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

Example 1 with MemoryPeakResults

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

the class ResequenceResults method run.

/*
	 * (non-)
	 * 
	 * @see ij.plugin.PlugIn#run(java.lang.String)
	 */
public void run(String arg) {
    SMLMUsageTracker.recordPlugin(this.getClass(), arg);
    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");
        return;
    }
    if (resequenceResults(results, start, block, skip, (logMapping) ? new IJTrackProgress() : null))
        IJ.showStatus("Resequenced " + results.getName());
}

Example 2 with MemoryPeakResults

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

the class ResultsManager method loadInputResults.

/**
	 * Load the results from the named input option
	 * 
	 * @param inputOption
	 * @param checkCalibration
	 *            Set to true to ensure the results have a valid calibration
	 * @return
	 */
public static MemoryPeakResults loadInputResults(String inputOption, boolean checkCalibration) {
    MemoryPeakResults results = null;
    PeakResultsReader reader = null;
    if (inputOption.equals(INPUT_NONE)) {
    } else if (inputOption.equals(INPUT_FILE)) {
        IJ.showStatus("Reading results file ...");
        reader = new PeakResultsReader(inputFilename);
        IJ.showStatus("Reading " + reader.getFormat() + " results file ...");
        ResultOption[] options = reader.getOptions();
        if (options != null)
            collectOptions(reader, options);
        reader.setTracker(new IJTrackProgress());
        results = reader.getResults();
        reader.getTracker().progress(1.0);
        if (results != null && results.size() > 0) {
            // If the name contains a .tif suffix then create an image source
            if (results.getName() != null && results.getName().contains(".tif") && results.getSource() == null) {
                int index = results.getName().indexOf(".tif");
                results.setSource(new IJImageSource(results.getName().substring(0, index)));
            }
        }
    } else {
        results = loadMemoryResults(inputOption);
    }
    if (results != null && results.size() > 0 && checkCalibration) {
        if (!checkCalibration(results, reader))
            results = null;
    }
    IJ.showStatus("");
    return results;
}

Example 3 with MemoryPeakResults

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

the class ResultsManager method cropToRoi.

private MemoryPeakResults cropToRoi(MemoryPeakResults results) {
    if (roiBounds == null)
        return results;
    // Adjust bounds relative to input results image
    double xscale = roiImageWidth / results.getBounds().width;
    double yscale = roiImageHeight / results.getBounds().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);
    // 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 4 with MemoryPeakResults

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

the class PeakFit method showResults.

protected void showResults() {
    IJ.showProgress(1.0);
    if (time >= 0) {
        if (silent) {
            results.end();
            return;
        }
        // Check if we are sorting
        IJ.showStatus("Finalising results ...");
        for (PeakResults r : results.toArray()) if (r instanceof MemoryPeakResults) {
            if (((MemoryPeakResults) r).isSortAfterEnd())
                IJ.showStatus("Sorting " + r.size() + " results ...");
            break;
        }
        results.end();
        String textTime = Utils.timeToString(time / 1000000.0);
        String textRunTime = Utils.timeToString(runTime / 1000000.0);
        int size = getSize();
        String message = String.format("%s. Fitting Time = %s. Run time = %s", Utils.pleural(size, "localisation"), textTime, textRunTime);
        if (resultsSettings.logProgress)
            IJ.log("-=-=-=-");
        IJ.log(message);
        IJ.showStatus(message);
    } else {
        IJ.showStatus("");
    }
}

Example 5 with MemoryPeakResults

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

the class PulseActivationAnalysis method runSimulation.

private void runSimulation() {
    TITLE += " Simulation";
    if (!showSimulationDialog())
        return;
    long start = System.currentTimeMillis();
    RandomDataGenerator rdg = getRandomDataGenerator();
    // Draw the molecule positions
    Utils.showStatus("Simulating molecules ...");
    float[][][] molecules = new float[3][][];
    MemoryPeakResults[] results = new MemoryPeakResults[3];
    Rectangle bounds = new Rectangle(0, 0, sim_size, sim_size);
    for (int c = 0; c < 3; c++) {
        molecules[c] = simulateMolecules(rdg, c);
        // Create a dataset to store the activations
        MemoryPeakResults r = new MemoryPeakResults();
        r.setCalibration(new Calibration(sim_nmPerPixel, 1, 100));
        r.setBounds(bounds);
        r.setName(TITLE + " C" + (c + 1));
        results[c] = r;
    }
    // Simulate activation
    Utils.showStatus("Simulating activations ...");
    for (int c = 0; c < 3; c++) simulateActivations(rdg, molecules, c, results);
    // Combine
    Utils.showStatus("Producing simulation output ...");
    MemoryPeakResults r = new MemoryPeakResults();
    r.setCalibration(new Calibration(sim_nmPerPixel, 1, 100));
    r.setBounds(new Rectangle(0, 0, sim_size, sim_size));
    r.setName(TITLE);
    ImageProcessor[] images = new ImageProcessor[3];
    for (int c = 0; c < 3; c++) {
        ArrayList<PeakResult> list = (ArrayList<PeakResult>) results[c].getResults();
        r.addAllf(list);
        // Draw the unmixed activations
        IJImagePeakResults image = ImagePeakResultsFactory.createPeakResultsImage(ResultsImage.LOCALISATIONS, true, true, TITLE, bounds, sim_nmPerPixel, 1, 1024.0 / sim_size, 0, ResultsMode.ADD);
        image.setLiveImage(false);
        image.setDisplayImage(false);
        image.begin();
        image.addAll(list);
        image.end();
        images[c] = image.getImagePlus().getProcessor();
    }
    displayComposite(images, TITLE);
    // Add to memory. Set the composite dataset first.
    MemoryPeakResults.addResults(r);
    for (int c = 0; c < 3; c++) MemoryPeakResults.addResults(results[c]);
    // TODO:
    // Show an image of what it looks like with no unmixing, i.e. colours allocated 
    // from the frame
    Utils.showStatus("Simulation complete: " + Utils.timeToString(System.currentTimeMillis() - start));
}