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

Example 1 with XyzrResultProcedure

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

the class TraceExporter method exportVbSpt.

@SuppressWarnings("resource")
private void exportVbSpt(MemoryPeakResults results) {
    // vbSPT file format:
    // https://sourceforge.net/projects/vbspt/
    // Matlab matrix file (.mat) containing at least one variable that is a cell
    // array where each element, representing a trajectory, is a matrix
    // where the rows define the coordinates in one, two or three dimensions
    // in subsequent timesteps. The number of dimensions to be used for the
    // analysis will be set by the runinputfile.
    // The units are arbitrary but vbSPT starting estimates must be in the same
    // units. Either nm or μm are recommended.
    // 3 columns for n rows of localisations
    // 1. x coordinate (μm)
    // 2. y coordinate (μm)
    // 3. z coordinate (μm)
    // 
    // Note: An extra column is added containing the frame. This allows results to
    // be uniquely identified using frame,x,y,z
    // Count the IDs. Each new result ID will increment the count.
    final FrameCounter idCounter = new FrameCounter(results.getFirst().getId() - 1);
    results.forEach((PeakResultProcedure) result -> {
        if (idCounter.advance(result.getId())) {
            idCounter.increment();
        }
    });
    // Create the cell array as 1xN
    final Cell out = Mat5.newCell(1, idCounter.getCount());
    // This will reset the counter to zero and ensure the current frame does not match
    // in the event of a single track
    idCounter.advanceAndReset(idCounter.currentFrame() + 1);
    final boolean is3d = results.is3D();
    // Write the tracks
    final LocalList<double[]> list = new LocalList<>();
    results.forEach(DistanceUnit.UM, (XyzrResultProcedure) (x, y, z, result) -> {
        if (idCounter.advance(result.getId())) {
            addTrack(out, idCounter.getCount() - 1, list, is3d);
            idCounter.increment();
            list.clear();
        }
        list.add(new double[] { x, y, z, result.getFrame() });
    });
    addTrack(out, idCounter.getCount() - 1, list, is3d);
    try (MatFile matFile = Mat5.newMatFile()) {
        matFile.addArray("tracks", out);
        Mat5.writeToFile(matFile, Paths.get(settings.directory, results.getName() + ".mat").toFile());
    } catch (final IOException ex) {
        handleException(ex);
    }
}

Example 2 with XyzrResultProcedure

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

the class ClassificationMatchCalculator method getCoordinates.

/**
 * Build a map between the peak id (time point) and a list of coordinates that pass the filter.
 *
 * @param results the results
 * @param test the test
 * @return the coordinates
 */
public static TIntObjectHashMap<List<PeakResultPoint>> getCoordinates(MemoryPeakResults results, Predicate<PeakResult> test) {
    final TIntObjectHashMap<List<PeakResultPoint>> 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();
        // Create list
        final LocalList<PeakResultPoint> tmpCoords = new LocalList<>();
        // Add the results for each frame
        final FrameCounter counter = results.newFrameCounter();
        results.forEach(DistanceUnit.PIXEL, (XyzrResultProcedure) (x, y, z, r) -> {
            if (counter.advance(r.getFrame()) && !tmpCoords.isEmpty()) {
                coords.put(counter.previousFrame(), tmpCoords.copy());
                tmpCoords.clear();
            }
            if (test.test(r)) {
                tmpCoords.add(new PeakResultPoint(r.getFrame(), x, y, z, r));
            }
        });
        if (!tmpCoords.isEmpty()) {
            coords.put(counter.currentFrame(), tmpCoords.copy());
        }
    }
    return coords;
}