Examples with MaximaSpotFilter gdsc.smlm.filters.MaximaSpotFilter used on opensource projects

Example 1 with MaximaSpotFilter

use of gdsc.smlm.filters.MaximaSpotFilter in project GDSC-SMLM by aherbert.

the class FitEngineConfiguration method createSpotFilter.

/**
	 * Create the spot filter for identifying candidate maxima. The actual border, search width and smoothing parameters
	 * can be configured relative to the configured standard deviations or left absolute. The standard deviation is used
	 * to determine the Half-Width at Half-Maximum (HWHM) for each dimension and the parameters set as follows.
	 * 
	 * <pre>
	 * 
	 * int search = (int) Math.ceil(getSearch() * hwhmMax);
	 * int border = (int) Math.floor(getBorder() * hwhmMax);
	 * // For each filter
	 * double smooth = getSmooth(i) * hwhmMin;
	 * 
	 * </pre>
	 * 
	 * @param relative
	 *            True if the parameters should be made relative to the configured standard deviations
	 * @return
	 */
public MaximaSpotFilter createSpotFilter(boolean relative) {
    final double hwhmMin, hwhmMax;
    if (relative) {
        // Get the half-width at half maximim
        hwhmMin = getHWHMMin();
        hwhmMax = getHWHMMax();
    } else {
        hwhmMin = hwhmMax = 1;
    }
    // Region for maxima finding
    int search = (int) Math.ceil(Maths.round(getSearch() * hwhmMax, 0.01));
    if (search < 1)
        search = 1;
    // Border where peaks are ignored
    int border = (int) Math.floor(Maths.round(getBorder() * hwhmMax, 0.01));
    if (border < 0)
        border = 0;
    DataProcessor processor0 = createDataProcessor(border, 0, hwhmMin);
    final int nFilters = Math.min(dataFilter.length, smooth.length);
    final MaximaSpotFilter spotFilter;
    switch(dataFilterType) {
        case JURY:
            if (nFilters > 1) {
                DataProcessor[] processors = new DataProcessor[nFilters];
                processors[0] = processor0;
                for (int i = 1; i < nFilters; i++) processors[i] = createDataProcessor(border, i, hwhmMin);
                spotFilter = new JurySpotFilter(search, border, processors);
                break;
            }
        case DIFFERENCE:
            if (nFilters > 1) {
                DataProcessor processor1 = createDataProcessor(border, 1, hwhmMin);
                spotFilter = new DifferenceSpotFilter(search, border, processor0, processor1);
                break;
            }
        case SINGLE:
        default:
            spotFilter = new SingleSpotFilter(search, border, processor0);
    }
    return spotFilter;
}

Example 2 with MaximaSpotFilter

use of gdsc.smlm.filters.MaximaSpotFilter in project GDSC-SMLM by aherbert.

the class SpotFinderPreview method run.

/*
	 * (non-Javadoc)
	 * 
	 * @see ij.plugin.filter.PlugInFilter#run(ij.process.ImageProcessor)
	 */
public void run(ImageProcessor ip) {
    Rectangle bounds = ip.getRoi();
    MaximaSpotFilter filter = config.createSpotFilter(true);
    // Crop to the ROI
    FloatProcessor fp = ip.crop().toFloat(0, null);
    float[] data = (float[]) fp.getPixels();
    int width = fp.getWidth();
    int height = fp.getHeight();
    Spot[] spots = filter.rank(data, width, height);
    data = filter.getPreprocessedData();
    fp = new FloatProcessor(width, height, data);
    ip = ip.duplicate();
    ip.insert(fp, bounds.x, bounds.y);
    //ip.resetMinAndMax();
    ip.setMinAndMax(fp.getMin(), fp.getMax());
    Overlay o = new Overlay();
    o.add(new ImageRoi(0, 0, ip));
    if (label != null) {
        // Get results for frame
        Coordinate[] actual = ResultsMatchCalculator.getCoordinates(actualCoordinates, imp.getCurrentSlice());
        Coordinate[] predicted = new Coordinate[spots.length];
        for (int i = 0; i < spots.length; i++) {
            predicted[i] = new BasePoint(spots[i].x + bounds.x, spots[i].y + bounds.y);
        }
        // Q. Should this use partial scoring with multi-matches allowed.
        // If so then this needs to be refactored out of the BenchmarkSpotFilter class.
        // TODO - compute AUC and max jaccard and plot			
        // Compute matches
        List<PointPair> matches = new ArrayList<PointPair>(Math.min(actual.length, predicted.length));
        List<Coordinate> FP = new ArrayList<Coordinate>(predicted.length);
        MatchResult result = MatchCalculator.analyseResults2D(actual, predicted, distance * fitConfig.getInitialPeakStdDev0(), null, FP, null, matches);
        // Show scores
        setLabel(String.format("P=%s, R=%s, J=%s", Utils.rounded(result.getPrecision()), Utils.rounded(result.getRecall()), Utils.rounded(result.getJaccard())));
        // Create Rois for TP and FP
        if (showTP) {
            float[] x = new float[matches.size()];
            float[] y = new float[x.length];
            int n = 0;
            for (PointPair pair : matches) {
                BasePoint p = (BasePoint) pair.getPoint2();
                x[n] = p.getX() + 0.5f;
                y[n] = p.getY() + 0.5f;
                n++;
            }
            addRoi(0, o, x, y, n, Color.green);
        }
        if (showFP) {
            float[] x = new float[predicted.length - matches.size()];
            float[] y = new float[x.length];
            int n = 0;
            for (Coordinate c : FP) {
                BasePoint p = (BasePoint) c;
                x[n] = p.getX() + 0.5f;
                y[n] = p.getY() + 0.5f;
                n++;
            }
            addRoi(0, o, x, y, n, Color.red);
        }
    } else {
        float[] x = new float[spots.length];
        float[] y = new float[x.length];
        for (int i = 0; i < spots.length; i++) {
            x[i] = spots[i].x + bounds.x + 0.5f;
            y[i] = spots[i].y + bounds.y + 0.5f;
        }
        PointRoi roi = new PointRoi(x, y);
        // Add options to configure colour and labels
        o.add(roi);
    }
    imp.setOverlay(o);
}

