Examples with PeakResult gdsc.smlm.results.PeakResult used on opensource projects

Example 66 with PeakResult

use of gdsc.smlm.results.PeakResult in project GDSC-SMLM by aherbert.

the class TraceFilter method setup.

@Override
public void setup(MemoryPeakResults peakResults) {
    ok = new HashSet<PeakResult>();
    // Trace molecules. Anything that is part of a trace is OK
    TraceManager tm = new TraceManager(peakResults);
    tm.traceMolecules(d, t);
    Trace[] traces = tm.getTraces();
    for (Trace trace : traces) {
        if (trace.size() > 1) {
            for (PeakResult result : trace.getPoints()) {
                ok.add(result);
            }
        }
    }
}

Example 67 with PeakResult

use of gdsc.smlm.results.PeakResult in project GDSC-SMLM by aherbert.

the class Filter method filter2.

/**
	 * Filter the results
	 * <p>
	 * The number of consecutive rejections are counted per frame. When the configured number of failures is reached all
	 * remaining results for the frame are rejected. This assumes the results are ordered by the frame.
	 * <p>
	 * Note that this method is to be used to score a set of results that may have been extracted from a larger set
	 * since the number of consecutive failures before each peak are expected to be stored in the origY property. Set
	 * this to zero and the results should be identical to {@link #filter(MemoryPeakResults, int)}
	 * 
	 * @param results
	 * @param failures
	 *            the number of failures to allow per frame before all peaks are rejected
	 * @return the filtered results
	 */
public MemoryPeakResults filter2(MemoryPeakResults results, int failures) {
    MemoryPeakResults newResults = new MemoryPeakResults();
    newResults.copySettings(results);
    setup(results);
    int frame = -1;
    int failCount = 0;
    for (PeakResult peak : results.getResults()) {
        if (frame != peak.getFrame()) {
            frame = peak.getFrame();
            failCount = 0;
        }
        failCount += peak.origY;
        // Reject all peaks if we have exceeded the fail count
        final boolean isPositive;
        if (failCount > failures) {
            isPositive = false;
        } else {
            // Otherwise assess the peak
            isPositive = accept(peak);
        }
        if (isPositive) {
            failCount = 0;
            newResults.add(peak);
        } else {
            failCount++;
        }
    }
    end();
    return newResults;
}

Example 68 with PeakResult

use of gdsc.smlm.results.PeakResult in project GDSC-SMLM by aherbert.

the class Filter method filterSubset.

/**
	 * Filter the results
	 * <p>
	 * Input PeakResults must be allocated a score for true positive, false positive, true negative and false negative
	 * (accessed via the object property get methods). The filter is run and results that pass accumulate scores for
	 * true positive and false positive, otherwise the scores are accumulated for true negative and false negative. The
	 * simplest scoring scheme is to mark valid results as tp=fn=1 and fp=tn=0 and invalid results the opposite.
	 * <p>
	 * The number of consecutive rejections are counted per frame. When the configured number of failures is reached all
	 * remaining results for the frame are rejected. This assumes the results are ordered by the frame.
	 * <p>
	 * The number of failures before each peak is stored in the origX property of the PeakResult.
	 * 
	 * @param results
	 * @param score
	 *            If not null will be populated with the fraction score [ tp, fp, tn, fn, p, n ]
	 * @return the filtered results
	 */
public MemoryPeakResults filterSubset(MemoryPeakResults results, double[] score) {
    MemoryPeakResults newResults = new MemoryPeakResults();
    newResults.copySettings(results);
    setup(results);
    int frame = -1;
    int failCount = 0;
    double fp = 0, fn = 0;
    double tp = 0, tn = 0;
    int p = 0;
    for (PeakResult peak : results.getResults()) {
        if (frame != peak.getFrame()) {
            frame = peak.getFrame();
            failCount = 0;
        }
        // Reject all peaks if we have exceeded the fail count
        final boolean isPositive = accept(peak);
        if (isPositive) {
            peak.origX = failCount;
            failCount = 0;
            newResults.add(peak);
        } else {
            failCount++;
        }
        if (isPositive) {
            p++;
            tp += peak.getTruePositiveScore();
            fp += peak.getFalsePositiveScore();
        } else {
            fn += peak.getFalseNegativeScore();
            tn += peak.getTrueNegativeScore();
        }
    }
    end();
    if (score != null && score.length > 5) {
        score[0] = tp;
        score[1] = fp;
        score[2] = tn;
        score[3] = fn;
        score[4] = p;
        score[5] = results.size() - p;
    }
    return newResults;
}

