Examples with PeakResultPoint gdsc.smlm.ij.plugins.ResultsMatchCalculator.PeakResultPoint used on opensource projects

Example 1 with PeakResultPoint

use of gdsc.smlm.ij.plugins.ResultsMatchCalculator.PeakResultPoint in project GDSC-SMLM by aherbert.

the class BenchmarkSmartSpotRanking method run.

private void run() {
    // Extract all the results in memory into a list per frame. This can be cached
    boolean refresh = false;
    if (lastId != simulationParameters.id) {
        // Do not get integer coordinates
        // The Coordinate objects will be PeakResultPoint objects that store the original PeakResult
        // from the MemoryPeakResults
        actualCoordinates = ResultsMatchCalculator.getCoordinates(results.getResults(), false);
        lastId = simulationParameters.id;
        refresh = true;
    }
    // Extract all the candidates into a list per frame. This can be cached if the settings have not changed
    if (refresh || lastFilterId != BenchmarkSpotFilter.filterResult.id || lastFractionPositives != fractionPositives || lastFractionNegativesAfterAllPositives != fractionNegativesAfterAllPositives || lastNegativesAfterAllPositives != negativesAfterAllPositives) {
        filterCandidates = subsetFilterResults(BenchmarkSpotFilter.filterResult.filterResults);
        lastFilterId = BenchmarkSpotFilter.filterResult.id;
        lastFractionPositives = fractionPositives;
        lastFractionNegativesAfterAllPositives = fractionNegativesAfterAllPositives;
        lastNegativesAfterAllPositives = negativesAfterAllPositives;
    }
    final ImageStack stack = imp.getImageStack();
    // Create a pool of workers
    final int nThreads = Prefs.getThreads();
    final 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, actualCoordinates, filterCandidates);
        Thread t = new Thread(worker);
        workers.add(worker);
        threads.add(t);
        t.start();
    }
    // Process the frames
    totalProgress = filterCandidates.size();
    stepProgress = Utils.getProgressInterval(totalProgress);
    progress = 0;
    filterCandidates.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();
        }
    }
    threads.clear();
    IJ.showProgress(1);
    if (Utils.isInterrupted()) {
        IJ.showStatus("Aborted");
        return;
    }
    IJ.showStatus("Collecting results ...");
    rankResultsId++;
    rankResults = new TIntObjectHashMap<RankResults>();
    for (Worker w : workers) {
        rankResults.putAll(w.results);
    }
    summariseResults(rankResults);
    IJ.showStatus("");
}

Example 2 with PeakResultPoint

use of gdsc.smlm.ij.plugins.ResultsMatchCalculator.PeakResultPoint in project GDSC-SMLM by aherbert.

the class BenchmarkSpotFit method run.

private void run() {
    // Extract all the results in memory into a list per frame. This can be cached
    boolean refresh = false;
    if (lastId != simulationParameters.id) {
        // Do not get integer coordinates
        // The Coordinate objects will be PeakResultPoint objects that store the original PeakResult
        // from the MemoryPeakResults
        actualCoordinates = ResultsMatchCalculator.getCoordinates(results.getResults(), false);
        lastId = simulationParameters.id;
        refresh = true;
    }
    // Extract all the candidates into a list per frame. This can be cached if the settings have not changed
    final int width = (config.isIncludeNeighbours()) ? config.getRelativeFitting() : 0;
    final Settings settings = new Settings(BenchmarkSpotFilter.filterResult.id, fractionPositives, fractionNegativesAfterAllPositives, negativesAfterAllPositives, width);
    if (refresh || !settings.equals(lastSettings)) {
        filterCandidates = subsetFilterResults(BenchmarkSpotFilter.filterResult.filterResults, width);
        lastSettings = settings;
        lastFilterId = BenchmarkSpotFilter.filterResult.id;
    }
    stopWatch = StopWatch.createStarted();
    final ImageStack stack = imp.getImageStack();
    clearFitResults();
    // Save results to memory
    MemoryPeakResults peakResults = new MemoryPeakResults();
    peakResults.copySettings(this.results);
    peakResults.setName(TITLE);
    MemoryPeakResults.addResults(peakResults);
    // 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, actualCoordinates, filterCandidates, peakResults);
        Thread t = new Thread(worker);
        workers.add(worker);
        threads.add(t);
        t.start();
    }
    // Fit the frames
    long runTime = System.nanoTime();
    totalProgress = stack.getSize();
    stepProgress = Utils.getProgressInterval(totalProgress);
    progress = 0;
    for (int i = 1; i <= totalProgress; 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();
    IJ.showProgress(1);
    runTime = System.nanoTime() - runTime;
    if (Utils.isInterrupted()) {
        return;
    }
    stopWatch.stop();
    final String timeString = stopWatch.toString();
    IJ.log("Spot fit time : " + timeString);
    IJ.showStatus("Collecting results ...");
    fitResultsId++;
    fitResults = new TIntObjectHashMap<FilterCandidates>();
    for (Worker w : workers) {
        fitResults.putAll(w.results);
    }
    // Assign a unique ID to each result
    int count = 0;
    // Materialise into an array since we use it twice
    FilterCandidates[] candidates = fitResults.values(new FilterCandidates[fitResults.size()]);
    for (FilterCandidates result : candidates) {
        for (int i = 0; i < result.fitResult.length; i++) {
            final MultiPathFitResult fitResult = result.fitResult[i];
            count += count(fitResult.getSingleFitResult());
            count += count(fitResult.getMultiFitResult());
            count += count(fitResult.getDoubletFitResult());
            count += count(fitResult.getMultiDoubletFitResult());
        }
    }
    PreprocessedPeakResult[] preprocessedPeakResults = new PreprocessedPeakResult[count];
    count = 0;
    for (FilterCandidates result : candidates) {
        for (int i = 0; i < result.fitResult.length; i++) {
            final MultiPathFitResult fitResult = result.fitResult[i];
            count = store(fitResult.getSingleFitResult(), count, preprocessedPeakResults);
            count = store(fitResult.getMultiFitResult(), count, preprocessedPeakResults);
            count = store(fitResult.getDoubletFitResult(), count, preprocessedPeakResults);
            count = store(fitResult.getMultiDoubletFitResult(), count, preprocessedPeakResults);
        }
    }
    summariseResults(fitResults, runTime, preprocessedPeakResults, count);
    IJ.showStatus("");
}