Examples with PeakResult gdsc.smlm.results.PeakResult used on opensource projects

Example 51 with PeakResult

use of gdsc.smlm.results.PeakResult in project GDSC-SMLM by aherbert.

the class ResultsMatchCalculator method getCoordinates.

/**
	 * Build a map between the peak id (time point) and a list of coordinates
	 * 
	 * @param results
	 * @param integerCoordinates
	 *            True if the values should be rounded down to integers
	 * @return
	 */
public static TIntObjectHashMap<ArrayList<Coordinate>> getCoordinates(List<PeakResult> results, boolean integerCoordinates) {
    TIntObjectHashMap<ArrayList<Coordinate>> coords = new TIntObjectHashMap<ArrayList<Coordinate>>();
    if (results.size() > 0) {
        ResultsMatchCalculator instance = new ResultsMatchCalculator();
        // 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
        Collections.sort(results);
        int minT = results.get(0).getFrame();
        int maxT = results.get(results.size() - 1).getEndFrame();
        // Create lists
        ArrayList<ArrayList<Coordinate>> tmpCoords = new ArrayList<ArrayList<Coordinate>>(maxT - minT + 1);
        for (int t = minT; t <= maxT; t++) {
            tmpCoords.add(new ArrayList<Coordinate>());
        }
        // Add the results to the lists
        for (PeakResult p : results) {
            final float x, y;
            if (integerCoordinates) {
                x = (int) p.getXPosition();
                y = (int) p.getYPosition();
            } else {
                x = p.getXPosition();
                y = p.getYPosition();
            }
            for (int t = p.getFrame() - minT, i = p.getEndFrame() - p.getFrame() + 1; i-- > 0; t++) tmpCoords.get(t).add(instance.new PeakResultPoint(t + minT, x, y, p));
        }
        // Put in the map
        for (int t = minT, i = 0; t <= maxT; t++, i++) {
            coords.put(t, tmpCoords.get(i));
        }
    }
    return coords;
}

Example 52 with PeakResult

use of gdsc.smlm.results.PeakResult in project GDSC-SMLM by aherbert.

the class PeakFit method addSingleFrameOverlay.

private void addSingleFrameOverlay() {
    // If a single frame was processed add the peaks as an overlay if they are in memory
    ImagePlus imp = this.imp;
    if (fitMaxima && singleFrame > 0) {
        if (source instanceof IJImageSource) {
            String title = source.getName();
            imp = WindowManager.getImage(title);
        }
    }
    if (singleFrame > 0 && imp != null) {
        MemoryPeakResults results = null;
        for (PeakResults r : this.results.toArray()) if (r instanceof MemoryPeakResults) {
            results = (MemoryPeakResults) r;
            break;
        }
        if (results == null || results.size() == 0)
            return;
        ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
        gd.enableYesNoCancel();
        gd.hideCancelButton();
        gd.addMessage("Add the fitted localisations as an overlay?");
        gd.showDialog();
        if (!gd.wasOKed())
            return;
        LUT lut = LUTHelper.createLUT(LutColour.ICE);
        Overlay o = new Overlay();
        ArrayList<PeakResult> list = (ArrayList<PeakResult>) results.getResults();
        for (int i = 0, j = results.size() - 1; i < results.size(); i++, j--) {
            PeakResult r = list.get(i);
            PointRoi roi = new PointRoi(r.getXPosition(), r.getYPosition());
            Color c = LUTHelper.getColour(lut, j, results.size());
            roi.setStrokeColor(c);
            roi.setFillColor(c);
            if (imp.getStackSize() > 1)
                roi.setPosition(singleFrame);
            o.add(roi);
        }
        imp.setOverlay(o);
        imp.getWindow().toFront();
    }
}

Example 53 with PeakResult

use of gdsc.smlm.results.PeakResult in project GDSC-SMLM by aherbert.

the class PulseActivationAnalysis method createActivations.

