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

Example 1 with TypeConverter

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

the class CreateData method setNoise.

/**
 * Sets the noise in the results if missing.
 *
 * @param results the results
 * @param imp the imp
 */
private static void setNoise(MemoryPeakResults results, ImagePlus imp) {
    // Loaded results do not have noise
    if (results.hasNoise()) {
        return;
    }
    IJ.showStatus("Estimating noise ...");
    // Compute noise per frame
    final ImageStack stack = imp.getImageStack();
    final int width = stack.getWidth();
    final int height = stack.getHeight();
    final IJImageSource source = new IJImageSource(imp);
    final float[] noise = new float[source.getFrames() + 1];
    source.setReadHint(ReadHint.SEQUENTIAL);
    source.open();
    for (int slice = 1; slice < noise.length; slice++) {
        final float[] data = source.next();
        // Use the trimmed method as there may be a lot of spots in the frame
        noise[slice] = FitWorker.estimateNoise(data, width, height, NoiseEstimatorMethod.QUICK_RESIDUALS_LEAST_TRIMMED_OF_SQUARES);
    }
    // Statistics stats = Statistics.create(Arrays.copyOfRange(noise, 1, noise.length));
    // System.out.printf("Noise = %.3f +/- %.3f (%d)\n", stats.getMean(),
    // stats.getStandardDeviation(), stats.getN());
    // Convert noise units from counts to the result format
    final TypeConverter<IntensityUnit> c = results.getIntensityConverter(IntensityUnit.COUNT);
    for (int i = 0; i < noise.length; i++) {
        noise[i] = c.convertBack(noise[i]);
    }
    results.forEach((PeakResultProcedure) result -> {
        if (result.getFrame() < noise.length) {
            result.setNoise(noise[result.getFrame()]);
        }
    });
}

Example 2 with TypeConverter

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

the class CreateData method loadBenchmarkData.

/**
 * Load benchmark data using an open image and a XYZ text file.
 */
private void loadBenchmarkData() {
    if (!showLoadDialog()) {
        // resetMemory();
        return;
    }
    // Load the image
    final ImagePlus imp = WindowManager.getImage(benchmarkImage);
    if (imp == null) {
        IJ.error(TITLE, "No benchmark image: " + benchmarkImage);
        // resetMemory();
        return;
    }
    // Load the results
    final MemoryPeakResults results = getSimulationResults();
    if (results == null) {
        IJ.error(TITLE, "No benchmark results: " + benchmarkResultsName);
        // resetMemory();
        return;
    }
    results.setName(imp.getTitle() + " (Results)");
    results.setBounds(new Rectangle(0, 0, imp.getWidth(), imp.getHeight()));
    final IJImageSource imageSource = new IJImageSource(imp);
    results.setSource(imageSource);
    // Load the settings as these are used in the dialog
    settings = SettingsManager.readCreateDataSettings(0).toBuilder();
    simulationParameters = showSimulationParametersDialog(imp, results);
    if (simulationParameters != null) {
        // Convert data to allow analysis as if a Gaussian2D PSF
        final boolean isGaussian2D = PsfHelper.isGaussian2D(results.getPsf());
        if (isGaussian2D) {
            Gaussian2DPeakResultHelper.addMeanIntensity(results.getPsf(), results);
        } else if (simulationParameters.sd > 0) {
            final TypeConverter<DistanceUnit> dc = results.getDistanceConverter(DistanceUnit.NM);
            final PSF.Builder psf = PsfProtosHelper.getDefaultPsf(PSFType.ONE_AXIS_GAUSSIAN_2D).toBuilder();
            psf.getParametersBuilder(0).setValue(dc.convertBack(simulationParameters.sd));
            results.setPsf(psf.build());
            // Update all the results. This assumes the results do not have data for a custom PSF,
            // i.e. the parameters only have [t,i,x,y,z]
            final LocalList<PeakResult> newResults = new LocalList<>(results.size());
            final float sd = (float) dc.convertBack(simulationParameters.sd);
            final double meanFactor = Gaussian2DPeakResultHelper.getMeanSignalUsingP05(1, sd, sd);
            results.forEach((PeakResultProcedure) r -> {
                final PeakResult peak = r.resize(PeakResult.STANDARD_PARAMETERS + 1);
                peak.setMeanIntensity((float) (peak.getIntensity() * meanFactor));
                peak.setParameter(PeakResult.STANDARD_PARAMETERS, sd);
                newResults.add(peak);
            });
            results.begin();
            results.addAll(newResults);
            results.end();
        }
        setBackground(results);
        setNoise(results, imp);
        setBenchmarkResults(imp, results);
        IJ.showStatus("Loaded " + TextUtils.pleural(results.size(), "result"));
    } else {
        resetMemory();
    }
}