Example 3 with MaximaSpotFilter

use of gdsc.smlm.filters.MaximaSpotFilter in project GDSC-SMLM by aherbert.

the class BenchmarkFilterAnalysis method createResults.

/**
	 * Create peak results.
	 *
	 * @param filterResults
	 *            The results from running the filter (or null)
	 * @param filter
	 *            the filter
	 */
private MemoryPeakResults createResults(PreprocessedPeakResult[] filterResults, DirectFilter filter, boolean withBorder) {
    if (filterResults == null) {
        final MultiPathFilter multiPathFilter = createMPF(filter, minimalFilter);
        //multiPathFilter.setDebugFile("/tmp/filter.txt");
        filterResults = filterResults(multiPathFilter);
    }
    MemoryPeakResults results = new MemoryPeakResults();
    results.copySettings(this.results);
    results.setName(TITLE);
    if (withBorder) {
        // To produce the same results as the PeakFit plugin we must implement the border
        // functionality used in the FitWorker. This respects the border of the spot filter.
        FitEngineConfiguration config = new FitEngineConfiguration(new FitConfiguration());
        updateAllConfiguration(config);
        MaximaSpotFilter spotFilter = config.createSpotFilter(true);
        final int border = spotFilter.getBorder();
        int[] bounds = getBounds();
        final int borderLimitX = bounds[0] - border;
        final int borderLimitY = bounds[1] - border;
        for (PreprocessedPeakResult spot : filterResults) {
            if (spot.getX() > border && spot.getX() < borderLimitX && spot.getY() > border && spot.getY() < borderLimitY) {
                double[] p = spot.toGaussian2DParameters();
                float[] params = new float[p.length];
                for (int j = 0; j < p.length; j++) params[j] = (float) p[j];
                int frame = spot.getFrame();
                int origX = (int) p[Gaussian2DFunction.X_POSITION];
                int origY = (int) p[Gaussian2DFunction.Y_POSITION];
                results.addf(frame, origX, origY, 0, 0, spot.getNoise(), params, null);
            }
        }
    } else {
        for (PreprocessedPeakResult spot : filterResults) {
            double[] p = spot.toGaussian2DParameters();
            float[] params = new float[p.length];
            for (int j = 0; j < p.length; j++) params[j] = (float) p[j];
            int frame = spot.getFrame();
            int origX = (int) p[Gaussian2DFunction.X_POSITION];
            int origY = (int) p[Gaussian2DFunction.Y_POSITION];
            results.addf(frame, origX, origY, 0, 0, spot.getNoise(), params, null);
        }
    }
    return results;
}

Example 4 with MaximaSpotFilter

use of gdsc.smlm.filters.MaximaSpotFilter in project GDSC-SMLM by aherbert.

the class BenchmarkSpotFilter method run.