Example 69 with PeakResult

use of gdsc.smlm.results.PeakResult in project GDSC-SMLM by aherbert.

the class ResultsManagerTest method checkEqual.

private void checkEqual(Spot[] spots, int channel, int slice, int position, int type, MemoryPeakResults actualResults) throws ArrayComparisonFailure {
    Assert.assertNotNull("Input results are null", actualResults);
    MemoryPeakResults expectedResults = extract(spots, channel, slice, position, type);
    Assert.assertEquals("Size differ", expectedResults.size(), actualResults.size());
    final float delta = 0;
    List<PeakResult> expected = expectedResults.getResults();
    List<PeakResult> actual = actualResults.getResults();
    for (int i = 0; i < actualResults.size(); i++) {
        PeakResult p1 = expected.get(i);
        PeakResult p2 = actual.get(i);
        Assert.assertEquals("Peak mismatch @ " + i, p1.getFrame(), p2.getFrame());
        Assert.assertEquals("Orig X mismatch @ " + i, p1.origX, p2.origX);
        Assert.assertEquals("Orig Y mismatch @ " + i, p1.origY, p2.origY);
        Assert.assertEquals("Orig value mismatch @ " + i, p1.origValue, p2.origValue, delta);
        Assert.assertEquals("Error mismatch @ " + i, p1.error, p2.error, 1e-6);
        Assert.assertEquals("Noise mismatch @ " + i, p1.noise, p2.noise, delta);
        Assert.assertNotNull("Params is null @ " + i, p2.params);
        Assert.assertEquals("Background mismatch @ " + i, p1.getBackground(), p2.getBackground(), delta);
        Assert.assertEquals("Signal mismatch @ " + i, p1.getSignal(), p2.getSignal(), delta);
        Assert.assertEquals("XPosition mismatch @ " + i, p1.getXPosition(), p2.getXPosition(), delta);
        Assert.assertEquals("YPosition mismatch @ " + i, p1.getYPosition(), p2.getYPosition(), delta);
        Assert.assertEquals("XSD mismatch @ " + i, p1.getXSD(), p2.getXSD(), 1e-6);
        Assert.assertEquals("YSD mismatch @ " + i, p1.getYSD(), p2.getYSD(), 1e-6);
        Assert.assertEquals("ID mismatch @ " + i, p1.getId(), p2.getId());
    }
}

Example 70 with PeakResult

use of gdsc.smlm.results.PeakResult in project GDSC-SMLM by aherbert.

the class FIRE method cropToRoi.

private MemoryPeakResults cropToRoi(MemoryPeakResults results) {
    if (roiBounds == null)
        return results;
    // Adjust bounds relative to input results image
    //Rectangle2D.Float bounds = results.getDataBounds();
    Rectangle bounds = results.getBounds(true);
    double xscale = roiImageWidth / bounds.width;
    double yscale = roiImageHeight / bounds.height;
    float minX = (float) (bounds.x + roiBounds.x / xscale);
    float maxX = (float) (minX + roiBounds.width / xscale);
    float minY = (float) (bounds.y + (roiBounds.y / yscale));
    float maxY = (float) (minY + roiBounds.height / yscale);
    // Create a new set of results within the bounds
    MemoryPeakResults newResults = new MemoryPeakResults();
    newResults.begin();
    for (PeakResult peakResult : results.getResults()) {
        float x = peakResult.params[Gaussian2DFunction.X_POSITION];
        float y = peakResult.params[Gaussian2DFunction.Y_POSITION];
        if (x < minX || x > maxX || y < minY || y > maxY)
            continue;
        newResults.add(peakResult);
    }
    newResults.end();
    newResults.copySettings(results);
    newResults.setBounds(new Rectangle((int) minX, (int) minY, (int) (maxX - minX), (int) (maxY - minY)));
    return newResults;
}