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Example 1 with SplitMix

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

the class ImageJ3DResultsViewer method getPoints.

/**
 * Gets the points.
 *
 * @param results the results
 * @param settings the settings
 * @return the points
 */
static LocalList<Point3f> getPoints(MemoryPeakResults results, ImageJ3DResultsViewerSettingsOrBuilder settings) {
    final LocalList<Point3f> points = new LocalList<>(results.size());
    if (results.is3D()) {
        results.forEach(DistanceUnit.NM, (XyzResultProcedure) (x, y, z) -> {
            points.push(new Point3f(x, y, z));
        });
    } else {
        results.forEach(DistanceUnit.NM, (XyResultProcedure) (x, y) -> {
            points.push(new Point3f(x, y, 0));
        });
        final double range = settings.getDepthRange();
        if (range > 0 && results.size() > 1) {
            final DepthMode mode = DepthMode.forNumber(settings.getDepthMode());
            final double min = -settings.getDepthRange() / 2;
            switch(mode) {
                case DITHER:
                    final SplitMix r = SplitMix.new64(settings.getDitherSeed());
                    for (int i = points.size(); i-- > 0; ) {
                        points.unsafeGet(i).z += (min + r.nextDouble() * range);
                    }
                    break;
                case INTENSITY:
                    // Rank by intensity, highest first
                    final StandardResultProcedure p = new StandardResultProcedure(results);
                    p.getI();
                    final int[] indices = SimpleArrayUtils.natural(results.size());
                    SortUtils.sortIndices(indices, p.intensity, true);
                    final double inc = range / indices.length;
                    for (int i = 0; i < indices.length; i++) {
                        // The standard rendering has +z going away so put the highest rank at min
                        points.unsafeGet(indices[i]).z += (min + i * inc);
                    }
                    break;
                case NONE:
                    break;
                default:
                    throw new IllegalStateException("Unknown depth mode: " + mode);
            }
        }
    }
    return points;
}
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Example 2 with SplitMix

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

the class PeakResultTableModelFrameDemo method main.

/**
 * Launch the application.
 *
 * @param args the arguments
 */
public static void main(String[] args) {
    final SplitMix r = SplitMix.new64(System.currentTimeMillis());
    final int n = 20;
    final ListSelectionModel selectionModel = new DefaultListSelectionModel();
    EventQueue.invokeLater((Runnable) () -> {
        try {
            final PeakResultStoreList store = new ArrayPeakResultStore(10);
            for (int i = n; i-- > 0; ) {
                store.add(new PeakResult(r.nextInt(), r.nextInt(), r.nextInt(), r.nextFloat(), r.nextDouble(), r.nextFloat(), r.nextFloat(), PeakResult.createParams(r.nextFloat(), r.nextFloat(), r.nextFloat(), r.nextFloat(), r.nextFloat()), null));
            }
            final CalibrationWriter cw = new CalibrationWriter();
            cw.setNmPerPixel(100);
            cw.setCountPerPhoton(10);
            cw.setDistanceUnit(DistanceUnit.PIXEL);
            cw.setIntensityUnit(IntensityUnit.COUNT);
            final ResultsTableSettings.Builder tableSettings = ResultsTableSettings.newBuilder();
            tableSettings.setDistanceUnit(DistanceUnit.NM);
            tableSettings.setIntensityUnit(IntensityUnit.PHOTON);
            tableSettings.setShowFittingData(true);
            tableSettings.setShowNoiseData(true);
            tableSettings.setShowPrecision(true);
            tableSettings.setRoundingPrecision(4);
            final PeakResultTableModel model = new PeakResultTableModel(store, cw.getCalibration(), null, tableSettings.build());
            final PeakResultTableModelFrame d = new PeakResultTableModelFrame(model, null, selectionModel);
            d.setTitle("D");
            d.setDefaultCloseOperation(javax.swing.JFrame.EXIT_ON_CLOSE);
            d.setVisible(true);
            // Selecting in one list activates the other list
            final PeakResultTableModelFrame d2 = new PeakResultTableModelFrame(model, null, selectionModel);
            d2.setTitle("D2");
            // Since we have the same selection model we need the same row sorter,
            // otherwise the selection is scrambled by sorting.
            // The alternative would be to get the source for the selection event (the table)
            // and get the row sorter to do the mapping.
            // However this breaks deletion of data as the row sorter double processes the deletion.
            // Basically only one table can use the same selection model when sorting is desired.
            // d2.table.setRowSorter(d.table.getRowSorter())
            d2.setDefaultCloseOperation(javax.swing.JFrame.EXIT_ON_CLOSE);
            d2.setVisible(true);
        } catch (final Exception ex) {
            ex.printStackTrace();
        }
    });
}
Also used : PeakResultStoreList(uk.ac.sussex.gdsc.smlm.results.PeakResultStoreList) SplitMix(uk.ac.sussex.gdsc.core.utils.rng.SplitMix) ListSelectionModel(javax.swing.ListSelectionModel) DefaultListSelectionModel(javax.swing.DefaultListSelectionModel) CalibrationWriter(uk.ac.sussex.gdsc.smlm.data.config.CalibrationWriter) DefaultListSelectionModel(javax.swing.DefaultListSelectionModel) ArrayPeakResultStore(uk.ac.sussex.gdsc.smlm.results.ArrayPeakResultStore) PeakResult(uk.ac.sussex.gdsc.smlm.results.PeakResult)

Aggregations

CustomLineMesh (customnode.CustomLineMesh)1 CustomMesh (customnode.CustomMesh)1 CustomMeshNode (customnode.CustomMeshNode)1 CustomPointMesh (customnode.CustomPointMesh)1 TFloatArrayList (gnu.trove.list.array.TFloatArrayList)1 TObjectIntHashMap (gnu.trove.map.hash.TObjectIntHashMap)1 IJ (ij.IJ)1 ImagePlus (ij.ImagePlus)1 WindowManager (ij.WindowManager)1 GUI (ij.gui.GUI)1 Roi (ij.gui.Roi)1 MacroRunner (ij.macro.MacroRunner)1 PlugIn (ij.plugin.PlugIn)1 LUT (ij.process.LUT)1 Content (ij3d.Content)1 ContentInstant (ij3d.ContentInstant)1 ContentNode (ij3d.ContentNode)1 DefaultUniverse (ij3d.DefaultUniverse)1 Image3DMenubar (ij3d.Image3DMenubar)1 Image3DUniverse (ij3d.Image3DUniverse)1