Examples with PeakResultsList uk.ac.sussex.gdsc.smlm.results.PeakResultsList used on opensource projects

Example 1 with PeakResultsList

use of uk.ac.sussex.gdsc.smlm.results.PeakResultsList in project GDSC-SMLM by aherbert.

the class PeakFit method createFitEngine.

/**
 * Creates a fitting engine using the current configuration.
 *
 * @param numberOfThreads the number of threads
 * @param queue the queue
 * @param queueSize the queue size
 * @return The fiting engine
 */
public FitEngine createFitEngine(int numberOfThreads, FitQueue queue, int queueSize) {
    // Ensure thread safety
    final PeakResultsList list = (numberOfThreads > 1) ? results.getThreadSafeList() : results;
    // Reduce to single object for speed
    final PeakResults r = (results.numberOfOutputs() == 1) ? list.toArray()[0] : list;
    // Update the configuration
    if (!updateFitConfiguration(config)) {
        return null;
    }
    final FitEngine engine = FitEngine.create(config, r, numberOfThreads, queue, queueSize);
    // Write settings out to the IJ log
    if (resultsSettings.getLogProgress()) {
        IJ.log(LOG_SPACER);
        IJ.log("Peak Fit");
        IJ.log(LOG_SPACER);
        ImageJUtils.log("Initial Peak SD = %s,%s", MathUtils.rounded(fitConfig.getInitialXSd()), MathUtils.rounded(fitConfig.getInitialYSd()));
        final SpotFilter spotFilter = engine.getSpotFilter();
        IJ.log("Spot Filter = " + spotFilter.getDescription());
        final int w = 2 * engine.getFitting() + 1;
        ImageJUtils.log("Fit window = %d x %d", w, w);
        if (!fitConfig.isDisableSimpleFilter()) {
            IJ.log("Coordinate shift = " + MathUtils.rounded(config.getFitConfiguration().getCoordinateShift()));
            IJ.log("Signal strength = " + MathUtils.rounded(fitConfig.getSignalStrength()));
        }
        if (fitConfig.isDirectFilter()) {
            IJ.log("Smart filter = " + fitConfig.getSmartFilter().getDescription());
        }
        if (extraOptions) {
            IJ.log("Noise = " + MathUtils.rounded(fitConfig.getNoise()));
        }
        IJ.log("Width factor = " + MathUtils.rounded(fitConfig.getMaxWidthFactor()));
        IJ.log(LOG_SPACER);
    }
    return engine;
}

Example 2 with PeakResultsList

use of uk.ac.sussex.gdsc.smlm.results.PeakResultsList in project GDSC-SMLM by aherbert.

the class TcPalmAnalysis method run.

@Override
public void run(String arg) {
    SmlmUsageTracker.recordPlugin(this.getClass(), arg);
    if (MemoryPeakResults.isMemoryEmpty()) {
        IJ.error(TITLE, "No localisations in memory");
        return;
    }
    // Only allow 1 instance to run
    if (!instanceLock.acquire()) {
        final Window w = WindowManager.getWindow(TITLE);
        if (w != null) {
            w.toFront();
            return;
        }
    // Fall through to allow the plugin to run. This may still have concurrency issues if
    // another version is running but the window is not currently showing/registered with
    // the window manager. Perhaps show a dialog asking to continue.
    }
    if (!showDialog()) {
        instanceLock.release();
        return;
    }
    // Load the results
    results = ResultsManager.loadInputResults(settings.getInputOption(), false, null, null);
    if (MemoryPeakResults.isEmpty(results)) {
        IJ.error(TITLE, "No results could be loaded");
        instanceLock.release();
        return;
    }
    // Allocate singles an id for analysis.
    results = results.copyAndAssignZeroIds();
    dataCalibration = new DataCalibration(results.getCalibration());
    // Show a super-resolution image where clusters can be selected.
    final Rectangle bounds = results.getBounds(true);
    final PeakResultsList resultsList = new PeakResultsList();
    resultsList.copySettings(results);
    ResultsManager.addImageResults(resultsList, settings.getResultsImageSettings(), bounds, 0);
    resultsList.begin();
    resultsList.addAll(results.toArray());
    resultsList.end();
    image = (ImageJImagePeakResults) resultsList.getOutput(0);
    // Note: Setting the lut name in the image only has an effect if the image is not showing
    // thus the lut is applied afterwards.
    final ImagePlus imp = image.getImagePlus();
    if (TextUtils.isNotEmpty(image.getLutName())) {
        imp.setLut(LutHelper.createLut(LutColour.forName(image.getLutName()), true));
    }
    // Set-up analysis processing:
    // Store latest image ROI bounds and analysis settings.
    // ConcurrentMonoStack to store next image ROI bounds and analysis settings.
    // When image is clicked submit for analysis.
    // When settings are changed submit for analysis.
    // Submit for analysis checks if ROI is area ROI. if so it:
    // - adds current settings to the next analysis monostack
    // - acquires a softlock and if available submits a runnable to do the analysis until
    // the monostack is empty
    lock = new SoftLock();
    workQueue = new ConcurrentMonoStack<>();
    // Use the current ROI (which may remain from previous plugin execution)
    previous = new Work(0, imp.getRoi(), settings.build());
    executor = Executors.newSingleThreadExecutor();
    // Create the bounds and activation times for each cluster
    clusterData = createClusterData(results);
    // Add interactive monitor to the image where clusters can be selected.
    // For all selected clusters show on an Activations-vs-Time plot.
    final RoiListener roiListener = new RoiListener() {