Example 3 with TypeConverter

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

the class TraceExporter method exportSpotOn.

private void exportSpotOn(MemoryPeakResults results) {
    try (BufferedWriter out = Files.newBufferedWriter(Paths.get(settings.directory, results.getName() + ".csv"))) {
        out.write("frame,t,trajectory,x,y");
        out.newLine();
        final TypeConverter<TimeUnit> converter = UnitConverterUtils.createConverter(TimeUnit.FRAME, TimeUnit.SECOND, results.getCalibrationReader().getExposureTime());
        @SuppressWarnings("resource") final BufferedWriter writer = out;
        results.forEach(DistanceUnit.UM, (XyrResultProcedure) (x, y, result) -> {
            try {
                if (result.hasEndFrame()) {
                    final String sId = Integer.toString(result.getId());
                    final String sx = Float.toString(x);
                    final String sy = Float.toString(y);
                    for (int t = result.getFrame(); t <= result.getEndFrame(); t++) {
                        writer.write(Integer.toString(t));
                        writer.write(",");
                        writer.write(Float.toString(converter.convert(t)));
                        writer.write(",");
                        writer.write(sId);
                        writer.write(",");
                        writer.write(sx);
                        writer.write(",");
                        writer.write(sy);
                        writer.newLine();
                    }
                } else {
                    writer.write(Integer.toString(result.getFrame()));
                    writer.write(",");
                    writer.write(Float.toString(converter.convert(result.getFrame())));
                    writer.write(",");
                    writer.write(Integer.toString(result.getId()));
                    writer.write(",");
                    writer.write(Float.toString(x));
                    writer.write(",");
                    writer.write(Float.toString(y));
                    writer.newLine();
                }
            } catch (final IOException ex) {
                throw new RuntimeException(ex);
            }
        });
    } catch (final IOException | RuntimeException ex) {
        handleException(ex);
    }
}

Example 4 with TypeConverter

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

the class TraceExporter method export.

