Examples with PeakResult uk.ac.sussex.gdsc.smlm.results.PeakResult used on opensource projects

Example 56 with PeakResult

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

the class PeakResultTableModelFrameDemo method main.

/**
 * Launch the application.
 *
 * @param args the arguments
 */
public static void main(String[] args) {
    final SplitMix r = SplitMix.new64(System.currentTimeMillis());
    final int n = 20;
    final ListSelectionModel selectionModel = new DefaultListSelectionModel();
    EventQueue.invokeLater((Runnable) () -> {
        try {
            final PeakResultStoreList store = new ArrayPeakResultStore(10);
            for (int i = n; i-- > 0; ) {
                store.add(new PeakResult(r.nextInt(), r.nextInt(), r.nextInt(), r.nextFloat(), r.nextDouble(), r.nextFloat(), r.nextFloat(), PeakResult.createParams(r.nextFloat(), r.nextFloat(), r.nextFloat(), r.nextFloat(), r.nextFloat()), null));
            }
            final CalibrationWriter cw = new CalibrationWriter();
            cw.setNmPerPixel(100);
            cw.setCountPerPhoton(10);
            cw.setDistanceUnit(DistanceUnit.PIXEL);
            cw.setIntensityUnit(IntensityUnit.COUNT);
            final ResultsTableSettings.Builder tableSettings = ResultsTableSettings.newBuilder();
            tableSettings.setDistanceUnit(DistanceUnit.NM);
            tableSettings.setIntensityUnit(IntensityUnit.PHOTON);
            tableSettings.setShowFittingData(true);
            tableSettings.setShowNoiseData(true);
            tableSettings.setShowPrecision(true);
            tableSettings.setRoundingPrecision(4);
            final PeakResultTableModel model = new PeakResultTableModel(store, cw.getCalibration(), null, tableSettings.build());
            final PeakResultTableModelFrame d = new PeakResultTableModelFrame(model, null, selectionModel);
            d.setTitle("D");
            d.setDefaultCloseOperation(javax.swing.JFrame.EXIT_ON_CLOSE);
            d.setVisible(true);
            // Selecting in one list activates the other list
            final PeakResultTableModelFrame d2 = new PeakResultTableModelFrame(model, null, selectionModel);
            d2.setTitle("D2");
            // Since we have the same selection model we need the same row sorter,
            // otherwise the selection is scrambled by sorting.
            // The alternative would be to get the source for the selection event (the table)
            // and get the row sorter to do the mapping.
            // However this breaks deletion of data as the row sorter double processes the deletion.
            // Basically only one table can use the same selection model when sorting is desired.
            // d2.table.setRowSorter(d.table.getRowSorter())
            d2.setDefaultCloseOperation(javax.swing.JFrame.EXIT_ON_CLOSE);
            d2.setVisible(true);
        } catch (final Exception ex) {
            ex.printStackTrace();
        }
    });
}

Example 57 with PeakResult

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

the class ResultsManagerTest method checkEqual.

private static void checkEqual(Spot[] spots, int channel, int slice, int position, int type, MemoryPeakResults actualResults) {
    Assertions.assertNotNull(actualResults, "Input results are null");
    final MemoryPeakResults expectedResults = extract(spots, channel, slice, position, type);
    Assertions.assertEquals(expectedResults.size(), actualResults.size(), "Size differ");
    final PeakResult[] expected = expectedResults.toArray();
    final PeakResult[] actual = actualResults.toArray();
    for (int i = 0; i < actualResults.size(); i++) {
        final int ii = i;
        final PeakResult p1 = expected[i];
        final PeakResult p2 = actual[i];
        Assertions.assertEquals(p1.getFrame(), p2.getFrame(), () -> "Peak mismatch @ " + ii);
        Assertions.assertEquals(p1.getOrigX(), p2.getOrigX(), () -> "Orig X mismatch @ " + ii);
        Assertions.assertEquals(p1.getOrigY(), p2.getOrigY(), () -> "Orig Y mismatch @ " + ii);
        Assertions.assertEquals(p1.getOrigValue(), p2.getOrigValue(), () -> "Orig value mismatch @ " + ii);
        Assertions.assertEquals(p1.getError(), p2.getError(), 1e-6, () -> "Error mismatch @ " + ii);
        Assertions.assertEquals(p1.getNoise(), p2.getNoise(), () -> "Noise mismatch @ " + ii);
        Assertions.assertNotNull(p2.getParameters(), () -> "Params is null @ " + ii);
        Assertions.assertEquals(p1.getBackground(), p2.getBackground(), () -> "Background mismatch @ " + ii);
        Assertions.assertEquals(p1.getIntensity(), p2.getIntensity(), () -> "Signal mismatch @ " + ii);
        Assertions.assertEquals(p1.getXPosition(), p2.getXPosition(), () -> "XPosition mismatch @ " + ii);
        Assertions.assertEquals(p1.getYPosition(), p2.getYPosition(), () -> "YPosition mismatch @ " + ii);
        Assertions.assertEquals(p1.getZPosition(), p2.getZPosition(), () -> "ZPosition mismatch @ " + ii);
        for (int j = PeakResult.STANDARD_PARAMETERS, size = p1.getNumberOfParameters(); j < size; j++) {
            Assertions.assertEquals(p1.getParameter(j), p2.getParameter(j), 1e-6, () -> "Parameter mismatch @ " + ii);
        }
        Assertions.assertEquals(p1.getId(), p2.getId(), () -> "ID mismatch @ " + ii);
    }
}

