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

Example 1 with PeakResults

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

the class PeakFit method createFitEngine.

/**
	 * Creates a fitting engine using the current configuration.
	 * 
	 * @param numberOfThreads
	 * @param queue
	 * @param queueSize
	 * @return The fiting engine
	 */
public FitEngine createFitEngine(int numberOfThreads, FitQueue queue, int queueSize) {
    PeakResults r = results;
    if (results.numberOfOutputs() == 1)
        // Reduce to single object for speed
        r = results.toArray()[0];
    // Update the configuration
    updateFitConfiguration(config);
    FitEngine engine = new FitEngine(config, r, numberOfThreads, queue, queueSize);
    // Write settings out to the IJ log
    if (resultsSettings.logProgress) {
        IJ.log("-=-=-=-");
        IJ.log("Peak Fit");
        IJ.log("-=-=-=-");
        Utils.log("Initial Peak SD = %s,%s", Utils.rounded(fitConfig.getInitialPeakStdDev0()), Utils.rounded(fitConfig.getInitialPeakStdDev1()));
        SpotFilter spotFilter = engine.getSpotFilter();
        IJ.log("Spot Filter = " + spotFilter.getDescription());
        int w = 2 * engine.getFitting() + 1;
        Utils.log("Fit window = %d x %d", w, w);
        if (!fitConfig.isDisableSimpleFilter()) {
            IJ.log("Coordinate shift = " + Utils.rounded(config.getFitConfiguration().getCoordinateShift()));
            IJ.log("Signal strength = " + Utils.rounded(fitConfig.getSignalStrength()));
        }
        if (fitConfig.isDirectFilter())
            IJ.log("Smart filter = " + fitConfig.getSmartFilter().getDescription());
        if (extraOptions)
            IJ.log("Noise = " + Utils.rounded(fitConfig.getNoise()));
        IJ.log("Width factor = " + Utils.rounded(fitConfig.getWidthFactor()));
        IJ.log("-=-=-=-");
    }
    return engine;
}

Example 2 with PeakResults

use of gdsc.smlm.results.PeakResults 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 3 with PeakResults

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

the class PeakFit method addFileResults.

private void addFileResults(PeakResultsList resultsList) {
    String filename = null;
    if (resultsSettings.resultsDirectory != null && new File(resultsSettings.resultsDirectory).exists()) {
        filename = resultsSettings.resultsDirectory + File.separatorChar + source.getName() + ".results." + resultsSettings.getResultsFileFormat().getExtension();
    } else if (resultsSettings.resultsFilename != null && resultsSettings.resultsFilename.length() > 0) {
        filename = resultsSettings.resultsFilename;
    }
    if (filename != null) {
        PeakResults r;
        switch(resultsSettings.getResultsFileFormat()) {
            case GDSC_BINARY:
                r = new BinaryFilePeakResults(filename, resultsSettings.showDeviations);
                break;
            case GDSC_TEXT:
                r = new FilePeakResults(filename, resultsSettings.showDeviations);
                break;
            case MALK:
                r = new MALKFilePeakResults(resultsSettings.resultsFilename);
                break;
            case TSF:
                r = new TSFPeakResultsWriter(resultsSettings.resultsFilename);
                break;
            default:
                throw new RuntimeException("Unsupported file format: " + resultsSettings.getResultsFileFormat());
        }
        if (r instanceof FilePeakResults) {
            FilePeakResults fr = (FilePeakResults) r;
            fr.setSortAfterEnd(Prefs.getThreads() > 1);
            fr.setPeakIdColumnName("Frame");
        }
        resultsList.addOutput(r);
    }
}

Example 4 with PeakResults

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

the class ResultsManager method run.

