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

Example 41 with MemoryPeakResults

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

the class PCPALMMolecules method cropToRoi.

private MemoryPeakResults cropToRoi(MemoryPeakResults results) {
    Rectangle bounds = results.getBounds(true);
    area = (bounds.width * bounds.height * results.getNmPerPixel() * results.getNmPerPixel()) / 1e6;
    if (roiBounds == null) {
        return results;
    }
    // Adjust bounds relative to input results image
    double xscale = (double) roiImageWidth / bounds.width;
    double yscale = (double) roiImageHeight / bounds.height;
    roiBounds.x /= xscale;
    roiBounds.width /= xscale;
    roiBounds.y /= yscale;
    roiBounds.height /= yscale;
    float minX = (int) (roiBounds.x);
    float maxX = (int) Math.ceil(roiBounds.x + roiBounds.width);
    float minY = (int) (roiBounds.y);
    float maxY = (int) Math.ceil(roiBounds.y + roiBounds.height);
    // Update the area with the cropped region
    area *= (maxX - minX) / bounds.width;
    area *= (maxY - minY) / bounds.height;
    // Create a new set of results within the bounds
    MemoryPeakResults newResults = new MemoryPeakResults();
    newResults.begin();
    for (PeakResult peakResult : results.getResults()) {
        float x = peakResult.params[Gaussian2DFunction.X_POSITION];
        float y = peakResult.params[Gaussian2DFunction.Y_POSITION];
        if (x < minX || x > maxX || y < minY || y > maxY)
            continue;
        newResults.add(peakResult);
    }
    newResults.end();
    newResults.copySettings(results);
    newResults.setBounds(new Rectangle((int) minX, (int) minY, (int) (maxX - minX), (int) (maxY - minY)));
    return newResults;
}

Example 42 with MemoryPeakResults

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

the class TraceMolecules method saveResults.

static MemoryPeakResults saveResults(MemoryPeakResults sourceResults, Trace[] traces, String name) {
    MemoryPeakResults tracedResults = TraceManager.convertToPeakResults(sourceResults, traces);
    tracedResults.setName(sourceResults.getName() + " " + name);
    MemoryPeakResults.addResults(tracedResults);
    return tracedResults;
}

Example 43 with MemoryPeakResults

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

the class TraceMolecules method saveCentroidResults.

static MemoryPeakResults saveCentroidResults(MemoryPeakResults sourceResults, Trace[] traces, String name) {
    MemoryPeakResults tracedResults = TraceManager.convertToCentroidPeakResults(sourceResults, traces);
    tracedResults.setName(sourceResults.getName() + " " + name);
    MemoryPeakResults.addResults(tracedResults);
    return tracedResults;
}

Example 44 with MemoryPeakResults

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

the class CreateData method saveFixedAndMoving.

private void saveFixedAndMoving(MemoryPeakResults results, String title) {
    if (simpleMode || benchmarkMode || spotMode)
        return;
    if (settings.diffusionRate <= 0 || settings.fixedFraction >= 1)
        return;
    MemoryPeakResults fixedResults = copyMemoryPeakResults("Fixed");
    MemoryPeakResults movingResults = copyMemoryPeakResults("Moving");
    List<PeakResult> peakResults = results.getResults();
    // Sort using the ID
    Collections.sort(peakResults, new Comparator<PeakResult>() {

        public int compare(PeakResult o1, PeakResult o2) {
            return o1.getId() - o2.getId();
        }
    });
    int currentId = -1;
    MemoryPeakResults currentResults = movingResults;
    for (PeakResult p : peakResults) {
        // The ID was stored in the result's parameter standard deviation array
        if (currentId != p.getId()) {
            currentId = p.getId();
            currentResults = (movingMolecules.contains(currentId)) ? movingResults : fixedResults;
        }
        currentResults.add(p);
    }
    movingResults.end();
    fixedResults.end();
    // Reset the input results
    results.sort();
}

Example 45 with MemoryPeakResults

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

the class BlinkEstimator method run.

/*
	 * (non-Javadoc)
	 * 
	 * @see ij.plugin.PlugIn#run(java.lang.String)
	 */
public void run(String arg) {
    SMLMUsageTracker.recordPlugin(this.getClass(), arg);
    // Require some fit results and selected regions
    if (MemoryPeakResults.isMemoryEmpty()) {
        IJ.error(TITLE, "There are no fitting results in memory");
        return;
    }
    if (!showDialog())
        return;
    MemoryPeakResults results = ResultsManager.loadInputResults(inputOption, true);
    if (results == null || results.size() == 0) {
        IJ.error(TITLE, "No results could be loaded");
        IJ.showStatus("");
        return;
    }
    msPerFrame = results.getCalibration().getExposureTime();
    Utils.log("%s: %d localisations", TITLE, results.size());
    showPlots = true;
    if (rangeFittedPoints > 0) {
        computeFitCurves(results, true);
    } else {
        computeBlinkingRate(results, true);
    }
}