Example 58 with PeakResult

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

the class ImageJImagePeakResults method addAll.

@Override
public void addAll(PeakResult[] results) {
    if (!imageActive) {
        return;
    }
    final int[] indices = new int[5];
    final float[] values = new float[4];
    int npoints = 0;
    int nvalues = 0;
    // Buffer output in batches
    final int[] allIndices = new int[100];
    final float[] allValues = new float[allIndices.length];
    // We add at most 4 indices for each peak
    final int limit = allIndices.length - 4;
    for (final PeakResult result : results) {
        final float x = mapX(result.getXPosition());
        final float y = mapY(result.getYPosition());
        // Check bounds
        if (x < 0 || x >= imageWidth || y < 0 || y >= imageHeight) {
            continue;
        }
        if (shouldUpdate(result.getFrame())) {
            addData(npoints, nvalues, allIndices, allValues);
            npoints = 0;
            nvalues = 0;
            updateToFrame(result.getFrame());
        }
        getValue(result.getFrame(), result.getId(), result.getParameters(), result.getError(), x, y, indices, values);
        for (int i = indices[4]; i-- > 0; ) {
            allIndices[nvalues] = indices[i];
            allValues[nvalues] = values[i];
            nvalues++;
        }
        npoints++;
        if (nvalues > limit) {
            addData(npoints, nvalues, allIndices, allValues);
            npoints = 0;
            nvalues = 0;
            updateImage();
            if (!imageActive) {
                return;
            }
        }
    }
    // Now add the values to the configured indices
    addData(npoints, nvalues, allIndices, allValues);
    updateImage();
}

Example 59 with PeakResult

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

the class ResultsImageSampler method getSample.

