Examples with Gaussian2DPeakResultCalculator uk.ac.sussex.gdsc.smlm.results.Gaussian2DPeakResultCalculator used on opensource projects

Example 1 with Gaussian2DPeakResultCalculator

use of uk.ac.sussex.gdsc.smlm.results.Gaussian2DPeakResultCalculator in project GDSC-SMLM by aherbert.

the class TraceDiffusion method calculatePrecision.

/**
 * Calculate the average precision of localisation in the traces.
 *
 * @param traces the traces
 * @param multi true if the traces were from multiple input results
 */
private void calculatePrecision(Trace[] traces, boolean multi) {
    // Check the diffusion simulation for a precision
    if (DiffusionRateTest.isSimulated(results.getName()) && !multi) {
        precision = DiffusionRateTest.getLastSimulationPrecision();
    } else {
        precision = 999;
        try {
            final Gaussian2DPeakResultCalculator calculator = Gaussian2DPeakResultHelper.create(results.getPsf(), results.getCalibration(), Gaussian2DPeakResultHelper.LSE_PRECISION);
            // Get the average precision of the localisations
            precision = 0;
            int count = 0;
            for (final Trace trace : traces) {
                for (int k = 0; k < trace.size(); k++) {
                    final PeakResult r = trace.get(k);
                    precision += calculator.getLsePrecision(r.getParameters(), r.getNoise());
                }
                count += trace.size();
            }
            precision /= count;
        } catch (final ConfigurationException ex) {
        // Ignore this and we will ask the user for the precision
        }
    }
    if (precision > 100) {
        final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
        gd.addMessage("The average precision of the traced results is " + MathUtils.rounded(precision, 4) + " nm.\nPlease verify the precision.");
        gd.addSlider("Precision (nm)", 5, 100, precision);
        gd.showDialog();
        if (!(gd.wasCanceled() || gd.invalidNumber())) {
            precision = Math.abs(gd.getNextNumber());
        }
    }
}

Example 2 with Gaussian2DPeakResultCalculator

use of uk.ac.sussex.gdsc.smlm.results.Gaussian2DPeakResultCalculator 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 the peak results
 * @param candidates the candidates
 * @return the search distance using candidates
 */
private double getSearchDistanceUsingCandidates(MemoryPeakResults peakResults, LinkedList<PeakResult> candidates) {
    final Gaussian2DPeakResultCalculator calculator = Gaussian2DPeakResultHelper.create(peakResults.getPsf(), peakResults.getCalibration(), Gaussian2DPeakResultHelper.LSE_PRECISION);
    double sum = 0;
    for (final PeakResult peakResult : candidates) {
        sum += calculator.getLsePrecision(peakResult.getParameters(), peakResult.getNoise());
    }
    final double nmPerPixel = peakResults.getNmPerPixel();
    return (sum / candidates.size()) * searchDistance / nmPerPixel;
}

Example 3 with Gaussian2DPeakResultCalculator

use of uk.ac.sussex.gdsc.smlm.results.Gaussian2DPeakResultCalculator 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();
}