Examples with Max org.apache.commons.math3.stat.descriptive.rank.Max used on opensource projects

Example 61 with Max

use of org.apache.commons.math3.stat.descriptive.rank.Max in project lucene-solr by apache.

the class HistogramEvaluator method evaluate.

public List<Map> evaluate(Tuple tuple) throws IOException {
    StreamEvaluator colEval1 = subEvaluators.get(0);
    List<Number> numbers1 = (List<Number>) colEval1.evaluate(tuple);
    double[] column1 = new double[numbers1.size()];
    for (int i = 0; i < numbers1.size(); i++) {
        column1[i] = numbers1.get(i).doubleValue();
    }
    int bins = 10;
    if (subEvaluators.size() == 2) {
        StreamEvaluator binsEval = subEvaluators.get(1);
        Number binsNum = (Number) binsEval.evaluate(tuple);
        bins = binsNum.intValue();
    }
    EmpiricalDistribution empiricalDistribution = new EmpiricalDistribution(bins);
    empiricalDistribution.load(column1);
    List<Map> binList = new ArrayList();
    List<SummaryStatistics> summaries = empiricalDistribution.getBinStats();
    for (SummaryStatistics statisticalSummary : summaries) {
        Map map = new HashMap();
        map.put("max", statisticalSummary.getMax());
        map.put("mean", statisticalSummary.getMean());
        map.put("min", statisticalSummary.getMin());
        map.put("stdev", statisticalSummary.getStandardDeviation());
        map.put("sum", statisticalSummary.getSum());
        map.put("N", statisticalSummary.getN());
        map.put("var", statisticalSummary.getVariance());
        binList.add(map);
    }
    return binList;
}

Example 62 with Max

use of org.apache.commons.math3.stat.descriptive.rank.Max in project GDSC-SMLM by aherbert.

the class SpotInspector method run.

/*
	 * (non-Javadoc)
	 * 
	 * @see ij.plugin.PlugIn#run(java.lang.String)
	 */
public void run(String arg) {
    SMLMUsageTracker.recordPlugin(this.getClass(), arg);
    if (MemoryPeakResults.isMemoryEmpty()) {
        IJ.error(TITLE, "No localisations in memory");
        return;
    }
    if (!showDialog())
        return;
    // Load the results
    results = ResultsManager.loadInputResults(inputOption, false);
    if (results == null || results.size() == 0) {
        IJ.error(TITLE, "No results could be loaded");
        IJ.showStatus("");
        return;
    }
    // Check if the original image is open
    ImageSource source = results.getSource();
    if (source == null) {
        IJ.error(TITLE, "Unknown original source image");
        return;
    }
    source = source.getOriginal();
    if (!source.open()) {
        IJ.error(TITLE, "Cannot open original source image: " + source.toString());
        return;
    }
    final float stdDevMax = getStandardDeviation(results);
    if (stdDevMax < 0) {
        // TODO - Add dialog to get the initial peak width
        IJ.error(TITLE, "Fitting configuration (for initial peak width) is not available");
        return;
    }
    // Rank spots
    rankedResults = new ArrayList<PeakResultRank>(results.size());
    final double a = results.getNmPerPixel();
    final double gain = results.getGain();
    final boolean emCCD = results.isEMCCD();
    for (PeakResult r : results.getResults()) {
        float[] score = getScore(r, a, gain, emCCD, stdDevMax);
        rankedResults.add(new PeakResultRank(r, score[0], score[1]));
    }
    Collections.sort(rankedResults);
    // Prepare results table. Get bias if necessary
    if (showCalibratedValues) {
        // Get a bias if required
        Calibration calibration = results.getCalibration();
        if (calibration.getBias() == 0) {
            ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
            gd.addMessage("Calibrated results requires a camera bias");
            gd.addNumericField("Camera_bias (ADUs)", calibration.getBias(), 2);
            gd.showDialog();
            if (!gd.wasCanceled()) {
                calibration.setBias(Math.abs(gd.getNextNumber()));
            }
        }
    }
    IJTablePeakResults table = new IJTablePeakResults(false, results.getName(), true);
    table.copySettings(results);
    table.setTableTitle(TITLE);
    table.setAddCounter(true);
    table.setShowCalibratedValues(showCalibratedValues);
    table.begin();
    // Add a mouse listener to jump to the frame for the clicked line
    textPanel = table.getResultsWindow().getTextPanel();
    // We must ignore old instances of this class from the mouse listeners
    id = ++currentId;
    textPanel.addMouseListener(this);
    // Add results to the table
    int n = 0;
    for (PeakResultRank rank : rankedResults) {
        rank.rank = n++;
        PeakResult r = rank.peakResult;
        table.add(r.getFrame(), r.origX, r.origY, r.origValue, r.error, r.noise, r.params, r.paramsStdDev);
    }
    table.end();
    if (plotScore || plotHistogram) {
        // Get values for the plots
        float[] xValues = null, yValues = null;
        double yMin, yMax;
        int spotNumber = 0;
        xValues = new float[rankedResults.size()];
        yValues = new float[xValues.length];
        for (PeakResultRank rank : rankedResults) {
            xValues[spotNumber] = spotNumber + 1;
            yValues[spotNumber++] = recoverScore(rank.score);
        }
        // Set the min and max y-values using 1.5 x IQR 
        DescriptiveStatistics stats = new DescriptiveStatistics();
        for (float v : yValues) stats.addValue(v);
        if (removeOutliers) {
            double lower = stats.getPercentile(25);
            double upper = stats.getPercentile(75);
            double iqr = upper - lower;
            yMin = FastMath.max(lower - iqr, stats.getMin());
            yMax = FastMath.min(upper + iqr, stats.getMax());
            IJ.log(String.format("Data range: %f - %f. Plotting 1.5x IQR: %f - %f", stats.getMin(), stats.getMax(), yMin, yMax));
        } else {
            yMin = stats.getMin();
            yMax = stats.getMax();
            IJ.log(String.format("Data range: %f - %f", yMin, yMax));
        }
        plotScore(xValues, yValues, yMin, yMax);
        plotHistogram(yValues, yMin, yMax);
    }
    // Extract spots into a stack
    final int w = source.getWidth();
    final int h = source.getHeight();
    final int size = 2 * radius + 1;
    ImageStack spots = new ImageStack(size, size, rankedResults.size());
    // To assist the extraction of data from the image source, process them in time order to allow 
    // frame caching. Then set the appropriate slice in the result stack
    Collections.sort(rankedResults, new Comparator<PeakResultRank>() {