/**
 * Gets the sample image. The image is a stack of the samples with an overlay of the localisation
 * positions. The info property is set with details of the localisations and the image is
 * calibrated.
 *
 * @param countNo the number of samples with no localisations
 * @param countLow the number of samples with low localisations
 * @param countHigh the number of samples with high localisations
 * @return the sample image (could be null if no samples were made)
 */
public ImagePlus getSample(int countNo, int countLow, int countHigh) {
    final ImageStack out = new ImageStack(size, size);
    if (!isValid()) {
        return null;
    }
    sampleList.clear();
    // empty
    for (final int i : RandomUtils.sample(countNo, no.length, rng)) {
        sampleList.add(ResultsSample.createEmpty(no[i]));
    }
    // low
    for (final int i : RandomUtils.sample(countLow, lower, rng)) {
        sampleList.add(data[i]);
    }
    // high
    for (final int i : RandomUtils.sample(countHigh, upper, rng)) {
        sampleList.add(data[i + lower]);
    }
    if (sampleList.isEmpty()) {
        return null;
    }
    double nmPerPixel = 1;
    if (results.hasCalibration()) {
        final CalibrationReader calibration = results.getCalibrationReader();
        if (calibration.hasNmPerPixel()) {
            nmPerPixel = calibration.getNmPerPixel();
        }
    }
    // Sort descending by number in the frame
    final ResultsSample[] samples = sampleList.toArray(new ResultsSample[0]);
    Arrays.sort(samples, ReverseCountComparator.INSTANCE);
    final int[] xyz = new int[3];
    final Rectangle stackBounds = new Rectangle(stack.getWidth(), stack.getHeight());
    final Overlay overlay = new Overlay();
    final StringBuilder sb = new StringBuilder();
    if (nmPerPixel == 1) {
        sb.append("Sample X Y Z Signal\n");
    } else {
        sb.append("Sample X(nm) Y(nm) Z(nm) Signal\n");
    }
    for (final ResultsSample sample : samples) {
        getXyz(sample.index, xyz);
        // Construct the region to extract
        Rectangle target = new Rectangle(xyz[0], xyz[1], size, size);
        target = target.intersection(stackBounds);
        if (target.width == 0 || target.height == 0) {
            continue;
        }
        // Extract the frame
        final int slice = xyz[2];
        final ImageProcessor ip = stack.getProcessor(slice);
        // Cut out the desired pixels (some may be blank if the block overruns the source image)
        final ImageProcessor ip2 = ip.createProcessor(size, size);
        for (int y = 0; y < target.height; y++) {
            for (int x = 0, i = y * size, index = (y + target.y) * ip.getWidth() + target.x; x < target.width; x++, i++, index++) {
                ip2.setf(i, ip.getf(index));
            }
        }
        final int sampleSize = sample.size();
        if (sampleSize > 0) {
            final float[] ox = new float[sampleSize];
            final float[] oy = new float[sampleSize];
            final int position = out.getSize() + 1;
            // Create an ROI with the localisations
            for (int i = 0; i < sampleSize; i++) {
                final PeakResult p = sample.list.get(i);
                ox[i] = p.getXPosition() - xyz[0];
                oy[i] = p.getYPosition() - xyz[1];
                sb.append(position).append(' ');
                sb.append(MathUtils.rounded(ox[i] * nmPerPixel)).append(' ');
                sb.append(MathUtils.rounded(oy[i] * nmPerPixel)).append(' ');
                sb.append(MathUtils.rounded(p.getZPosition() * nmPerPixel)).append(' ');
                sb.append(MathUtils.rounded(p.getIntensity())).append('\n');
            }
            final PointRoi roi = new OffsetPointRoi(ox, oy, sampleSize);
            roi.setPosition(position);
            overlay.add(roi);
        }
        out.addSlice(String.format("Frame=%d @ %d,%d px (n=%d)", slice, xyz[0], xyz[1], sampleSize), ip2.getPixels());
    }
    if (out.getSize() == 0) {
        return null;
    }
    final ImagePlus imp = new ImagePlus("Sample", out);
    imp.setOverlay(overlay);
    // Note: Only the info property can be saved to a TIFF file
    imp.setProperty("Info", sb.toString());
    if (nmPerPixel != 1) {
        final ij.measure.Calibration cal = new ij.measure.Calibration();
        cal.setUnit("nm");
        cal.pixelHeight = cal.pixelWidth = nmPerPixel;
        imp.setCalibration(cal);
    }
    return imp;
}

Example 60 with PeakResult

use of uk.ac.sussex.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 failures before each peak is stored in the origX property of the PeakResult.
 *
 * @param results the 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) {
    final MemoryPeakResults newResults = new MemoryPeakResults();
    final FrameCounter counter = new FrameCounter();
    newResults.copySettings(results);
    setup(results);
    final double[] s = new double[4];
    final Counter p = new Counter();
    results.forEach((PeakResultProcedure) peak -> {
        counter.advanceAndReset(peak.getFrame());
        final boolean isPositive = accept(peak);
        if (isPositive) {
            peak.setOrigX(counter.getCount());
            counter.reset();
            newResults.add(peak);
        } else {
            counter.increment();
        }
        if (isPositive) {
            p.increment();
            s[TP] += peak.getTruePositiveScore();
            s[FP] += peak.getFalsePositiveScore();
        } else {
            s[FN] += peak.getFalseNegativeScore();
            s[TN] += peak.getTrueNegativeScore();
        }
    });
    end();
    if (score != null && score.length > 5) {
        score[0] = s[TP];
        score[1] = s[FP];
        score[2] = s[TN];
        score[3] = s[FN];
        score[4] = p.getCount();
        score[5] = (double) results.size() - p.getCount();
    }
    return newResults;
}