Example usage for java.lang Math log10

Introduction

In this page you can find the example usage for java.lang Math log10.

Prototype

@HotSpotIntrinsicCandidate
public static double log10(double a) 

Source Link

Document

Returns the base 10 logarithm of a double value.

Usage

From source file:com.android.stockbrowser.WebStorageSizeManager.java

static long calculateGlobalLimit(long fileSystemSizeBytes, long freeSpaceBytes) {
    if (fileSystemSizeBytes <= 0 || freeSpaceBytes <= 0 || freeSpaceBytes > fileSystemSizeBytes) {
        return 0;
    }//from   w ww. jav  a  2 s . c  o  m

    long fileSystemSizeRatio = 2 << ((int) Math.floor(Math.log10(fileSystemSizeBytes / (1024 * 1024))));
    long maxSizeBytes = (long) Math.min(Math.floor(fileSystemSizeBytes / fileSystemSizeRatio),
            Math.floor(freeSpaceBytes / 2));
    // Round maxSizeBytes up to a multiple of 1024KB (but only if
    // maxSizeBytes > 1MB).
    long maxSizeStepBytes = 1024 * 1024;
    if (maxSizeBytes < maxSizeStepBytes) {
        return 0;
    }
    long roundingExtra = maxSizeBytes % maxSizeStepBytes == 0 ? 0 : 1;
    return (maxSizeStepBytes * ((maxSizeBytes / maxSizeStepBytes) + roundingExtra));
}

---

From source file:edu.ucuenca.authorsdisambiguation.nwd.NWD.java

public double NGD(String a, String b) throws IOException, SQLException {

    a = a.trim();/*from  w w w. j av  a  2s .com*/
    b = b.trim();

    if (a.compareToIgnoreCase(b) == 0) {
        return 0;
    }

    //double n0 = getResultsCount(""+a+"");
    //double n1 = getResultsCount(""+b+"");
    //String c = ""+a+" "+b+"";
    String _a = "\"" + a + "\"~10";
    String _b = "\"" + b + "\"~10";
    String c = "\"" + a + " " + b + "\"~50";
    if (Cache.getInstance().config.get("relaxMode").getAsBoolean().value()) {
        _a = "" + a;
        _b = "" + b;
        c = a + " " + b;
    }

    double n0 = getResultsCount(_a);
    double n1 = getResultsCount(_b);
    double n2 = 0;

    if (n0 == 0 || n1 == 0) {
        n2 = 0;
    } else {
        n2 = getResultsCount(c);
    }

    //double m = 5026040.0 * 590;
    double m = getResultsCount("the");

    double distance = 0;

    int Measure = 0;

    double l1 = Math.max(Math.log10(n0), Math.log10(n1)) - Math.log10(n2);
    double l2 = Math.log10(m) - Math.min(Math.log10(n0), Math.log10(n1));

    if (Measure == 0) {
        distance = l1 / l2;
    }

    if (Measure == 1) {
        distance = 1 - (Math.log10(n2) / Math.log10(n0 + n1 - n2));
    }

    if (n0 == 0 || n1 == 0 || n2 == 0) {
        distance = 1;
    }

    //System.out.println("n0="+n0);
    //System.out.println("n1="+n1);
    //System.out.println("n2="+n2);
    //System.out.println(a + "," + b + "=" + distance2);
    return distance;
}

---

From source file:uk.ac.babraham.FastQC.Modules.KmerContent.java

public boolean raisesError() {
    if (!calculated)
        calculateEnrichment();//from   w w w  .j ava 2 s  . c om

    // We raise an error if the most enriched kmer is seen more than 100 times
    // more frequently than we expect.

    if (enrichedKmers.length > 0
            && 0 - Math.log10(enrichedKmers[0].pValue()) > ModuleConfig.getParam("kmer", "error"))
        return true;
    return false;
}

---

From source file:org.broadinstitute.gatk.engine.recalibration.RecalDatumNode.java

