Examples with FitEngine gdsc.smlm.engine.FitEngine used on opensource projects

Example 6 with FitEngine

use of gdsc.smlm.engine.FitEngine in project GDSC-SMLM by aherbert.

the class PeakFit method runMaximaFitting.

/**
	 * Load the selected results from memory. All multiple frame results are added directly to the results. All single
	 * frame
	 * results are added to a list of candidate maxima per frame and fitted using the configured parameters.
	 */
private void runMaximaFitting() {
    MemoryPeakResults results = ResultsManager.loadInputResults(inputOption, false);
    if (results == null || results.size() == 0) {
        log("No results for maxima fitting");
        return;
    }
    // No check for imageSource since this has been check in the calling method
    int totalFrames = source.getFrames();
    // Store the indices of each new time-frame
    results.sort();
    List<PeakResult> candidateMaxima = results.getResults();
    // Use the FitEngine to allow multi-threading.
    FitEngine engine = createFitEngine(getNumberOfThreads(totalFrames));
    final int step = Utils.getProgressInterval(totalFrames);
    runTime = System.nanoTime();
    boolean shutdown = false;
    int slice = candidateMaxima.get(0).getFrame();
    ArrayList<PeakResult> sliceCandidates = new ArrayList<PeakResult>();
    Iterator<PeakResult> iter = candidateMaxima.iterator();
    while (iter.hasNext()) {
        PeakResult r = iter.next();
        if (slice != r.getFrame()) {
            if (escapePressed()) {
                shutdown = true;
                break;
            }
            if (slice % step == 0) {
                if (Utils.showStatus("Slice: " + slice + " / " + totalFrames))
                    IJ.showProgress(slice, totalFrames);
            }
            // Process results
            if (!processResults(engine, sliceCandidates, slice))
                break;
            sliceCandidates.clear();
        }
        slice = r.getFrame();
        sliceCandidates.add(r);
    }
    // Process final results
    if (!shutdown)
        processResults(engine, sliceCandidates, slice);
    engine.end(shutdown);
    time = engine.getTime();
    runTime = System.nanoTime() - runTime;
    showResults();
    source.close();
}