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

Example 36 with PeakResult

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

the class HysteresisFilter method setup.

@Override
public void setup(MemoryPeakResults peakResults) {
    ok = new HashSet<>();
    // Create a set of candidates and valid peaks
    final MemoryPeakResults traceResults = new MemoryPeakResults();
    // Initialise peaks to check
    final LinkedList<PeakResult> candidates = new LinkedList<>();
    peakResults.forEach((PeakResultProcedure) result -> {
        switch(getStatus(result)) {
            case OK:
                ok.add(result);
                traceResults.add(result);
                break;
            case CANDIDATE:
                candidates.add(result);
                traceResults.add(result);
                break;
            default:
                break;
        }
    });
    if (candidates.isEmpty()) {
        // No candidates for tracing so just return
        return;
    }
    double distanceThreshold;
    switch(searchDistanceMode) {
        case 1:
            distanceThreshold = searchDistance / peakResults.getNmPerPixel();
            break;
        case 0:
        default:
            distanceThreshold = getSearchDistanceUsingCandidates(peakResults, candidates);
    }
    if (distanceThreshold <= 0) {
        return;
    }
    // This must be in frames
    int myTimeThreshold;
    if (timeThresholdMode == 1) {
        // time threshold is in Seconds.
        // Default to 1 frame if not calibrated.
        myTimeThreshold = 1;
        if (peakResults.hasCalibration()) {
            // Convert time threshold in seconds to frames
            final CalibrationReader cr = peakResults.getCalibrationReader();
            final double et = cr.getExposureTime();
            if (et > 0) {
                myTimeThreshold = (int) Math.round((this.timeThreshold / et));
            }
        }
    } else {
        // frames
        myTimeThreshold = (int) this.timeThreshold;
    }
    if (myTimeThreshold <= 0) {
        return;
    }
    // Trace through candidates
    final TraceManager tm = new TraceManager(traceResults);
    tm.setTraceMode(TraceMode.LATEST_FORERUNNER);
    tm.traceMolecules(distanceThreshold, myTimeThreshold);
    final Trace[] traces = tm.getTraces();
    for (final Trace trace : traces) {
        if (trace.size() > 1) {
            // Check if the trace touches a valid point
            boolean isOk = false;
            for (int i = 0; i < trace.size(); i++) {
                if (ok.contains(trace.get(i))) {
                    isOk = true;
                    break;
                }
            }
            // Add the entire trace to the OK points
            if (isOk) {
                for (int i = 0; i < trace.size(); i++) {
                    ok.add(trace.get(i));
                }
            }
        }
    }
}

Example 37 with PeakResult

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

the class Filter method score.

/**
 * Filter the results and return the performance score. Allows benchmarking the filter by marking
 * the results as true or false.
 *
 * <p>Any input PeakResult with an original value that is not zero will be treated as a true
 * result, all other results are false. The filter is run and the results are marked as true
 * positive, false negative and false positive.
 *
 * <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.
 *
 * @param resultsList a list of results to analyse
 * @param failures the number of failures to allow per frame before all peaks are rejected
 * @return the score
 */
public ClassificationResult score(List<MemoryPeakResults> resultsList, final int failures) {
    final int[] s = new int[4];
    for (final MemoryPeakResults peakResults : resultsList) {
        setup(peakResults);
        final FrameCounter counter = new FrameCounter();
        peakResults.forEach((PeakResultProcedure) peak -> {
            counter.advanceAndReset(peak.getFrame());
            final boolean isTrue = peak.getOrigValue() != 0;
            final boolean isPositive;
            if (counter.getCount() > failures) {
                isPositive = false;
            } else {
                isPositive = accept(peak);
            }
            if (isPositive) {
                counter.reset();
            } else {
                counter.increment();
            }
            if (isTrue) {
                if (isPositive) {
                    s[TP]++;
                } else {
                    s[FN]++;
                }
            } else if (isPositive) {
                s[FP]++;
            } else {
                s[TN]++;
            }
        });
        end();
    }
    return new ClassificationResult(s[TP], s[FP], s[TN], s[FN]);
}

Example 38 with PeakResult

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

the class PeakResultTableModel method createTableStructure.