/*
	 * (non-Javadoc)
	 * 
	 * @see ij.plugin.PlugIn#run(java.lang.String)
	 */
public void run(String arg) {
    SMLMUsageTracker.recordPlugin(this.getClass(), arg);
    if (arg != null && arg.startsWith("clear")) {
        Collection<MemoryPeakResults> allResults;
        boolean removeAll = false;
        if (arg.contains("multi")) {
            MultiDialog md = new MultiDialog(TITLE, new MultiDialog.MemoryResultsItems());
            md.addSelected(selected);
            md.showDialog();
            if (md.wasCanceled())
                return;
            selected = md.getSelectedResults();
            if (selected.isEmpty())
                return;
            allResults = new ArrayList<MemoryPeakResults>(selected.size());
            for (String name : selected) {
                MemoryPeakResults r = MemoryPeakResults.getResults(name);
                if (r != null)
                    allResults.add(r);
            }
        } else {
            removeAll = true;
            allResults = MemoryPeakResults.getAllResults();
        }
        if (allResults.isEmpty())
            return;
        long memorySize = 0;
        int size = 0;
        for (MemoryPeakResults results : allResults) {
            memorySize += MemoryPeakResults.estimateMemorySize(results.getResults());
            size += results.size();
        }
        String memory = MemoryPeakResults.memorySizeString(memorySize);
        String count = Utils.pleural(size, "result");
        String sets = Utils.pleural(allResults.size(), "set");
        GenericDialog gd = new GenericDialog(TITLE);
        gd.addMessage(String.format("Do you want to remove %s from memory (%s, %s)?", count, sets, memory));
        gd.enableYesNoCancel();
        gd.showDialog();
        if (!gd.wasOKed())
            return;
        if (removeAll)
            MemoryPeakResults.clearMemory();
        else {
            for (MemoryPeakResults results : allResults) MemoryPeakResults.removeResults(results.getName());
        }
        SummariseResults.clearSummaryTable();
        IJ.log(String.format("Cleared %s (%s, %s)", count, sets, memory));
        return;
    }
    if (!showDialog())
        return;
    MemoryPeakResults results = loadResults(inputOption);
    if (results == null || results.size() == 0) {
        IJ.error(TITLE, "No results could be loaded");
        IJ.showStatus("");
        return;
    }
    results = cropToRoi(results);
    if (results.size() == 0) {
        IJ.error(TITLE, "No results within the crop region");
        return;
    }
    if (resultsSettings.resultsInMemory && fileInput)
        MemoryPeakResults.addResults(results);
    IJ.showStatus("Processing outputs ...");
    Rectangle bounds = results.getBounds(true);
    boolean showDeviations = resultsSettings.showDeviations && canShowDeviations(results);
    boolean showEndFrame = canShowEndFrame(results);
    boolean showId = canShowId(results);
    // Display the configured output
    PeakResultsList outputList = new PeakResultsList();
    outputList.copySettings(results);
    //String title = results.getSource();
    //if (title == null || title.length() == 0)
    //	output.setSource(TITLE);
    addTableResults(results, outputList, showDeviations, showEndFrame);
    addImageResults(outputList, results.getName(), bounds, results.getNmPerPixel(), results.getGain());
    addFileResults(outputList, showDeviations, showEndFrame, showId);
    // Reduce to single object for speed
    PeakResults output = (outputList.numberOfOutputs() == 1) ? outputList.toArray()[0] : outputList;
    output.begin();
    // Process in batches to provide progress
    List<PeakResult> list = results.getResults();
    int progress = 0;
    int totalProgress = list.size();
    int stepProgress = Utils.getProgressInterval(totalProgress);
    TurboList<PeakResult> batch = new TurboList<PeakResult>(stepProgress);
    for (PeakResult result : list) {
        if (progress % stepProgress == 0) {
            IJ.showProgress(progress, totalProgress);
        }
        progress++;
        batch.addf(result);
        if (batch.size() == stepProgress) {
            output.addAll(batch);
            batch.clearf();
            if (isInterrupted())
                break;
        }
    }
    IJ.showProgress(1);
    output.end();
    IJ.showStatus(String.format("Processed %d result%s", results.size(), (results.size() > 1) ? "s" : ""));
}

Example 5 with PeakResults

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

the class ResultsManager method addFileResults.

private void addFileResults(PeakResultsList resultsList, boolean showDeviations, boolean showEndFrame, boolean showId) {
    if (resultsSettings.resultsFilename != null && resultsSettings.resultsFilename.length() > 0) {
        // Remove extension
        resultsSettings.resultsFilename = Utils.replaceExtension(resultsSettings.resultsFilename, resultsSettings.getResultsFileFormat().getExtension());
        if (fileInput && inputFilename.equals(resultsSettings.resultsFilename)) {
            IJ.log(TITLE + ": Input and output files are the same, skipping output ...");
            return;
        }
        // Check if file exists
        File file = new File(resultsSettings.resultsFilename);
        if (file.exists()) {
            YesNoCancelDialog d = new YesNoCancelDialog(IJ.getInstance(), TITLE, "Overwrite existing file?\n" + resultsSettings.resultsFilename);
            if (!d.yesPressed())
                return;
        }
        File parent = file.getParentFile();
        if (parent != null && parent.exists()) {
            PeakResults r;
            switch(resultsSettings.getResultsFileFormat()) {
                case GDSC_BINARY:
                    r = new BinaryFilePeakResults(resultsSettings.resultsFilename, showDeviations, showEndFrame, showId);
                    break;
                case GDSC_TEXT:
                    r = new FilePeakResults(resultsSettings.resultsFilename, showDeviations, showEndFrame, showId);
                    break;
                case MALK:
                    r = new MALKFilePeakResults(resultsSettings.resultsFilename);
                    break;
                case TSF:
                    r = new TSFPeakResultsWriter(resultsSettings.resultsFilename);
                    break;
                default:
                    throw new RuntimeException("Unsupported file format: " + resultsSettings.getResultsFileFormat());
            }
            if (r instanceof FilePeakResults) {
                FilePeakResults fr = (FilePeakResults) r;
                fr.setPeakIdColumnName("Frame");
            }
            resultsList.addOutput(r);
        }
    }
}