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

Example 1 with RelativeParameterProvider

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

the class SpotFinderPreview method showDialog.

@Override
public int showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr) {
    settings = Settings.load();
    this.overlay = imp.getOverlay();
    this.imp = imp;
    // Saved by reference so do it once now
    settings.save();
    // The image is locked by the PlugInFilterRunner so unlock it to allow scroll.
    // This should be OK as the image data is not modified and only the overlay is
    // adjusted. If another plugin changes the image then the preview should update
    // the overlay and it will be obvious to the user to turn this plugin off.
    imp.unlock();
    config = SettingsManager.readFitEngineConfiguration(0);
    fitConfig = config.getFitConfiguration();
    gd = new NonBlockingExtendedGenericDialog(TITLE);
    gd.addHelp(HelpUrls.getUrl("spot-finder-preview"));
    gd.addMessage("Preview candidate maxima");
    final String[] templates = ConfigurationTemplate.getTemplateNames(true);
    gd.addChoice("Template", templates, templates[0]);
    final String[] models = CameraModelManager.listCameraModels(true);
    gd.addChoice("Camera_model_name", models, fitConfig.getCameraModelName());
    PeakFit.addPsfOptions(gd, (FitConfigurationProvider) () -> fitConfig);
    final PeakFit.SimpleFitEngineConfigurationProvider provider = new PeakFit.SimpleFitEngineConfigurationProvider(config);
    PeakFit.addDataFilterOptions(gd, provider);
    gd.addChoice("Spot_filter_2", SettingsManager.getDataFilterMethodNames(), config.getDataFilterMethod(1, settings.defaultDataFilterMethod).ordinal());
    PeakFit.addRelativeParameterOptions(gd, new RelativeParameterProvider(2.5, 4.5, "Smoothing_2", provider) {

        @Override
        void setAbsolute(boolean absolute) {
            final FitEngineConfiguration c = fitEngineConfigurationProvider.getFitEngineConfiguration();
            final DataFilterMethod m = c.getDataFilterMethod(1, settings.defaultDataFilterMethod);
            final double smooth = c.getDataFilterParameterValue(1, settings.defaultSmooth);
            c.setDataFilter(m, smooth, absolute, 1);
        }

        @Override
        boolean isAbsolute() {
            return fitEngineConfigurationProvider.getFitEngineConfiguration().getDataFilterParameterAbsolute(1, false);
        }

        @Override
        double getValue() {
            return fitEngineConfigurationProvider.getFitEngineConfiguration().getDataFilterParameterValue(1, settings.defaultSmooth);
        }
    });
    PeakFit.addSearchOptions(gd, provider);
    PeakFit.addBorderOptions(gd, provider);
    // Find if this image was created with ground truth data
    if (imp.getID() == CreateData.getImageId()) {
        final MemoryPeakResults results = CreateData.getResults();
        if (results != null) {
            gd.addSlider("Match_distance", 0, 2.5, settings.distance);
            gd.addSlider("Lower_match_distance (%)", 0, 100, settings.lowerDistance);
            gd.addCheckbox("Multiple_matches", settings.multipleMatches);
            gd.addCheckbox("Show_TP", settings.showTP);
            gd.addCheckbox("Show_FP", settings.showFP);
            gd.addMessage("");
            label = (Label) gd.getMessage();
            final boolean integerCoords = false;
            actualCoordinates = ResultsMatchCalculator.getCoordinates(results, integerCoords);
        }
    }
    if (label == null) {
        // If no ground truth data add options to show the spots by their rank
        // and number of neighbours
        gd.addSlider("Top_N", 0, 100, settings.topN);
        topNScrollBar = gd.getLastScrollbar();
        gd.addSlider("Select", 0, 100, settings.select);
        selectScrollBar = gd.getLastScrollbar();
        gd.addSlider("Neigbour_radius", 0, 10, settings.neighbourRadius);
    }
    ImageListener imageListener = null;
    if (ImageJUtils.isShowGenericDialog()) {
        // Listen for changes in the dialog options
        gd.addOptionCollectedListener(event -> {
            // Just run on the current processor
            if (preview) {
                run(imp.getProcessor());
            }
        });
        // Listen for changes to an image
        imageListener = new ImageAdapter() {

            @Override
            public void imageUpdated(ImagePlus imp) {
                if (SpotFinderPreview.this.imp.getID() == imp.getID() && preview && imp.getCurrentSlice() != currentSlice && filter != null) {
                    run(imp.getProcessor(), filter);
                }
            }
        };
        ImagePlus.addImageListener(imageListener);
        // Support template settings
        final Vector<TextField> numerics = gd.getNumericFields();
        final Vector<Choice> choices = gd.getChoices();
        final Iterator<TextField> nu = numerics.iterator();
        final Iterator<Choice> ch = choices.iterator();
        final Choice textTemplate = ch.next();
        textTemplate.removeItemListener(gd);
        textTemplate.removeKeyListener(gd);
        textTemplate.addItemListener(this::itemStateChanged);
        textCameraModelName = ch.next();
        textPsf = ch.next();
        textDataFilterType = ch.next();
        textDataFilterMethod = ch.next();
        textSmooth = nu.next();
        textDataFilterMethod2 = ch.next();
        textSmooth2 = nu.next();
        textSearch = nu.next();
        textBorder = nu.next();
    }
    gd.addPreviewCheckbox(pfr);
    gd.addDialogListener(this::dialogItemChanged);
    gd.setOKLabel("Save");
    gd.setCancelLabel("Close");
    gd.showDialog();
    if (imageListener != null) {
        ImagePlus.removeImageListener(imageListener);
    }
    if (!gd.wasCanceled() && !SettingsManager.writeSettings(config, SettingsManager.FLAG_SILENT)) {
        IJ.error(TITLE, "Failed to save settings");
    }
    // Reset
    imp.setOverlay(overlay);
    return DONE;
}