/**
	 * Creates the activations. This splits the input traces into continuous chains of localisations. Each chain is an
	 * activation. A new activation is created if there are more than the configured number of dark frames since the
	 * last localisation. The start frame for the activation defines the channel the activation is assigned to (this may
	 * be channel 0 if the start frame is not in a pulse start frame).
	 */
private void createActivations() {
    TurboList<Activation> activations = new TurboList<Activation>(traces.length);
    // Activations are only counted if there are at least 
    // n frames between localisations.
    final int n = darkFramesForNewActivation + 1;
    for (Trace trace : traces) {
        // Time-order
        trace.sort();
        ArrayList<PeakResult> points = trace.getPoints();
        // Define the frame for a new activation 
        int nextActivationStartFrame = Integer.MIN_VALUE;
        Trace current = null;
        int channel = 0;
        for (int j = 0; j < points.size(); j++) {
            PeakResult p = points.get(j);
            // Check if this is an activation
            if (p.getFrame() >= nextActivationStartFrame) {
                if (current != null)
                    // Store the last
                    activations.add(new Activation(current, channel));
                // Create a new activation
                current = new Trace(p);
                channel = getChannel(p);
            } else {
                // This is the same chain of localisations
                current.add(p);
            }
            nextActivationStartFrame = p.getEndFrame() + n;
        }
        if (current != null)
            activations.add(new Activation(current, channel));
    }
    save(activations);
}

Example 54 with PeakResult

use of gdsc.smlm.results.PeakResult in project GDSC-SMLM by aherbert.

the class ResultsImageSampler method createResultSamples.

/**
	 * Creates the result samples.
	 * Do this by storing the coordinates at the region index.
	 */
private void createResultSamples() {
    TLongObjectHashMap<ResultsSample> map = new TLongObjectHashMap<ResultsSample>(results.size());
    ResultsSample next = ResultsSample.create(-1);
    for (PeakResult p : results) {
        // Avoid invalid slices
        if (p.getFrame() < 1 || p.getFrame() > stack.getSize())
            continue;
        long index = getIndex(p.getXPosition(), p.getYPosition(), p.getFrame());
        ResultsSample current = map.putIfAbsent(index, next);
        if (current == null) {
            // If the return value is null then this is a new insertion.
            // Set the current value as the one we just added and create the next insertion object.
            current = next;
            current.index = index;
            next = ResultsSample.create(-1);
        }
        current.add(p);
    }
    // Create an array of all the sample entries.
    // This is used to sample regions by density.
    data = new ResultsSample[map.size()];
    map.values(data);
}

Example 55 with PeakResult

use of gdsc.smlm.results.PeakResult in project GDSC-SMLM by aherbert.

the class IJImagePeakResults method addAll.

/*
	 * (non-Javadoc)
	 * 
	 * @see gdsc.utils.fitting.results.PeakResults#addAll(java.util.Collection)
	 */
public void addAll(Collection<PeakResult> results) {
    if (!imageActive)
        return;
    int[] indices = new int[5];
    float[] values = new float[4];
    int nPoints = 0;
    int nValues = 0;
    // Buffer output in batches
    int[] allIndices = new int[100];
    float[] allValues = new float[allIndices.length];
    boolean replace = ((displayFlags & DISPLAY_REPLACE) != 0);
    // We add at most 4 indices for each peak
    int limit = allIndices.length - 4;
    for (PeakResult result : results) {
        float x = mapX(result.getXPosition());
        float y = mapY(result.getYPosition());
        // Check bounds
        if (x < 0 || x >= imageWidth || y < 0 || y >= imageHeight)
            continue;
        if (shouldUpdate(result.getFrame())) {
            addData(nPoints, nValues, allIndices, allValues);
            nPoints = 0;
            nValues = 0;
            updateToFrame(result.getFrame());
        }
        getValue(result.getFrame(), result.params, result.error, x, y, indices, values);
        for (int i = indices[4]; i-- > 0; ) {
            allIndices[nValues] = indices[i];
            allValues[nValues] = values[i];
            nValues++;
        }
        nPoints++;
        if (nValues > limit || replace) {
            addData(nPoints, nValues, allIndices, allValues);
            nPoints = 0;
            nValues = 0;
            updateImage();
            if (!imageActive)
                return;
        }
    }
    // Now add the values to the configured indices
    addData(nPoints, nValues, allIndices, allValues);
    updateImage();
}