correct range is returned
        Assert.assertEquals(startFrame, source.getStartFrameNumber());
        Assert.assertEquals(endFrame, source.getEndFrameNumber());
        // Check the data is collated correctly
        float[] all = new float[data[0].length];
        for (; e <= endE; e++) {
            int frame = expected[e] - 1;
            for (int j = 0; j < all.length; j++) all[j] += data[frame][j];
        }
        Assert.assertArrayEquals(all, d, 0);
    }
    // Check all the data is valid but skipped interlaced points return null 
    for (int i = 0; i < data.length; i++) {
        int frame = i + 1;
        Assert.assertTrue(source.isValid(frame));
        if (!isExpected(frame, expected))
            Assert.assertNull(source.get(frame));
    }
    Assert.assertFalse(source.isValid(0));
    Assert.assertFalse(source.isValid(data.length + 1));
}