        @Override
        public void roiModified(ImagePlus imp2, int id) {
            if (imp2 != null && imp.getID() == imp2.getID()) {
                addWork(imp.getRoi());
            }
        }
    };
    Roi.addRoiListener(roiListener);
    // Add monitor for the selection of clusters in the current clusters table
    clusterSelectedListener = new ClusterSelectedListener();
    // Initialise the loop view
    loopImage = new LoopImage().setSettings(previous.settings).setColourMap(colourMap);
    // steepness parameter: local window size (sec) and activation rate (per sec)
    try {
        showAnalysisDialog();
    } finally {
        Roi.removeRoiListener(roiListener);
        // Remove the action from the single instance of the current clusters table
        removeListener(currentGroupsTable.get());
        removeListener(currentClustersTable.get());
        removeListener(allClustersTable.get());
        executor.shutdown();
        instanceLock.release();
        SettingsManager.writeSettings(settings);
    }
}

Example 3 with PeakResultsList

use of uk.ac.sussex.gdsc.smlm.results.PeakResultsList in project GDSC-SMLM by aherbert.

the class ResultsManager method run.

@Override
public void run(String arg) {
    extraOptions = ImageJUtils.isExtraOptions();
    SmlmUsageTracker.recordPlugin(this.getClass(), arg);
    if ("load".equals(arg)) {
        batchLoad();
        return;
    }
    if ("save".equals(arg)) {
        batchSave();
        return;
    }
    if (StringUtils.startsWith(arg, "clear")) {
        runClearMemory(arg);
        return;
    }
    if (!showDialog()) {
        return;
    }
    final MemoryPeakResults results = loadResults(settings.inputOption);
    if (MemoryPeakResults.isEmpty(results)) {
        IJ.error(TITLE, "No results could be loaded");
        IJ.showStatus("");
        return;
    }
    IJ.showStatus("Loaded " + TextUtils.pleural(results.size(), "result"));
    boolean saved = false;
    if (resultsSettings.getResultsInMemorySettings().getInMemory() && fileInput) {
        if (!addResultsToMemory(results, settings.inputFilename)) {
            IJ.showStatus("");
            return;
        }
        saved = true;
    }
    if (resultsSettings.getResultsTableSettings().getResultsTableFormatValue() <= 0 && resultsSettings.getResultsImageSettings().getImageTypeValue() <= 0 && TextUtils.isNullOrEmpty(resultsSettings.getResultsFileSettings().getResultsFilename())) {
        // No outputs. Error if results were not saved to memory
        if (!saved) {
            IJ.error(TITLE, "No output selected");
        }
        return;
    }
    final Rectangle bounds = results.getBounds(true);
    final boolean showDeviations = resultsSettings.getShowDeviations() && canShowDeviations(results);
    final boolean showEndFrame = canShowEndFrame(results);
    final boolean showId = canShowId(results);
    final boolean showCategory = canShowCategory(results);
    // Display the configured output
    final PeakResultsList outputList = new PeakResultsList();
    outputList.copySettings(results);
    final int tableFormat = resultsSettings.getResultsTableSettings().getResultsTableFormatValue();
    if (tableFormat == ResultsTableFormat.IMAGEJ_VALUE) {
        addImageJTableResults(outputList, resultsSettings.getResultsTableSettings(), showDeviations, showEndFrame, results.is3D(), showId, showCategory);
    } else if (tableFormat == ResultsTableFormat.INTERACTIVE_VALUE) {
        showInteractiveTable(results, resultsSettings.getResultsTableSettings());
    }
    addImageResults(outputList, resultsSettings.getResultsImageSettings(), bounds, (extraOptions) ? FLAG_EXTRA_OPTIONS : 0);
    addFileResults(outputList, showDeviations, showEndFrame, showId, showCategory);
    if (outputList.numberOfOutputs() == 0) {
        // This occurs when only using the interactive table
        IJ.showStatus("Processed " + TextUtils.pleural(results.size(), "result"));
        return;
    }
    IJ.showStatus("Processing outputs ...");
    // Reduce to single object for speed
    final PeakResults output = (outputList.numberOfOutputs() == 1) ? outputList.toArray()[0] : outputList;
    output.begin();
    // Note: We could add a batch iterator to the MemoryPeakResults.
    // However the speed increase will be marginal as the main time
    // taken is in processing the outputs.
    // Process in batches to provide progress
    final Counter progress = new Counter();
    final int totalProgress = results.size();
    final int batchSize = Math.max(100, totalProgress / 10);
    final FixedPeakResultList batch = new FixedPeakResultList(batchSize);
    IJ.showProgress(0);
    results.forEach((PeakResultProcedureX) result -> {
        batch.add(result);
        if (batch.size == batchSize) {
            if (IJ.escapePressed()) {
                batch.clear();
                return true;
            }
            output.addAll(batch.results);
            batch.clear();
            IJ.showProgress(progress.incrementAndGet(batchSize), totalProgress);
        }
        return false;
    });
    // Will be empty if interrupted
    if (batch.isNotEmpty()) {
        output.addAll(batch.toArray());
    }
    IJ.showProgress(1);
    output.end();
    if (output.size() == results.size()) {
        IJ.showStatus("Processed " + TextUtils.pleural(results.size(), "result"));
    } else {
        IJ.showStatus(String.format("A %d/%s", output.size(), TextUtils.pleural(results.size(), "result")));
    }
}