private BenchmarkFilterResult run(FitEngineConfiguration config, boolean relativeDistances, boolean batchSummary) {
    if (Utils.isInterrupted())
        return null;
    MaximaSpotFilter spotFilter = config.createSpotFilter(relativeDistances);
    // Extract all the results in memory into a list per frame. This can be cached
    if (// || lastRelativeDistances != relativeDistances)
    lastId != simulationParameters.id) {
        // Always use float coordinates.
        // The Worker adds a pixel offset for the spot coordinates.
        TIntObjectHashMap<ArrayList<Coordinate>> coordinates = ResultsMatchCalculator.getCoordinates(results.getResults(), false);
        actualCoordinates = new TIntObjectHashMap<PSFSpot[]>();
        lastId = simulationParameters.id;
        //lastRelativeDistances = relativeDistances;
        // Store these so we can reset them
        final int total = totalProgress;
        final String prefix = progressPrefix;
        // Spot PSFs may overlap so we must determine the amount of signal overlap and amplitude effect 
        // for each spot...
        IJ.showStatus("Computing PSF overlap ...");
        final int nThreads = Prefs.getThreads();
        final BlockingQueue<Integer> jobs = new ArrayBlockingQueue<Integer>(nThreads * 2);
        List<OverlapWorker> workers = new LinkedList<OverlapWorker>();
        List<Thread> threads = new LinkedList<Thread>();
        for (int i = 0; i < nThreads; i++) {
            OverlapWorker worker = new OverlapWorker(jobs, coordinates);
            Thread t = new Thread(worker);
            workers.add(worker);
            threads.add(t);
            t.start();
        }
        // Process the frames
        totalProgress = coordinates.size();
        stepProgress = Utils.getProgressInterval(totalProgress);
        progress = 0;
        coordinates.forEachKey(new TIntProcedure() {

            public boolean execute(int value) {
                put(jobs, value);
                return true;
            }
        });
        // Finish all the worker threads by passing in a null job
        for (int i = 0; i < threads.size(); i++) {
            put(jobs, -1);
        }
        // Wait for all to finish
        for (int i = 0; i < threads.size(); i++) {
            try {
                threads.get(i).join();
            } catch (InterruptedException e) {
                e.printStackTrace();
            }
            actualCoordinates.putAll(workers.get(i).coordinates);
        }
        threads.clear();
        IJ.showProgress(-1);
        IJ.showStatus("");
        setupProgress(total, prefix);
    }
    if (!batchMode)
        IJ.showStatus("Computing results ...");
    final ImageStack stack = imp.getImageStack();
    float background = 0;
    if (spotFilter.isAbsoluteIntensity()) {
        // To allow the signal factor to be computed we need to lower the image by the background so 
        // that the intensities correspond to the results amplitude.
        // Just assume the background is uniform.
        double sum = 0;
        for (PeakResult r : results) sum += r.getBackground();
        background = (float) (sum / results.size());
    }
    // Create a pool of workers
    final int nThreads = Prefs.getThreads();
    BlockingQueue<Integer> jobs = new ArrayBlockingQueue<Integer>(nThreads * 2);
    List<Worker> workers = new LinkedList<Worker>();
    List<Thread> threads = new LinkedList<Thread>();
    for (int i = 0; i < nThreads; i++) {
        Worker worker = new Worker(jobs, stack, spotFilter, background);
        Thread t = new Thread(worker);
        workers.add(worker);
        threads.add(t);
        t.start();
    }
    // Fit the frames
    for (int i = 1; i <= stack.getSize(); i++) {
        put(jobs, i);
    }
    // Finish all the worker threads by passing in a null job
    for (int i = 0; i < threads.size(); i++) {
        put(jobs, -1);
    }
    // Wait for all to finish
    for (int i = 0; i < threads.size(); i++) {
        try {
            threads.get(i).join();
        } catch (InterruptedException e) {
            e.printStackTrace();
        }
    }
    threads.clear();
    if (Utils.isInterrupted())
        return null;
    if (!batchMode) {
        IJ.showProgress(-1);
        IJ.showStatus("Collecting results ...");
    }
    TIntObjectHashMap<FilterResult> filterResults = new TIntObjectHashMap<FilterResult>();
    time = 0;
    for (Worker w : workers) {
        time += w.time;
        filterResults.putAll(w.results);
    }
    // Show a table of the results
    BenchmarkFilterResult filterResult = summariseResults(filterResults, config, spotFilter, relativeDistances, batchSummary);
    if (!batchMode)
        IJ.showStatus("");
    return filterResult;
}

Example 5 with MaximaSpotFilter

use of gdsc.smlm.filters.MaximaSpotFilter in project GDSC-SMLM by aherbert.

the class SmoothImage method run.

/*
	 * (non-Javadoc)
	 * 
	 * @see ij.plugin.filter.PlugInFilter#run(ij.process.ImageProcessor)
	 */
public void run(ImageProcessor ip) {
    Rectangle bounds = ip.getRoi();
    // Crop to the ROI
    FloatProcessor fp = ip.crop().toFloat(0, null);
    float[] data = (float[]) fp.getPixels();
    MaximaSpotFilter filter = createSpotFilter();
    int width = fp.getWidth();
    int height = fp.getHeight();
    data = filter.preprocessData(data, width, height);
    //System.out.println(filter.getDescription());
    fp = new FloatProcessor(width, height, data);
    ip.insert(fp, bounds.x, bounds.y);
    //ip.resetMinAndMax();
    ip.setMinAndMax(fp.getMin(), fp.getMax());
}