Examples with DataException uk.ac.sussex.gdsc.core.data.DataException used on opensource projects

Example 11 with DataException

use of uk.ac.sussex.gdsc.core.data.DataException in project GDSC-SMLM by aherbert.

the class BackgroundEstimator method drawPlot.

/**
 * Build a plot of the noise estimate from the current frame. Limit the preview to 100 frames.
 */
private void drawPlot() {
    IJ.showStatus("Estimating background ...");
    final int start = imp.getCurrentSlice();
    final int end = Math.min(imp.getStackSize(), start + 100);
    final int size = end - start + 1;
    final double[] xValues = new double[size];
    final double[] noise1 = new double[size];
    final double[] noise2 = new double[size];
    final double[] background = new double[size];
    final double[] threshold = new double[size];
    final double[] percentile = new double[size];
    final ImageStack stack = imp.getImageStack();
    final Rectangle bounds = imp.getProcessor().getRoi();
    float[] buffer = null;
    for (int slice = start, i = 0; slice <= end; slice++, i++) {
        IJ.showProgress(i, size);
        final ImageProcessor ip = stack.getProcessor(slice);
        buffer = ImageJImageConverter.getData(ip.getPixels(), ip.getWidth(), ip.getHeight(), bounds, buffer);
        final DataEstimator de = new DataEstimator(buffer, bounds.width, bounds.height);
        de.setFraction(settings.fraction);
        de.setHistogramSize(settings.histogramSize);
        de.setThresholdMethod(settings.thresholdMethod);
        xValues[i] = slice;
        try {
            noise1[i] = de.getNoise();
            noise2[i] = de.getNoise(FitProtosHelper.convertNoiseEstimatorMethod(settings.noiseMethod));
            background[i] = de.getBackground();
            threshold[i] = de.getThreshold();
            percentile[i] = de.getPercentile(settings.percentile);
        } catch (final Exception ex) {
            throw new DataException("Failed to estimate the background", ex);
        }
    }
    IJ.showProgress(1);
    IJ.showStatus("Plotting background ...");
    final WindowOrganiser wo = new WindowOrganiser();
    plot(wo, xValues, noise1, noise2, null, "Noise", "Background Noise", "Global Noise", null);
    plot(wo, xValues, background, threshold, percentile, "Background", "Background", "Threshold", "Percentile");
    wo.tile();
    IJ.showStatus("");
}

Example 12 with DataException

use of uk.ac.sussex.gdsc.core.data.DataException in project GDSC-SMLM by aherbert.

the class BlinkEstimator method calculateAveragePrecision.

private double calculateAveragePrecision(MemoryPeakResults results, boolean verbose) {
    double fittedAverage = 0;
    try {
        final PcPalmMolecules fitter = new PcPalmMolecules();
        final List<Molecule> molecules = fitter.extractLocalisations(results);
        final String title = (verbose) ? TITLE + " Localisation Precision" : null;
        fittedAverage = fitter.calculateAveragePrecision(molecules, title, settings.histogramBins, true, true);
    } catch (final DataException ex) {
    // This is thrown when the data cannot be converted for precision computation
    }
    // Sense check the precision
    if (fittedAverage < 5 || fittedAverage > 60) {
        final GenericDialog gd = new GenericDialog(TITLE);
        gd.addMessage("Estimated precision is not within expected bounds.\nPlease enter an estimate:");
        gd.addSlider("Precision", 5, 60, fittedAverage);
        gd.showDialog();
        if (!gd.wasCanceled()) {
            fittedAverage = gd.getNextNumber();
        }
    }
    // The fitter does checks for a good fit to the histogram so just return the value
    return fittedAverage;
}

Example 13 with DataException

use of uk.ac.sussex.gdsc.core.data.DataException in project GDSC-SMLM by aherbert.

the class SummariseResults method createSummary.

