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

Example 1 with FixedPeakResultList

use of uk.ac.sussex.gdsc.smlm.results.FixedPeakResultList 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")));
    }
}