private void export(MemoryPeakResults results) {
    // Copy to allow manipulation
    results = results.copy();
    // Strip results with no trace Id
    results.removeIf(result -> result.getId() <= 0);
    // Sort by ID then time
    results.sort(IdFramePeakResultComparator.INSTANCE);
    // Split traces with big jumps and long tracks into smaller tracks
    results = splitTraces(results);
    results = splitLongTraces(results);
    // Count each ID and remove short traces
    int id = 0;
    int count = 0;
    int tracks = 0;
    int maxLength = 0;
    final TIntHashSet remove = new TIntHashSet();
    for (int i = 0, size = results.size(); i < size; i++) {
        final PeakResult result = results.get(i);
        if (result.getId() != id) {
            if (count < settings.minLength) {
                remove.add(id);
            } else {
                tracks++;
                maxLength = Math.max(maxLength, count);
            }
            count = 0;
            id = result.getId();
        }
        count += getLength(result);
    }
    // Final ID
    if (count < settings.minLength) {
        remove.add(id);
    } else {
        tracks++;
        maxLength = Math.max(maxLength, count);
    }
    if (!remove.isEmpty()) {
        results.removeIf(result -> remove.contains(result.getId()));
        results.sort(IdFramePeakResultComparator.INSTANCE);
    }
    if (settings.wobble > 0) {
        // Just leave any exceptions to trickle up and kill the plugin
        final TypeConverter<DistanceUnit> c = results.getDistanceConverter(DistanceUnit.NM);
        final double w = c.convertBack(settings.wobble);
        final UniformRandomProvider rng = UniformRandomProviders.create();
        final NormalizedGaussianSampler gauss = SamplerUtils.createNormalizedGaussianSampler(rng);
        final boolean is3D = results.is3D();
        results.forEach((PeakResultProcedure) peakResult -> {
            peakResult.setXPosition((float) (peakResult.getXPosition() + w * gauss.sample()));
            peakResult.setYPosition((float) (peakResult.getYPosition() + w * gauss.sample()));
            if (is3D) {
                peakResult.setZPosition((float) (peakResult.getZPosition() + w * gauss.sample()));
            }
        });
    }
    if (settings.format == 2) {
        exportVbSpt(results);
    } else if (settings.format == 1) {
        exportAnaDda(results);
    } else {
        exportSpotOn(results);
    }
    ImageJUtils.log("Exported %s: %s in %s", results.getName(), TextUtils.pleural(results.size(), "localisation"), TextUtils.pleural(tracks, "track"));
    if (settings.showTraceLengths) {
        // We store and index (count-1)
        final int[] h = new int[maxLength];
        id = 0;
        for (int i = 0, size = results.size(); i < size; i++) {
            final PeakResult result = results.get(i);
            if (result.getId() != id) {
                h[count - 1]++;
                count = 0;
                id = result.getId();
            }
            count += getLength(result);
        }
        h[count - 1]++;
        final String title = TITLE + ": " + results.getName();
        final Plot plot = new Plot(title, "Length", "Frequency");
        plot.addPoints(SimpleArrayUtils.newArray(h.length, 1, 1.0f), SimpleArrayUtils.toFloat(h), Plot.BAR);
        plot.setLimits(SimpleArrayUtils.findIndex(h, i -> i != 0), maxLength + 1, 0, Double.NaN);
        ImageJUtils.display(title, plot);
    }
}

Example 5 with TypeConverter

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

the class SpotInspector method mouseClicked.

private void mouseClicked(MouseEvent event) {
    if (id != currentId.get()) {
        return;
    }
    // Show the result that was double clicked in the result table
    if (event.getClickCount() > 1) {
        final int rank = textPanel.getSelectionStart() + 1;
        // Show the spot that was double clicked
        final ImagePlus imp = WindowManager.getImage(TITLE);
        if (imp != null && rank > 0 && rank <= imp.getStackSize()) {
            imp.setSlice(rank);
            if (imp.getWindow() != null) {
                imp.getWindow().toFront();
            }
            final PeakResult r = rankedResults.get(rank - 1).peakResult;
            final TypeConverter<DistanceUnit> dc = results.getDistanceConverter(DistanceUnit.PIXEL);
            final float rx = dc.convert(r.getXPosition());
            final float ry = dc.convert(r.getYPosition());
            final int x = (int) rx;
            final int y = (int) ry;
            // Find bounds
            final int minX = x - settings.radius;
            final int minY = y - settings.radius;
            // Require the Shift key to add all spots
            if (!event.isShiftDown()) {
                // Add the single clicked spot
                imp.setRoi(new OffsetPointRoi(rx - minX, ry - minY));
                return;
            }
            // Add all the spots
            final int maxX = x + settings.radius + 1;
            final int maxY = y + settings.radius + 1;
            // Create ROIs
            final HashSet<Point2D.Float> spots = new HashSet<>();
            results.forEach(DistanceUnit.PIXEL, (XyResultProcedure) (xp, yp) -> {
                if (xp > minX && xp < maxX && yp > minY && yp < maxY) {
                    // Use only unique points
                    spots.add(new Point2D.Float(xp - minX, yp - minY));
                }
            });
            final int points = spots.size();
            final float[] ox = new float[points];
            final float[] oy = new float[points];
            final Counter c = new Counter();
            spots.forEach(p -> {
                ox[c.getCount()] = p.x;
                oy[c.getAndIncrement()] = p.y;
            });
            imp.setRoi(new OffsetPointRoi(ox, oy, points));
        }
    }
}