/**
 * Return a freshly allocated tree where all mergable nodes with < maxPenalty are merged
 *
 * Note that nodes must have fixed penalties to this algorithm will fail.
 *
 * @param maxPenaltyIn the maximum penalty we are allowed to incur for a merge
 * @param applyBonferroniCorrection if true, we will adjust penalty by the phred-scaled bonferroni correction
 *                                  for the size of the initial tree.  That is, if there are 10 nodes in the
 *                                  tree and maxPenalty is 20 we will actually enforce 10^-2 / 10 = 10^-3 = 30
 *                                  penalty for multiple testing
 * @return/*w w  w  . ja v a2  s  .c  o m*/
 */
public RecalDatumNode<T> pruneToNoMoreThanPenalty(final double maxPenaltyIn,
        final boolean applyBonferroniCorrection) {
    RecalDatumNode<T> root = this;

    final double bonferroniCorrection = 10 * Math.log10(this.size());
    final double maxPenalty = applyBonferroniCorrection ? maxPenaltyIn + bonferroniCorrection : maxPenaltyIn;

    if (applyBonferroniCorrection)
        logger.info(String.format(
                "Applying Bonferroni correction for %d nodes = %.2f to initial penalty %.2f for total "
                        + "corrected max penalty of %.2f",
                this.size(), bonferroniCorrection, maxPenaltyIn, maxPenalty));

    while (true) {
        final Pair<RecalDatumNode<T>, Double> minPenaltyNode = root.getMinPenaltyAboveLeafNode();

        if (minPenaltyNode == null || minPenaltyNode.getSecond() > maxPenalty) {
            // nothing to merge, or the best candidate is above our max allowed
            if (minPenaltyNode == null) {
                if (logger.isDebugEnabled())
                    logger.debug("Stopping because no candidates could be found");
            } else {
                if (logger.isDebugEnabled())
                    logger.debug("Stopping because node " + minPenaltyNode.getFirst() + " has penalty "
                            + minPenaltyNode.getSecond() + " > max " + maxPenalty);
            }
            break;
        } else {
            // remove the lowest penalty element, and continue
            if (logger.isDebugEnabled())
                logger.debug("Removing node " + minPenaltyNode.getFirst() + " with penalty "
                        + minPenaltyNode.getSecond());
            root = root.removeLowestPenaltyNode();
        }
    }

    // no more candidates exist with penalty < maxPenalty
    return root;
}

---

From source file:msi.gaml.operators.Stats.java

@operator(value = "split", can_be_const = true, content_type = IType.LIST, expected_content_type = { IType.INT,
        IType.FLOAT }, category = { IOperatorCategory.STATISTICAL,
                IOperatorCategory.CONTAINER }, concept = { IConcept.STATISTIC })
@doc(see = { "split_in",
        "split_using" }, value = "Splits a list of numbers into n=(1+3.3*log10(elements)) bins. The splitting is strict (i.e. elements are in the ith bin if they are strictly smaller than the ith bound")

public static <T extends Number> IList<IList<T>> split(final IScope scope, final IList<T> list) {
    final int nb = (int) (1 + 3.3 * Math.log10(list.size()));
    return split_in(scope, list, nb);
}

---

From source file:org.nuxeo.ecm.automation.server.jaxrs.batch.BatchManagerFixture.java

@Test
public void testBatchConcurrency() throws Exception {

    BatchManager bm = Framework.getService(BatchManager.class);

    // Initialize batches with one file concurrently
    int nbBatches = 100;
    String[] batchIds = new String[nbBatches];
    ThreadPoolExecutor tpe = new ThreadPoolExecutor(5, 5, 500L, TimeUnit.MILLISECONDS,
            new LinkedBlockingQueue<Runnable>(nbBatches + 1));

    for (int i = 0; i < nbBatches; i++) {
        final int batchIndex = i;
        tpe.submit(new Runnable() {
            @Override/*from   w w  w.  j a  va  2s .  c om*/
            public void run() {
                try {
                    String batchId = bm.initBatch();
                    bm.addStream(batchId, "0",
                            new ByteArrayInputStream(
                                    ("SomeContent_" + batchId).getBytes(StandardCharsets.UTF_8)),
                            "MyBatchFile.txt", "text/plain");
                    batchIds[batchIndex] = batchId;
                } catch (IOException e) {
                    fail(e.getMessage());
                }
            }
        });
    }

    tpe.shutdown();
    boolean finish = tpe.awaitTermination(20, TimeUnit.SECONDS);
    assertTrue("timeout", finish);

    // Check batches
    for (String batchId : batchIds) {
        assertNotNull(batchId);
    }
    // Test indexes 0, 9, 99, ..., nbFiles - 1
    int nbDigits = (int) (Math.log10(nbBatches) + 1);
    int divisor = nbBatches;
    for (int i = 0; i < nbDigits; i++) {
        int batchIndex = nbBatches / divisor - 1;
        String batchId = batchIds[batchIndex];
        Blob blob = bm.getBlob(batchId, "0");
        assertNotNull(blob);
        assertEquals("MyBatchFile.txt", blob.getFilename());
        assertEquals("SomeContent_" + batchId, blob.getString());
        divisor = divisor / 10;
    }