        public int compare(PeakResultRank o1, PeakResultRank o2) {
            if (o1.peakResult.getFrame() < o2.peakResult.getFrame())
                return -1;
            if (o1.peakResult.getFrame() > o2.peakResult.getFrame())
                return 1;
            return 0;
        }
    });
    for (PeakResultRank rank : rankedResults) {
        PeakResult r = rank.peakResult;
        // Extract image
        // Note that the coordinates are relative to the middle of the pixel (0.5 offset)
        // so do not round but simply convert to int
        final int x = (int) (r.params[Gaussian2DFunction.X_POSITION]);
        final int y = (int) (r.params[Gaussian2DFunction.Y_POSITION]);
        // Extract a region but crop to the image bounds
        int minX = x - radius;
        int minY = y - radius;
        int maxX = FastMath.min(x + radius + 1, w);
        int maxY = FastMath.min(y + radius + 1, h);
        int padX = 0, padY = 0;
        if (minX < 0) {
            padX = -minX;
            minX = 0;
        }
        if (minY < 0) {
            padY = -minY;
            minY = 0;
        }
        int sizeX = maxX - minX;
        int sizeY = maxY - minY;
        float[] data = source.get(r.getFrame(), new Rectangle(minX, minY, sizeX, sizeY));
        // Prevent errors with missing data
        if (data == null)
            data = new float[sizeX * sizeY];
        ImageProcessor spotIp = new FloatProcessor(sizeX, sizeY, data, null);
        // Pad if necessary, i.e. the crop is too small for the stack
        if (padX > 0 || padY > 0 || sizeX < size || sizeY < size) {
            ImageProcessor spotIp2 = spotIp.createProcessor(size, size);
            spotIp2.insert(spotIp, padX, padY);
            spotIp = spotIp2;
        }
        int slice = rank.rank + 1;
        spots.setPixels(spotIp.getPixels(), slice);
        spots.setSliceLabel(Utils.rounded(rank.originalScore), slice);
    }
    source.close();
    ImagePlus imp = Utils.display(TITLE, spots);
    imp.setRoi((PointRoi) null);
    // Make bigger		
    for (int i = 10; i-- > 0; ) imp.getWindow().getCanvas().zoomIn(imp.getWidth() / 2, imp.getHeight() / 2);
}

Example 63 with Max

use of org.apache.commons.math3.stat.descriptive.rank.Max in project gatk by broadinstitute.

the class OptimizationUtils method argmax.

public static double argmax(final Function<Double, Double> function, final double min, final double max, final double guess, final double relativeTolerance, final double absoluteTolerance, final int maxEvaluations) {
    final BrentOptimizer optimizer = new BrentOptimizer(relativeTolerance, absoluteTolerance);
    final SearchInterval interval = new SearchInterval(min, max, guess);
    return optimizer.optimize(new UnivariateObjectiveFunction(function::apply), GoalType.MAXIMIZE, interval, new MaxEval(maxEvaluations)).getPoint();
}

Example 64 with Max

use of org.apache.commons.math3.stat.descriptive.rank.Max in project gatk-protected by broadinstitute.

the class ReadCountCollectionUtilsUnitTest method testRemoveTargetsWithTooManyZeros.