/**
 * Called when the structure of the table should be created. If the structure has not changed or
 * no live table are attached then this does nothing.
 *
 * @param changed Set to true if a property controlling the structure has changed
 */
private void createTableStructure(boolean changed) {
    if (changed) {
        columnsComputed.set(false);
    }
    // so it can be turned off by PeakResultTableModelFrame.
    if (liveCount.get() == 0 || columnsComputed.get()) {
        return;
    }
    columnsComputed.set(true);
    rounder = RounderUtils.create(tableSettings.getRoundingPrecision());
    // Create the converters
    final PeakResultConversionHelper helper = new PeakResultConversionHelper(calibration, psf);
    helper.setIntensityUnit(tableSettings.getIntensityUnit());
    helper.setDistanceUnit(tableSettings.getDistanceUnit());
    helper.setAngleUnit(tableSettings.getAngleUnit());
    final Converter[] converters = helper.getConverters();
    final Converter ic = converters[PeakResult.INTENSITY];
    final String[] paramNames = helper.getNames();
    final String[] unitNames = helper.getUnitNames();
    // Calibration tableCalibration = (helper.isCalibrationChanged()) ? helper.getCalibration() :
    // calibration;
    // Organise the data columns.
    // This is done as per the IJTablePeakResults for consistency
    final LocalList<PeakResultData<?>> valuesList = new LocalList<>();
    final LocalList<String> namesList = new LocalList<>();
    rowCounter = tableSettings.getShowRowCounter();
    if (rowCounter) {
        valuesList.add(new PeakResultDataFrame());
        namesList.add("#");
    }
    valuesList.add(new PeakResultDataFrame());
    addName(valuesList, namesList);
    if (showEndFrame) {
        valuesList.add(new PeakResultDataEndFrame());
        addName(valuesList, namesList);
    }
    if (showId) {
        valuesList.add(new PeakResultDataId());
        addName(valuesList, namesList);
    }
    if (showCategory) {
        valuesList.add(new PeakResultDataCategory());
        addName(valuesList, namesList);
    }
    if (tableSettings.getShowFittingData()) {
        valuesList.add(new PeakResultDataOrigX());
        addName(valuesList, namesList);
        valuesList.add(new PeakResultDataOrigY());
        addName(valuesList, namesList);
        valuesList.add(new PeakResultDataOrigValue());
        addName(valuesList, namesList);
        valuesList.add(new PeakResultDataError());
        addName(valuesList, namesList);
    }
    if (tableSettings.getShowNoiseData()) {
        // Must be converted
        valuesList.add(new PeakResultDataFloat() {

            @Override
            public Float getValue(PeakResult result) {
                return ic.convert(result.getNoise());
            }
        });
        addName("Noise", namesList, unitNames[PeakResult.INTENSITY]);
        valuesList.add(new PeakResultDataFloat() {

            @Override
            public Float getValue(PeakResult result) {
                return ic.convert(result.getMeanIntensity());
            }
        });
        addName("Mean" + paramNames[PeakResult.INTENSITY], namesList, unitNames[PeakResult.INTENSITY]);
        valuesList.add(new PeakResultDataSnr());
        addName(valuesList, namesList);
    }
    int[] outIndices = SimpleArrayUtils.natural(converters.length);
    if (!showZ) {
        final TIntArrayList list = new TIntArrayList(outIndices);
        list.remove(PeakResult.Z);
        outIndices = list.toArray();
    }
    for (final int i : outIndices) {
        // Must be converted
        valuesList.add(new PeakResultDataParameterConverter(converters[i], i));
        addName(paramNames[i], namesList, unitNames[i]);
        if (showDeviations) {
            valuesList.add(new PeakResultDataParameterDeviationConverter(converters[i], i));
            namesList.add("+/-");
        }
    }
    if (tableSettings.getShowPrecision()) {
        PeakResultDataPrecision precision = null;
        try {
            final Gaussian2DPeakResultCalculator calculator = Gaussian2DPeakResultHelper.create(getPsf(), calibration, Gaussian2DPeakResultHelper.LSE_PRECISION);
            precision = new PeakResultDataPrecision() {

                @Override
                public Double getValue(PeakResult result) {
                    if (result.hasPrecision()) {
                        return result.getPrecision();
                    }
                    if (calculator != null) {
                        return calculator.getLsePrecision(result.getParameters(), result.getNoise());
                    }
                    return 0.0;
                }
            };
        } catch (final ConfigurationException | ConversionException ex) {
        // Ignore
        }
        if (precision == null) {
            precision = new PeakResultDataPrecision();
        }
        valuesList.add(precision);
        namesList.add("Precision (nm)");
    }
    values = valuesList.toArray(new PeakResultData<?>[0]);
    names = namesList.toArray(new String[0]);
    fireTableStructureChanged();
}

Example 39 with PeakResult

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

the class TcPalmAnalysis method createBurstLocalisations.

/**
 * Creates the burst localisations using the ranges of the current bursts.
 *
 * @param clusters the clusters
 * @param bursts the bursts
 * @return the burst localisations
 */
private static LocalList<LocalList<PeakResult>> createBurstLocalisations(LocalList<ClusterData> clusters, LocalList<int[]> bursts) {
    final LocalList<LocalList<PeakResult>> burstsLocalisations = new LocalList<>();
    // TODO: Make more efficient. Order clusters by frame and burst by frame
    // Do a single sweep over the clusters and extract the peaks within the burst ranges.
    bursts.forEach(range -> {
        final int min = range[0];
        final int max = range[1];
        final LocalList<PeakResult> list = new LocalList<>();
        // Build from the current selection
        clusters.forEach(cluster -> {
            cluster.results.forEach(peak -> {
                final int t = peak.getFrame();
                if (t >= min && t <= max) {
                    list.add(peak);
                }
            });
        });
        burstsLocalisations.add(list);
    });
    return burstsLocalisations;
}

Example 40 with PeakResult

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

the class SpotInspector method run.