    // Check storage size
    TransientStore ts = bm.getTransientStore();
    assertTrue(((AbstractTransientStore) ts).getStorageSize() > 12 * nbBatches);

    // Clean batches
    for (String batchId : batchIds) {
        bm.clean(batchId);
    }
    assertEquals(ts.getStorageSizeMB(), 0);
}

---

From source file:org.broadinstitute.gatk.tools.walkers.annotator.ExcessHet.java

protected double calculateEH(final VariantContext vc, final GenotypesContext genotypes) {
    HeterozygosityUtils heterozygosityUtils = new HeterozygosityUtils(RETURN_ROUNDED);
    final double[] genotypeCountsDoubles = heterozygosityUtils.getGenotypeCountsForRefVsAllAlts(vc, genotypes);
    sampleCount = heterozygosityUtils.getSampleCount();
    final int[] genotypeCounts = new int[genotypeCountsDoubles.length];
    for (int i = 0; i < genotypeCountsDoubles.length; i++) {
        genotypeCounts[i] = (int) genotypeCountsDoubles[i];
    }/* w  w w .j  a  v a 2  s . co m*/

    double pval = exactTest(genotypeCounts);

    //If the actual phredPval would be infinity we will probably still filter out just a very large number
    if (pval == 0) {
        return Integer.MAX_VALUE;
    }
    double phredPval = -10.0 * Math.log10(pval);

    return phredPval;
}

---

From source file:uk.ac.babraham.FastQC.Modules.KmerContent.java

public boolean raisesWarning() {
    if (!calculated)
        calculateEnrichment();//  w  ww .j av  a2  s.  c  o  m

    // We raise a warning if there are any enriched kmers
    if (enrichedKmers.length > 0
            && 0 - Math.log10(enrichedKmers[0].pValue()) > ModuleConfig.getParam("kmer", "warn"))
        return true;
    return false;
}

---

From source file:org.esa.nest.gpf.CosmoSkymedCalibrator.java

public void computeTile(Band targetBand, Tile targetTile, ProgressMonitor pm) throws OperatorException {

    final Rectangle targetTileRectangle = targetTile.getRectangle();
    final int x0 = targetTileRectangle.x;
    final int y0 = targetTileRectangle.y;
    final int w = targetTileRectangle.width;
    final int h = targetTileRectangle.height;

    Tile sourceRaster1 = null;/*  ww  w  .ja v a 2s.co  m*/
    ProductData srcData1 = null;
    ProductData srcData2 = null;
    Band sourceBand1 = null;

    final String[] srcBandNames = targetBandNameToSourceBandName.get(targetBand.getName());
    if (srcBandNames.length == 1) {
        sourceBand1 = sourceProduct.getBand(srcBandNames[0]);
        sourceRaster1 = calibrationOp.getSourceTile(sourceBand1, targetTileRectangle);
        srcData1 = sourceRaster1.getDataBuffer();
    } else {
        sourceBand1 = sourceProduct.getBand(srcBandNames[0]);
        final Band sourceBand2 = sourceProduct.getBand(srcBandNames[1]);
        sourceRaster1 = calibrationOp.getSourceTile(sourceBand1, targetTileRectangle);
        final Tile sourceRaster2 = calibrationOp.getSourceTile(sourceBand2, targetTileRectangle);
        srcData1 = sourceRaster1.getDataBuffer();
        srcData2 = sourceRaster2.getDataBuffer();
    }

    final Unit.UnitType bandUnit = Unit.getUnitType(sourceBand1);

    // copy band if unit is phase
    if (bandUnit == Unit.UnitType.PHASE) {
        targetTile.setRawSamples(sourceRaster1.getRawSamples());
        return;
    }

    final String pol = OperatorUtils.getBandPolarization(srcBandNames[0], absRoot).toUpperCase();
    double Ks = 1.0;
    if (pol != null && !pol.isEmpty() && applyConstantCorrection) {
        Ks = calibrationFactor.get(pol);
    }

    final ProductData trgData = targetTile.getDataBuffer();
    final TileIndex srcIndex = new TileIndex(sourceRaster1);
    final TileIndex tgtIndex = new TileIndex(targetTile);

    final int maxY = y0 + h;
    final int maxX = x0 + w;

