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

Example 1 with XyrResultProcedure

use of uk.ac.sussex.gdsc.smlm.results.procedures.XyrResultProcedure 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 2 with XyrResultProcedure

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

the class TraceMatchCalculator method extractPulses.

@Nullable
private static Pulse[] extractPulses(MemoryPeakResults results) {
    if (results == null) {
        return null;
    }
    final Pulse[] pulses = new Pulse[results.size()];
    final Counter i = new Counter();
    results.forEach(DistanceUnit.PIXEL, (XyrResultProcedure) (x, y, result) -> pulses[i.getAndIncrement()] = new Pulse(x, y, result.getFrame(), result.getEndFrame()));
    return pulses;
}

Example 3 with XyrResultProcedure

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

the class SpotAnalysis method addCandidateFrames.

private void addCandidateFrames(String title) {
    for (final MemoryPeakResults r : MemoryPeakResults.getAllResults()) {
        if (r.getSource() instanceof IJImageSource && r.getSource().getName().equals(title)) {
            final float minx = areaBounds.x;
            final float maxx = minx + areaBounds.width;
            final float miny = areaBounds.y;
            final float maxy = miny + areaBounds.height;
            r.forEach(DistanceUnit.PIXEL, (XyrResultProcedure) (x, y, result) -> {
                if (result.getXPosition() >= minx && result.getXPosition() <= maxx && result.getYPosition() >= miny && result.getYPosition() <= maxy) {
                    candidateFrames.add(result.getFrame());
                }
            });
        }
    }
}

Example 4 with XyrResultProcedure

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

the class DriftCalculator method findSpots.

private static Spot[] findSpots(MemoryPeakResults results, Rectangle bounds, int[] limits) {
    final LocalList<Spot> list = new LocalList<>(limits[1] - limits[0] + 1);
    final float minx = bounds.x;
    final float miny = bounds.y;
    final float maxx = (float) bounds.x + bounds.width;
    final float maxy = (float) bounds.y + bounds.height;
    // Find spots within the ROI
    results.forEach(DistanceUnit.PIXEL, (XyrResultProcedure) (x, y, result) -> {
        if (x > minx && x < maxx && y > miny && y < maxy) {
            list.add(new Spot(result.getFrame(), x, y, result.getIntensity()));
        }
    });
    // For each frame pick the strongest spot
    Collections.sort(list, Spot::compare);
    final LocalList<Spot> newList = new LocalList<>(list.size());
    int currentT = -1;
    for (final Spot spot : list) {
        if (currentT != spot.time) {
            newList.add(spot);
            currentT = spot.time;
        }
    }
    return newList.toArray(new Spot[0]);
}

Example 5 with XyrResultProcedure

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

the class CropResults method cropResults.

/**
 * Apply the filters to the data.
 */
private void cropResults() {
    final MemoryPeakResults newResults = createNewResults();
    // These bounds are integer. But this is because the results are meant to come from an image.
    final Rectangle integerBounds = results.getBounds(true);
    // The crop bounds can be floating point...
    // Border
    final double border = settings.getBorder();
    final double xx = integerBounds.x + border;
    final double yy = integerBounds.y + border;
    final double w = Math.max(0, integerBounds.width - 2 * border);
    final double h = Math.max(0, integerBounds.height - 2 * border);
    Rectangle2D pixelBounds = new Rectangle2D.Double(xx, yy, w, h);
    // Bounding box
    if (settings.getSelectRegion()) {
        final Rectangle2D boxBounds = new Rectangle2D.Double(settings.getX(), settings.getY(), settings.getWidth(), settings.getHeight());
        pixelBounds = pixelBounds.createIntersection(boxBounds);
    }
    // and create another intersection
    if (myUseRoi) {
        final ImagePlus imp = WindowManager.getImage(settings.getRoiImage());
        if (imp != null && imp.getRoi() != null) {
            final Rectangle roi = imp.getRoi().getBounds();
            final int roiImageWidth = imp.getWidth();
            final int roiImageHeight = imp.getHeight();
            final double xscale = (double) roiImageWidth / integerBounds.width;
            final double yscale = (double) roiImageHeight / integerBounds.height;
            final Rectangle2D roiBounds = new Rectangle2D.Double(roi.x / xscale, roi.y / yscale, roi.width / xscale, roi.height / yscale);
            pixelBounds = pixelBounds.createIntersection(roiBounds);
        }
    }
    final Rectangle2D bounds = pixelBounds;
    final Predicate<PeakResult> testZ = getZFilter();
    // Copy the results if the origin is reset
    final Consumer<PeakResult> consumer = settings.getResetOrigin() ? r -> newResults.add(r.copy()) : newResults::add;
    if (bounds.getWidth() > 0 && bounds.getHeight() > 0) {
        results.forEach(DistanceUnit.PIXEL, (XyrResultProcedure) (x, y, result) -> {
            if (bounds.contains(x, y) && testZ.test(result)) {
                consumer.accept(result);
            }
        });
    }
    if (settings.getPreserveBounds()) {
        newResults.setBounds(integerBounds);
    } else {
        // Get the lower and upper integer limits
        final int x = (int) Math.floor(bounds.getX());
        final int y = (int) Math.floor(bounds.getY());
        final int ux = (int) Math.ceil(bounds.getX() + bounds.getWidth());
        final int uy = (int) Math.ceil(bounds.getY() + bounds.getHeight());
        // Ensure the width and height are at least 1
        newResults.setBounds(new Rectangle(x, y, Math.max(1, ux - x), Math.max(1, uy - y)));
        if (settings.getResetOrigin()) {
            newResults.translate(-x, -y);
        }
    }
    IJ.showStatus(newResults.size() + " Cropped localisations");
}