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

Example 6 with PeakResult

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

the class FilterResults method filterResults.

/**
	 * Apply the filters to the data
	 */
private void filterResults() {
    checkLimits();
    MemoryPeakResults newResults = new MemoryPeakResults();
    newResults.copySettings(results);
    newResults.setName(results.getName() + " Filtered");
    // Initialise the mask
    ByteProcessor mask = getMask(filterSettings.maskTitle);
    MaskDistribution maskFilter = null;
    final float centreX = results.getBounds().width / 2.0f;
    final float centreY = results.getBounds().height / 2.0f;
    if (mask != null) {
        double scaleX = (double) results.getBounds().width / mask.getWidth();
        double scaleY = (double) results.getBounds().height / mask.getHeight();
        maskFilter = new MaskDistribution((byte[]) mask.getPixels(), mask.getWidth(), mask.getHeight(), 0, scaleX, scaleY);
    }
    int i = 0;
    final int size = results.size();
    final double maxVariance = filterSettings.maxPrecision * filterSettings.maxPrecision;
    for (PeakResult result : results.getResults()) {
        if (i % 64 == 0)
            IJ.showProgress(i, size);
        if (getDrift(result) > filterSettings.maxDrift)
            continue;
        if (result.getSignal() < filterSettings.minSignal)
            continue;
        if (getSNR(result) < filterSettings.minSNR)
            continue;
        if (getVariance(result) > maxVariance)
            continue;
        final float width = getWidth(result);
        if (width < filterSettings.minWidth || width > filterSettings.maxWidth)
            continue;
        if (maskFilter != null) {
            // Check the coordinates are inside the mask
            double[] xy = new double[] { result.getXPosition() - centreX, result.getYPosition() - centreY };
            if (!maskFilter.isWithinXY(xy))
                continue;
        }
        // Passed all filters. Add to the results
        newResults.add(result);
    }
    IJ.showProgress(1);
    IJ.showStatus(newResults.size() + " Filtered localisations");
    MemoryPeakResults.addResults(newResults);
}

Example 7 with PeakResult

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

the class FilterResults method analyseResults.

/**
	 * Analyse the results and determine the range for each filter
	 */
private void analyseResults() {
    IJ.showStatus("Analysing results ...");
    nmPerPixel = results.getNmPerPixel();
    gain = results.getGain();
    emCCD = results.isEMCCD();
    double maxVariance = maxPrecision * maxPrecision;
    double minVariance = minPrecision * minPrecision;
    int size = results.size();
    int i = 0;
    for (PeakResult result : results.getResults()) {
        if (i % 64 == 0)
            IJ.showProgress(i, size);
        final float drift = getDrift(result);
        if (maxDrift < drift)
            maxDrift = drift;
        if (minDrift > drift)
            minDrift = drift;
        final float signal = result.getSignal();
        if (maxSignal < signal)
            maxSignal = signal;
        if (minSignal > signal)
            minSignal = signal;
        final float snr = getSNR(result);
        if (maxSNR < snr)
            maxSNR = snr;
        if (minSNR > snr)
            minSNR = snr;
        // Use variance to avoid sqrt()
        final double variance = getVariance(result);
        if (maxVariance < variance)
            maxVariance = variance;
        if (minVariance > variance)
            minVariance = variance;
        final float width = getWidth(result);
        averageWidth += width;
        if (maxWidth < width)
            maxWidth = width;
        if (minWidth > width)
            minWidth = width;
    }
    averageWidth /= results.size();
    maxPrecision = Math.sqrt(maxVariance);
    minPrecision = Math.sqrt(minVariance);
    IJ.showProgress(1);
    IJ.showStatus("");
}

Example 8 with PeakResult

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

the class LoadLocalisations method getZDepth.

private boolean getZDepth(MemoryPeakResults results) {
    // The z-depth is stored in pixels in the error field
    double min = results.getHead().error;
    double max = min;
    for (PeakResult peak : results.getResults()) {
        if (min > peak.error)
            min = peak.error;
        else if (max < peak.error)
            max = peak.error;
    }
    // No z-depth
    if (min == max && min == 0)
        return true;
    maxz = FastMath.min(maxz, max);
    minz = FastMath.max(minz, min);
    // Display in nm
    final double pp = results.getNmPerPixel();
    min *= pp;
    max *= pp;
    String msg = String.format("%d localisations with %.2f <= z <= %.2f", results.size(), min, max);
    min = Math.floor(min);
    max = Math.ceil(max);
    GenericDialog gd = new GenericDialog(TITLE);
    gd.addMessage(msg);
    gd.addCheckbox("Limit Z-depth", limitZ);
    gd.addSlider("minZ", min, max, minz * pp);
    gd.addSlider("maxZ", min, max, maxz * pp);
    gd.showDialog();
    if (gd.wasCanceled() || gd.invalidNumber()) {
        return false;
    }
    myLimitZ = limitZ = gd.getNextBoolean();
    minz = gd.getNextNumber() / pp;
    maxz = gd.getNextNumber() / pp;
    return true;
}

Example 9 with PeakResult

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

the class FIRE method canCalculatePrecision.

private boolean canCalculatePrecision(MemoryPeakResults results) {
    // Calibration is required to compute the precision
    Calibration cal = results.getCalibration();
    if (cal == null)
        return false;
    if (!cal.hasNmPerPixel() || !cal.hasGain() || !cal.hasEMCCD())
        return false;
    // Check all have a width and signal
    PeakResult[] data = results.toArray();
    for (int i = 0; i < data.length; i++) {
        PeakResult p = data[i];
        if (p.getSD() <= 0 || p.getSignal() <= 0)
            return true;
    }
    // Check for variable width that is not 1 and a variable signal
    for (int i = 0; i < data.length; i++) {
        PeakResult p = data[i];
        // Check this is valid
        if (p.getSD() != 1) {
            // Check the rest for a different value
            float w1 = p.getSD();
            float s1 = p.getSignal();
            for (int j = i + 1; j < data.length; j++) {
                PeakResult p2 = data[j];
                if (p2.getSD() != 1 && p2.getSD() != w1 && p2.getSignal() != s1)
                    return true;
            }
            // All the results are the same, this is not valid
            break;
        }
    }
    return false;
}

Example 10 with PeakResult

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

the class HysteresisFilter method getSearchDistanceUsingCandidates.

/**
	 * Find average precision of the candidates and use it for the search
	 * distance
	 * 
	 * @param peakResults
	 * @param candidates
	 * @return
	 */
private double getSearchDistanceUsingCandidates(MemoryPeakResults peakResults, LinkedList<PeakResult> candidates) {
    SummaryStatistics stats = new SummaryStatistics();
    final double nmPerPixel = peakResults.getNmPerPixel();
    final double gain = peakResults.getGain();
    final boolean emCCD = peakResults.isEMCCD();
    for (PeakResult peakResult : candidates) {
        stats.addValue(peakResult.getPrecision(nmPerPixel, gain, emCCD));
    }
    double distanceThreshold = stats.getMean() * searchDistance / nmPerPixel;
    return distanceThreshold;
}