Example 4 with PeakResultsList

use of uk.ac.sussex.gdsc.smlm.results.PeakResultsList in project GDSC-SMLM by aherbert.

the class PeakFit method initialiseImage.

/**
 * Initialise a new image.
 *
 * <p>Does not set-up for fitting. This can be done using a subsequent call to
 * {@link #initialiseFitting()}.
 *
 * <p>This mechanism allows additional result outputs to be added after initialisation using
 * {@link #addPeakResults(PeakResults)}.
 *
 * @param imageSource The image source
 * @param bounds The region to process from the image
 * @param ignoreBoundsForNoise Set to true if the bounds should be ignored when computing the
 *        noise estimate for each frame
 * @return True if the image was valid and the initialisation was successful
 */
public boolean initialiseImage(ImageSource imageSource, Rectangle bounds, boolean ignoreBoundsForNoise) {
    // Initialise for image processing
    if (!setSource(imageSource)) {
        return false;
    }
    if (bounds == null) {
        // No region so no need to ignore the bounds.
        this.bounds = new Rectangle(0, 0, source.getWidth(), source.getHeight());
        this.ignoreBoundsForNoise = false;
    } else {
        // The bounds must fit in the image
        try {
            imageSource.checkBounds(bounds);
        } catch (final IllegalArgumentException ex) {
            return false;
        }
        this.bounds = bounds;
        this.ignoreBoundsForNoise = ignoreBoundsForNoise;
    }
    results = new PeakResultsList();
    time = 0;
    return true;
}

Example 5 with PeakResultsList

use of uk.ac.sussex.gdsc.smlm.results.PeakResultsList in project GDSC-SMLM by aherbert.

the class PulseActivationAnalysis method createOutput.

private PeakResultsList createOutput(int channel) {
    final PeakResultsList outputList = new PeakResultsList();
    outputList.copySettings(results);
    if (settings.channels > 1) {
        outputList.setName(results.getName() + " " + title + " C" + channel);
    } else {
        outputList.setName(results.getName() + " " + title);
    }
    // Store the set in memory
    final MemoryPeakResults memoryResults = new MemoryPeakResults(this.results.size());
    outputList.addOutput(memoryResults);
    MemoryPeakResults.addResults(memoryResults);
    // Draw the super-resolution image
    final Rectangle bounds = results.getBounds(true);
    addImageResults(outputList, results.getName(), bounds, results.getNmPerPixel(), resultsSettingsBuilder.getResultsImageSettings());
    outputList.begin();
    return outputList;
}