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

Example 11 with PeakResultProcedure

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

the class ImageJ3DResultsViewer method createRankById.

private static float[] createRankById(MemoryPeakResults results) {
    if (results.hasId()) {
        final TFloatArrayList list = new TFloatArrayList(results.size());
        results.forEach((PeakResultProcedure) r -> list.add(r.getId()));
        return list.toArray();
    }
    return null;
}

Example 12 with PeakResultProcedure

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

the class PeakResultsReader method simplifyTwoAxis.

/**
 * Simplify two axis Gaussian 2D data.
 *
 * @param results the results
 * @param removeTheta the remove theta flag
 */
private void simplifyTwoAxis(MemoryPeakResults results, boolean removeTheta) {
    final int[] indices = PsfHelper.getGaussian2DWxWyIndices(psf);
    final int isx = indices[0];
    final int isy = indices[1];
    // Columns to remove
    int remove = (removeTheta) ? 1 : 0;
    // New PSF type
    PSFType psfType;
    // Determine if sy is redundant
    if (results.forEach((PeakResultProcedureX) peakResult -> peakResult.getParameter(isx) != peakResult.getParameter(isy))) {
        if (!removeTheta) {
            // Already a TwoAxis Gaussian
            return;
        }
        // Otherwise this was a TwoAxisAndTheta with 1 column to remove
        // so it should be simplified
        psfType = PSFType.TWO_AXIS_GAUSSIAN_2D;
    } else {
        // sy is redundant so remove another column
        psfType = PSFType.ONE_AXIS_GAUSSIAN_2D;
        remove++;
    }
    // Update the PSF
    final PSF.Builder builder = psf.toBuilder();
    builder.setPsfType(psfType);
    psf = builder.build();
    results.setPsf(psf);
    // Update the results.
    // We can directly manipulate the params array
    final int newLength = results.getf(0).getNumberOfParameters() - remove;
    if (deviations) {
        results.forEach((PeakResultProcedure) peakResult -> {
            peakResult.resizeParameters(newLength);
            peakResult.resizeParameterDeviations(newLength);
        });
    } else {
        results.forEach((PeakResultProcedure) peakResult -> peakResult.resizeParameters(newLength));
    }
}

Example 13 with PeakResultProcedure

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

the class BenchmarkFilterAnalysis method getCoordinates.

private static TIntObjectHashMap<UniqueIdPeakResult[]> getCoordinates(MemoryPeakResults results) {
    final TIntObjectHashMap<UniqueIdPeakResult[]> coords = new TIntObjectHashMap<>();
    if (results.size() > 0) {
        // Do not use HashMap directly to build the coords object since there
        // will be many calls to getEntry(). Instead sort the results and use
        // a new list for each time point
        results.sort();
        final Counter uniqueId = new Counter();
        final FrameCounter counter = new FrameCounter();
        final LocalList<PeakResult> tmp = new LocalList<>();
        // Add the results to the lists
        results.forEach((PeakResultProcedure) result -> {
            if (counter.advanceAndReset(result.getFrame()) && !tmp.isEmpty()) {
                coords.put(counter.previousFrame(), tmp.toArray(new UniqueIdPeakResult[0]));
                tmp.clear();
            }
            tmp.add(new UniqueIdPeakResult(tmp.size(), uniqueId.getAndIncrement(), result));
        });
        if (!tmp.isEmpty()) {
            coords.put(counter.currentFrame(), tmp.toArray(new UniqueIdPeakResult[0]));
        }
    }
    return coords;
}

Example 14 with PeakResultProcedure

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

the class TranslateResults method run.

@Override
public void run(String arg) {
    SmlmUsageTracker.recordPlugin(this.getClass(), arg);
    if (MemoryPeakResults.isMemoryEmpty()) {
        IJ.error(TITLE, "There are no fitting results in memory");
        return;
    }
    final TranslateResultsSettings.Builder settings = SettingsManager.readTranslateResultsSettings(0).toBuilder();
    // Show a dialog allowing the results set to be filtered
    final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addMessage("Select a dataset to translate");
    ResultsManager.addInput(gd, settings.getInputOption(), InputSource.MEMORY);
    gd.addNumericField("x", settings.getDx(), 3);
    gd.addNumericField("y", settings.getDy(), 3);
    gd.addNumericField("z", settings.getDz(), 3);
    gd.addChoice("Distance_unit", SettingsManager.getDistanceUnitNames(), settings.getDistanceUnitValue());
    gd.addHelp(HelpUrls.getUrl("translate-results"));
    gd.showDialog();
    if (gd.wasCanceled()) {
        return;
    }
    settings.setInputOption(ResultsManager.getInputSource(gd));
    settings.setDx(gd.getNextNumber());
    settings.setDy(gd.getNextNumber());
    settings.setDz(gd.getNextNumber());
    settings.setDistanceUnitValue(gd.getNextChoiceIndex());
    SettingsManager.writeSettings(settings);
    final MemoryPeakResults results = ResultsManager.loadInputResults(settings.getInputOption(), false, null, null);
    if (MemoryPeakResults.isEmpty(results)) {
        IJ.error(TITLE, "No results could be loaded");
        return;
    }
    TypeConverter<DistanceUnit> converter;
    try {
        converter = results.getDistanceConverter(settings.getDistanceUnit());
    } catch (final DataException ex) {
        IJ.error(TITLE, "Unit conversion error: " + ex.getMessage());
        return;
    }
    final float x = (float) converter.convertBack(settings.getDx());
    final float y = (float) converter.convertBack(settings.getDy());
    final float z = (float) converter.convertBack(settings.getDz());
    // Reset the 2D bounds
    if (x != 0 || y != 0) {
        results.setBounds(null);
    }
    results.forEach((PeakResultProcedure) peakResult -> {
        final float[] params = peakResult.getParameters();
        params[PeakResult.X] += x;
        params[PeakResult.Y] += y;
        params[PeakResult.Z] += z;
    });
}

Example 15 with PeakResultProcedure

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

the class TraceMolecules method convertToClusterPoints.

/**
 * Convert a list of peak results into points for the clustering engine.
 *
 * @param results the results
 * @return the list of clusters
 */
public static List<ClusterPoint> convertToClusterPoints(MemoryPeakResults results) {
    final ArrayList<ClusterPoint> points = new ArrayList<>(results.size());
    final Counter counter = new Counter();
    results.forEach((PeakResultProcedure) result -> points.add(ClusterPoint.newTimeClusterPoint(counter.getAndIncrement(), result.getXPosition(), result.getYPosition(), result.getIntensity(), result.getFrame(), result.getEndFrame())));
    return points;
}