private static String createSummary(StringBuilder sb, MemoryPeakResults result, int[] removeNullResults) {
    sb.setLength(0);
    final DescriptiveStatistics[] stats = new DescriptiveStatistics[2];
    for (int i = 0; i < stats.length; i++) {
        stats[i] = new DescriptiveStatistics();
    }
    if (result.hasNullResults()) {
        IJ.log("Null results in dataset: " + result.getName());
        if (removeNullResults[0] == UNKNOWN) {
            final GenericDialog gd = new GenericDialog(TITLE);
            gd.addMessage("There are invalid results in memory.\n \nClean these results?");
            gd.enableYesNoCancel();
            gd.hideCancelButton();
            gd.showDialog();
            removeNullResults[0] = (gd.wasOKed()) ? YES : NO;
        }
        if (removeNullResults[0] == NO) {
            result = result.copy();
        }
        result.removeNullResults();
    }
    final CalibrationReader calibration = result.getCalibrationReader();
    PrecisionMethod precisionMethod = PrecisionMethod.PRECISION_METHOD_NA;
    boolean stored = false;
    final int size = result.size();
    if (size > 0) {
        // Precision
        try {
            final PrecisionResultProcedure p = new PrecisionResultProcedure(result);
            // Use stored precision if possible
            stored = result.hasPrecision();
            precisionMethod = p.getPrecision(stored);
            for (final double v : p.precisions) {
                stats[0].addValue(v);
            }
        } catch (final DataException ex) {
        // Ignore
        }
        // SNR
        try {
            final SnrResultProcedure p = new SnrResultProcedure(result);
            p.getSnr();
            for (final double v : p.snr) {
                stats[1].addValue(v);
            }
        } catch (final DataException ex) {
        // Ignore
        }
    }
    sb.append(result.getName());
    int maxT = 0;
    if (result.size() == 0) {
        sb.append("\t0\t0");
    } else {
        sb.append('\t').append(result.size());
        maxT = result.getMaxFrame();
        sb.append('\t').append(maxT);
    }
    if (calibration != null && calibration.hasExposureTime()) {
        sb.append('\t').append(TextUtils.millisToString((long) Math.ceil(maxT * calibration.getExposureTime())));
    } else {
        sb.append("\t-");
    }
    if (size > 0) {
        final boolean includeDeviations = result.hasDeviations();
        final long memorySize = MemoryPeakResults.estimateMemorySize(size, includeDeviations);
        final String memory = TextUtils.bytesToString(memorySize);
        sb.append('\t').append(memory);
    } else {
        sb.append("\t-");
    }
    final Rectangle bounds = result.getBounds(true);
    TextUtils.formatTo(sb, "\t%d,%d,%d,%d", bounds.x, bounds.y, bounds.x + bounds.width, bounds.y + bounds.height);
    if (calibration != null) {
        sb.append('\t').append(calibration.hasNmPerPixel() ? MathUtils.rounded(calibration.getNmPerPixel()) : '-');
        sb.append('\t').append(calibration.hasExposureTime() ? MathUtils.rounded(calibration.getExposureTime()) : '-');
        if (calibration.hasCameraType()) {
            sb.append('\t').append(CalibrationProtosHelper.getName(calibration.getCameraType()));
            if (calibration.isCcdCamera()) {
                sb.append(" bias=").append(calibration.getBias());
                sb.append(" gain=").append(calibration.getCountPerPhoton());
            }
        } else {
            sb.append("\t-");
        }
        sb.append('\t').append(calibration.hasDistanceUnit() ? UnitHelper.getShortName(calibration.getDistanceUnit()) : '-');
        sb.append('\t').append(calibration.hasIntensityUnit() ? UnitHelper.getShortName(calibration.getIntensityUnit()) : '-');
    } else {
        sb.append("\t\t\t\t\t");
    }
    if (result.is3D()) {
        sb.append("\tY");
    } else {
        sb.append("\tN");
    }
    sb.append("\t").append(FitProtosHelper.getName(precisionMethod));
    if (stored) {
        sb.append(" (Stored)");
    }
    for (int i = 0; i < stats.length; i++) {
        if (Double.isNaN(stats[i].getMean())) {
            sb.append("\t-\t-\t-\t-");
        } else {
            sb.append('\t').append(IJ.d2s(stats[i].getMean(), 3));
            sb.append('\t').append(IJ.d2s(stats[i].getPercentile(50), 3));
            sb.append('\t').append(IJ.d2s(stats[i].getMin(), 3));
            sb.append('\t').append(IJ.d2s(stats[i].getMax(), 3));
        }
    }
    return sb.toString();
}

Example 14 with DataException

use of uk.ac.sussex.gdsc.core.data.DataException in project GDSC-SMLM by aherbert.

the class UpdateResultsBounds method showDialog.