@Override
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(settings.inputOption, false, DistanceUnit.PIXEL, null);
    if (MemoryPeakResults.isEmpty(results)) {
        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();
    source.setReadHint(ReadHint.NONSEQUENTIAL);
    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<>(results.size());
    // Data for the sorting
    final PrecisionResultProcedure pp;
    if (settings.sortOrderIndex == 1) {
        pp = new PrecisionResultProcedure(results);
        pp.getPrecision();
    } else {
        pp = null;
    }
    // Build procedures to get:
    // Shift = position in pixels - originXY
    final StandardResultProcedure sp;
    if (settings.sortOrderIndex == 9) {
        sp = new StandardResultProcedure(results, DistanceUnit.PIXEL);
        sp.getXyr();
    } else {
        sp = null;
    }
    // SD = gaussian widths only for Gaussian PSFs
    final WidthResultProcedure wp;
    if (settings.sortOrderIndex >= 6 && settings.sortOrderIndex <= 8) {
        wp = new WidthResultProcedure(results, DistanceUnit.PIXEL);
        wp.getWxWy();
    } else {
        wp = null;
    }
    // Amplitude for Gaussian PSFs
    final HeightResultProcedure hp;
    if (settings.sortOrderIndex == 2) {
        hp = new HeightResultProcedure(results, IntensityUnit.PHOTON);
        hp.getH();
    } else {
        hp = null;
    }
    final Counter c = new Counter();
    results.forEach((PeakResultProcedure) result -> {
        final float[] score = getScore(result, c.getAndIncrement(), pp, sp, wp, hp, stdDevMax);
        rankedResults.add(new PeakResultRank(result, score[0], score[1]));
    });
    Collections.sort(rankedResults, PeakResultRank::compare);
    // Prepare results table
    final ImageJTablePeakResults table = new ImageJTablePeakResults(false, results.getName(), true);
    table.copySettings(results);
    table.setTableTitle(TITLE);
    table.setAddCounter(true);
    table.setShowZ(results.is3D());
    // TODO - Add to settings
    table.setShowFittingData(true);
    table.setShowNoiseData(true);
    if (settings.showCalibratedValues) {
        table.setDistanceUnit(DistanceUnit.NM);
        table.setIntensityUnit(IntensityUnit.PHOTON);
    } else {
        table.setDistanceUnit(DistanceUnit.PIXEL);
        table.setIntensityUnit(IntensityUnit.COUNT);
    }
    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.incrementAndGet();
    textPanel.addMouseListener(new MouseAdapter() {

        @Override
        public void mouseClicked(MouseEvent event) {
            SpotInspector.this.mouseClicked(event);
        }
    });
    // Add results to the table
    int count = 0;
    for (final PeakResultRank rank : rankedResults) {
        rank.rank = count++;
        table.add(rank.peakResult);
    }
    table.end();
    if (settings.plotScore || settings.plotHistogram) {
        // Get values for the plots
        float[] xValues = null;
        float[] yValues = null;
        double yMin;
        double yMax;
        int spotNumber = 0;
        xValues = new float[rankedResults.size()];
        yValues = new float[xValues.length];
        for (final PeakResultRank rank : rankedResults) {
            xValues[spotNumber] = spotNumber + 1;
            yValues[spotNumber++] = recoverScore(rank.score);
        }
        // Set the min and max y-values using 1.5 x IQR
        final DescriptiveStatistics stats = new DescriptiveStatistics();
        for (final float v : yValues) {
            stats.addValue(v);
        }
        if (settings.removeOutliers) {
            final double lower = stats.getPercentile(25);
            final double upper = stats.getPercentile(75);
            final double iqr = upper - lower;
            yMin = Math.max(lower - iqr, stats.getMin());
            yMax = Math.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);
    }
    // Extract spots into a stack
    final int w = source.getWidth();
    final int h = source.getHeight();
    final int size = 2 * settings.radius + 1;
    final 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, (o1, o2) -> Integer.compare(o1.peakResult.getFrame(), o2.peakResult.getFrame()));
    for (final PeakResultRank rank : rankedResults) {
        final 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.getXPosition());
        final int y = (int) (r.getYPosition());
        // Extract a region but crop to the image bounds
        int minX = x - settings.radius;
        int minY = y - settings.radius;
        final int maxX = Math.min(x + settings.radius + 1, w);
        final int maxY = Math.min(y + settings.radius + 1, h);
        int padX = 0;
        int padY = 0;
        if (minX < 0) {
            padX = -minX;
            minX = 0;
        }
        if (minY < 0) {
            padY = -minY;
            minY = 0;
        }
        final int sizeX = maxX - minX;
        final 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) {
            final ImageProcessor spotIp2 = spotIp.createProcessor(size, size);
            spotIp2.insert(spotIp, padX, padY);
            spotIp = spotIp2;
        }
        final int slice = rank.rank + 1;
        spots.setPixels(spotIp.getPixels(), slice);
        spots.setSliceLabel(MathUtils.rounded(rank.originalScore), slice);
    }
    source.close();
    // Reset to the rank order
    Collections.sort(rankedResults, PeakResultRank::compare);
    final ImagePlus imp = ImageJUtils.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);
    }
}