    double sigma, dn, i, q;
    int srcIdx, tgtIdx;
    final double powFactor = FastMath.pow(referenceSlantRange, 2 * referenceSlantRangeExp);
    final double sinRefIncidenceAngle = FastMath.sin(referenceIncidenceAngle);
    final double rescaleCalFactor = rescalingFactor * rescalingFactor * Ks;

    for (int y = y0; y < maxY; ++y) {
        srcIndex.calculateStride(y);
        tgtIndex.calculateStride(y);

        for (int x = x0; x < maxX; ++x) {
            srcIdx = srcIndex.getIndex(x);
            tgtIdx = tgtIndex.getIndex(x);

            if (bandUnit == Unit.UnitType.AMPLITUDE) {
                dn = srcData1.getElemDoubleAt(srcIdx);
                sigma = dn * dn;
            } else if (bandUnit == Unit.UnitType.INTENSITY) {
                sigma = srcData1.getElemDoubleAt(srcIdx);
            } else if (bandUnit == Unit.UnitType.REAL || bandUnit == Unit.UnitType.IMAGINARY) {
                i = srcData1.getElemDoubleAt(srcIdx);
                q = srcData2.getElemDoubleAt(srcIdx);
                sigma = i * i + q * q;
            } else if (bandUnit == Unit.UnitType.INTENSITY_DB) {
                sigma = FastMath.pow(10, srcData1.getElemDoubleAt(srcIdx) / 10.0); // convert dB to linear scale
            } else {
                throw new OperatorException("CosmoSkymed Calibration: unhandled unit");
            }

            if (applyRangeSpreadingLossCorrection)
                sigma *= powFactor;

            if (applyIncidenceAngleCorrection)
                sigma *= sinRefIncidenceAngle;

            sigma /= rescaleCalFactor;

            if (outputImageScaleInDb) { // convert calibration result to dB
                if (sigma < underFlowFloat) {
                    sigma = -underFlowFloat;
                } else {
                    sigma = 10.0 * Math.log10(sigma);
                }
            }

            trgData.setElemDoubleAt(tgtIdx, sigma);
        }
    }
}

---

From source file:edu.umn.cs.spatialHadoop.nasa.MultiHDFPlot.java

/**
 * Draws a scale used with the heat map//from  w ww.  j av  a  2  s .  co  m
 * @param output
 * @param valueRange
 * @param width
 * @param height
 * @throws IOException
 */
private static void drawVerticalScale(Path output, double min, double max, int width, int height,
        OperationsParams params) throws IOException {
    BufferedImage image = new BufferedImage(width, height, BufferedImage.TYPE_INT_ARGB);
    Graphics2D g = image.createGraphics();
    g.setBackground(Color.BLACK);
    g.clearRect(0, 0, width, height);

    // fix this part to work according to color1, color2 and gradient type
    HDFPlot.HDFRasterizer gradient = new HDFPlot.HDFRasterizer();
    gradient.configure(params);
    HDFRasterLayer gradientLayer = (HDFRasterLayer) gradient.createCanvas(0, 0, new Rectangle());
    for (int y = 0; y < height; y++) {
        Color color = gradientLayer.calculateColor(height - y, 0, height);
        g.setColor(color);
        g.drawRect(width * 3 / 4, y, width / 4, 1);
    }

    int fontSize = 24;
    g.setFont(new Font("Arial", Font.BOLD, fontSize));
    double step = (max - min) * fontSize * 5 / height;
    step = (int) (Math.pow(10.0, Math.round(Math.log10(step))));
    double min_value = Math.floor(min / step) * step;
    double max_value = Math.floor(max / step) * step;

    g.setColor(Color.WHITE);
    for (double value = min_value; value <= max_value; value += step) {
        double y = ((value - min) + (max - value) * (height - fontSize)) / (max - min);
        g.drawString(String.valueOf((int) value), 5, (int) y);
    }

    g.dispose();

    FileSystem fs = output.getFileSystem(new Configuration());
    FSDataOutputStream outStream = fs.create(output, true);
    ImageIO.write(image, "png", outStream);
    outStream.close();
}

---

• «
• 1
• 2
• 3
• 4
• 5
• 6
• 7
• 8
• 9
• 10
• 11
• 12
• 13
• 14
• 15
• 16
• 17
• 18
• 19
• 20
• 21
• 22
• 23
• 24
• 25
• 26
• 27
• 28
• 29
• 30
• 31
• 32
• 33
• 34
• 35
• 36
• 37
• 38
• 39
• 40
• 41
• 42
• 43
• 44
• 45
• »