private static boolean showDialog(MemoryPeakResults results) {
    final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addHelp(HelpUrls.getUrl("update-results-bounds"));
    // Force computation of bounds
    Rectangle currentBounds = results.getBounds();
    results.setBounds(null);
    Rectangle autoBounds;
    try {
        autoBounds = results.getBounds(true);
    } catch (final DataException ex) {
        IJ.error(TITLE, "No calibration found to convert to pixel units");
        return false;
    } finally {
        // Reset after forcing computation
        if (currentBounds != null) {
            results.setBounds(currentBounds);
        }
    }
    // Re-acquire the bounds (either the existing bounds or the auto-bounds)
    currentBounds = results.getBounds();
    gd.addMessage(TextUtils.wrap("Set the bounds of the original source image.\n \nAuto-bounds = " + format(autoBounds) + "\n \nThe new bounds will be the union of the auto-bounds and specified bounds " + "to ensure all data is within the bounds.", 80));
    gd.addNumericField("Min_x", currentBounds.x, 0, 6, "px");
    gd.addNumericField("Min_y", currentBounds.y, 0, 6, "px");
    gd.addNumericField("Width", currentBounds.width, 0, 6, "px");
    gd.addNumericField("Height", currentBounds.height, 0, 6, "px");
    gd.showDialog();
    if (gd.wasCanceled()) {
        return false;
    }
    final int x = (int) gd.getNextNumber();
    final int y = (int) gd.getNextNumber();
    final int width = (int) gd.getNextNumber();
    final int height = (int) gd.getNextNumber();
    // Check the bounds are not smaller than the auto-bounds
    final Rectangle newBounds = new Rectangle(x, y, width, height).union(autoBounds);
    if (newBounds.isEmpty()) {
        IJ.error(TITLE, "New bounds are not valid: " + format(newBounds));
        return false;
    }
    results.setBounds(newBounds);
    return true;
}

Example 15 with DataException

use of uk.ac.sussex.gdsc.core.data.DataException in project GDSC-SMLM by aherbert.

the class FilterResults method analyseResults.

/**
 * Analyse the results and determine the range for each filter.
 */
private boolean analyseResults() {
    IJ.showStatus("Analysing results ...");
    final ArrayList<String> error = new ArrayList<>();
    try {
        wp = new WidthResultProcedure(results, DistanceUnit.PIXEL);
        wp.getW();
        final float[] limits = MathUtils.limits(wp.wx);
        maxWidth = limits[1];
        minWidth = limits[0];
        averageWidth = MathUtils.sum(wp.wx) / wp.size();
    } catch (final DataException ex) {
        error.add(ex.getMessage());
        wp = null;
        maxWidth = minWidth = 0;
    }
    try {
        pp = new PrecisionResultProcedure(results);
        pp.getPrecision();
        final double[] limits = MathUtils.limits(pp.precisions);
        maxPrecision = limits[1];
        minPrecision = limits[0];
    } catch (final DataException ex) {
        error.add(ex.getMessage());
        pp = null;
        maxPrecision = minPrecision = 0;
    }
    try {
        sp = new StandardResultProcedure(results, DistanceUnit.PIXEL);
        sp.getXyr();
        // Re-use for convenience
        sp.intensity = new float[sp.x.length];
        sp.background = new float[sp.x.length];
        sp.z = new float[sp.x.length];
        for (int i = 0; i < sp.size(); i++) {
            if (i % 64 == 0) {
                IJ.showProgress(i, sp.size());
            }
            final PeakResult result = sp.peakResults[i];
            final float drift = getDrift(result, sp.x[i], sp.y[i]);
            if (maxDrift < drift) {
                maxDrift = drift;
            }
            if (minDrift > drift) {
                minDrift = drift;
            }
            final float signal = result.getIntensity();
            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;
            }
            // for convenience
            sp.z[i] = drift;
            sp.intensity[i] = signal;
            sp.background[i] = snr;
        }
    } catch (final DataException ex) {
        error.add(ex.getMessage());
        sp = null;
    }
    if (error.size() == 3 || sp == null) {
        final StringBuilder sb = new StringBuilder("Unable to analyse the results:\n");
        for (final String s : error) {
            sb.append(s).append(".\n");
        }
        IJ.error(TITLE, sb.toString());
        return false;
    }
    ImageJUtils.finished();
    return true;
}