@Test(dataProvider = "tooManyZerosData")
public void testRemoveTargetsWithTooManyZeros(final ReadCountCollection readCount) {
    final RealMatrix counts = readCount.counts();
    final int[] numberOfZeros = IntStream.range(0, counts.getRowDimension()).map(i -> (int) DoubleStream.of(counts.getRow(i)).filter(d -> d == 0.0).count()).toArray();
    final int maximumNumberOfZeros = IntStream.of(numberOfZeros).max().getAsInt();
    for (int maxZeros = 0; maxZeros < maximumNumberOfZeros; maxZeros++) {
        final int maxZerosThres = maxZeros;
        final int expectedRemainingCount = (int) IntStream.of(numberOfZeros).filter(i -> i <= maxZerosThres).count();
        if (expectedRemainingCount == 0) {
            try {
                ReadCountCollectionUtils.removeTargetsWithTooManyZeros(readCount, maxZeros, false, NULL_LOGGER);
            } catch (final UserException.BadInput ex) {
                // expected.
                continue;
            }
            Assert.fail("expects an exception");
        }
        final ReadCountCollection rc = ReadCountCollectionUtils.removeTargetsWithTooManyZeros(readCount, maxZeros, false, NULL_LOGGER);
        Assert.assertEquals(rc.targets().size(), expectedRemainingCount);
        int nextIndex = 0;
        for (int i = 0; i < readCount.targets().size(); i++) {
            final Target target = readCount.targets().get(i);
            final int newIndex = rc.targets().indexOf(target);
            if (numberOfZeros[i] <= maxZeros) {
                Assert.assertTrue(newIndex >= 0, " " + numberOfZeros[i] + " " + maxZeros);
                Assert.assertEquals(newIndex, nextIndex++);
            } else {
                Assert.assertEquals(newIndex, -1);
            }
        }
        Assert.assertEquals(nextIndex, expectedRemainingCount);
    }
}

Example 65 with Max

use of org.apache.commons.math3.stat.descriptive.rank.Max in project gatk-protected by broadinstitute.

the class ReadCountCollectionUtilsUnitTest method testRemoveColumnsWithTooManyZeros.

@Test(dataProvider = "tooManyZerosData")
public void testRemoveColumnsWithTooManyZeros(final ReadCountCollection readCount) {
    final RealMatrix counts = readCount.counts();
    final int[] numberOfZeros = IntStream.range(0, counts.getColumnDimension()).map(i -> (int) DoubleStream.of(counts.getColumn(i)).filter(d -> d == 0.0).count()).toArray();
    final int maximumNumberOfZeros = IntStream.of(numberOfZeros).max().getAsInt();
    for (int maxZeros = 0; maxZeros < maximumNumberOfZeros; maxZeros++) {
        final int maxZerosThres = maxZeros;
        final int expectedRemainingCount = (int) IntStream.of(numberOfZeros).filter(i -> i <= maxZerosThres).count();
        if (expectedRemainingCount == 0) {
            try {
                ReadCountCollectionUtils.removeColumnsWithTooManyZeros(readCount, maxZeros, false, NULL_LOGGER);
            } catch (final UserException.BadInput ex) {
                // expected.
                continue;
            }
            Assert.fail("expects an exception");
        }
        final ReadCountCollection rc = ReadCountCollectionUtils.removeColumnsWithTooManyZeros(readCount, maxZeros, false, NULL_LOGGER);
        Assert.assertEquals(rc.columnNames().size(), expectedRemainingCount);
        final int[] newIndices = new int[expectedRemainingCount];
        int nextIndex = 0;
        for (int i = 0; i < readCount.columnNames().size(); i++) {
            final String name = readCount.columnNames().get(i);
            final int newIndex = rc.columnNames().indexOf(name);
            if (numberOfZeros[i] <= maxZeros) {
                Assert.assertTrue(newIndex >= 0);
                newIndices[nextIndex++] = i;
            } else {
                Assert.assertEquals(newIndex, -1);
            }
        }
        Assert.assertEquals(nextIndex, expectedRemainingCount);
        for (int i = 1; i < newIndices.length; i++) {
            Assert.assertTrue(newIndices[i - 1] < newIndices[i]);
        }
    }
}