Examples with ConfigurationTemplate uk.ac.sussex.gdsc.smlm.ij.plugins.ConfigurationTemplate used on opensource projects

Example 1 with ConfigurationTemplate

use of uk.ac.sussex.gdsc.smlm.ij.plugins.ConfigurationTemplate in project GDSC-SMLM by aherbert.

the class BenchmarkFilterAnalysis method saveTemplate.

/**
 * Save PeakFit configuration template using the current benchmark settings.
 *
 * @param topFilterSummary the top filter summary
 */
private void saveTemplate(String topFilterSummary) {
    final FitEngineConfiguration config = new FitEngineConfiguration();
    if (!updateAllConfiguration(config, true)) {
        IJ.log("Unable to create the template configuration");
        return;
    }
    // Remove the PSF width to make the template generic
    config.getFitConfiguration().setInitialPeakStdDev(0);
    // Only get this once when doing iterative analysis
    String filename;
    final boolean localSaveTemplateIsSet = saveTemplateIsSet;
    if (localSaveTemplateIsSet) {
        filename = settings.templateFilename;
    } else {
        filename = getFilename("Template_File", settings.templateFilename);
        saveTemplateIsSet = true;
    }
    if (filename != null) {
        settings.templateFilename = filename;
        Prefs.set(Settings.KEY_TEMPLATE_FILENAME, filename);
        final TemplateSettings.Builder templateSettings = TemplateSettings.newBuilder();
        getNotes(templateSettings, topFilterSummary);
        templateSettings.setFitEngineSettings(config.getFitEngineSettings());
        if (!SettingsManager.toJson(templateSettings.build(), filename, SettingsManager.FLAG_SILENT | SettingsManager.FLAG_JSON_WHITESPACE)) {
            IJ.log("Unable to save the template configuration");
            return;
        }
        // This need only be performed once as the sample image is the same for all iterations.
        if (localSaveTemplateIsSet) {
            return;
        }
        // Save some random frames from the test image data
        final ImagePlus imp = CreateData.getImage();
        if (imp == null) {
            return;
        }
        // Get the number of frames
        final ResultsImageSampler sampler = getSampler(results, imp);
        if (!sampler.isValid()) {
            return;
        }
        // Iteratively show the example until the user is happy.
        // Yes = OK, No = Repeat, Cancel = Do not save
        final String keyNo = "nNo";
        final String keyLow = "nLower";
        final String keyHigh = "nHigher";
        if (ImageJUtils.isMacro()) {
            // Collect the options if running in a macro
            final String options = Macro.getOptions();
            settings.countNo = Integer.parseInt(Macro.getValue(options, keyNo, Integer.toString(settings.countNo)));
            settings.countLow = Integer.parseInt(Macro.getValue(options, keyLow, Integer.toString(settings.countLow)));
            settings.countHigh = Integer.parseInt(Macro.getValue(options, keyHigh, Integer.toString(settings.countHigh)));
        } else if (settings.countLow + settings.countHigh == 0) {
            settings.countLow = settings.countHigh = 1;
        }
        final ImagePlus[] out = new ImagePlus[1];
        out[0] = sampler.getSample(settings.countNo, settings.countLow, settings.countHigh);
        if (!ImageJUtils.isMacro()) {
            // Show the template results
            final ConfigurationTemplate configTemplate = new ConfigurationTemplate();
            // Interactively show the sample image data
            final boolean[] close = new boolean[1];
            final ImagePlus[] outImp = new ImagePlus[1];
            if (out[0] != null) {
                final WindowOrganiser windowOrganiser = new WindowOrganiser();
                outImp[0] = display(out[0], windowOrganiser);
                if (windowOrganiser.isNotEmpty()) {
                    close[0] = true;
                    // Zoom a bit
                    final ImageWindow iw = outImp[0].getWindow();
                    for (int i = 7; i-- > 0 && Math.max(iw.getWidth(), iw.getHeight()) < 512; ) {
                        iw.getCanvas().zoomIn(0, 0);
                    }
                }
                configTemplate.createResults(outImp[0]);
            }
            // TODO - fix this when a second sample is made as the results are not updated.
            final ImageListener listener = new ImageListener() {

                @Override
                public void imageOpened(ImagePlus imp) {
                // Do nothing
                }

                @Override
                public void imageClosed(ImagePlus imp) {
                // Do nothing
                }

                @Override
                public void imageUpdated(ImagePlus imp) {
                    if (imp != null && imp == outImp[0]) {
                        configTemplate.updateResults(imp.getCurrentSlice());
                    }
                }
            };
            ImagePlus.addImageListener(listener);
            // Turn off the recorder when the dialog is showing
            final boolean record = Recorder.record;
            Recorder.record = false;
            final NonBlockingGenericDialog gd = new NonBlockingGenericDialog(TITLE);
            ImageJUtils.addMessage(gd, "Showing image data for the template example.\n \nSample Frames:\nEmpty = %d\n" + "Lower density = %d\nHigher density = %d\n", sampler.getNumberOfEmptySamples(), sampler.getNumberOfLowDensitySamples(), sampler.getNumberOfHighDensitySamples());
            gd.addSlider(keyNo, 0, 10, settings.countNo);
            gd.addSlider(keyLow, 0, 10, settings.countLow);
            gd.addSlider(keyHigh, 0, 10, settings.countHigh);
            gd.addDialogListener((genDialog, event) -> {
                // image the user has not seen.
                if (event == null) {
                    return true;
                }
                settings.countNo = (int) genDialog.getNextNumber();
                settings.countLow = (int) genDialog.getNextNumber();
                settings.countHigh = (int) genDialog.getNextNumber();
                out[0] = sampler.getSample(settings.countNo, settings.countLow, settings.countHigh);
                if (out[0] != null) {
                    final WindowOrganiser windowOrganiser = new WindowOrganiser();
                    outImp[0] = display(out[0], windowOrganiser);
                    if (windowOrganiser.isNotEmpty()) {
                        close[0] = true;
                        // Zoom a bit
                        final ImageWindow iw = outImp[0].getWindow();
                        for (int i = 7; i-- > 0 && Math.max(iw.getWidth(), iw.getHeight()) < 512; ) {
                            iw.getCanvas().zoomIn(0, 0);
                        }
                    }
                    configTemplate.createResults(outImp[0]);
                }
                return true;
            });
            gd.showDialog();
            if (gd.wasCanceled()) {
                out[0] = null;
                // For the recorder
                settings.countNo = settings.countLow = settings.countHigh = 0;
            }
            if (close[0]) {
                // Because closing the image sets the stack pixels array to null
                if (out[0] != null) {
                    out[0] = out[0].duplicate();
                }
                outImp[0].close();
            }
            configTemplate.closeResults();
            ImagePlus.removeImageListener(listener);
            if (record) {
                Recorder.record = true;
                Recorder.recordOption(keyNo, Integer.toString(settings.countNo));
                Recorder.recordOption(keyLow, Integer.toString(settings.countLow));
                Recorder.recordOption(keyHigh, Integer.toString(settings.countHigh));
            }
        }
        if (out[0] == null) {
            return;
        }
        final ImagePlus example = out[0];
        filename = FileUtils.replaceExtension(filename, ".tif");
        IJ.save(example, filename);
    }
}