Examples with ImageAdapter uk.ac.sussex.gdsc.core.ij.ImageAdapter used on opensource projects

Example 1 with ImageAdapter

use of uk.ac.sussex.gdsc.core.ij.ImageAdapter in project GDSC-SMLM by aherbert.

the class ConfigurationTemplate method showTemplateImages.

/**
 * Show template images.
 *
 * @param settings the settings
 */
private void showTemplateImages(ConfigurationTemplateSettings.Builder settings) {
    title = "Template Example Images";
    final String[] names = getTemplateNamesWithImage();
    if (names.length == 0) {
        IJ.error(title, "No templates with example images");
        return;
    }
    // Follow when the image slice is changed
    ImageListener listener;
    if (imp != null) {
        listener = new ImageAdapter() {

            @Override
            public void imageUpdated(ImagePlus imp) {
                if (imp == ConfigurationTemplate.this.imp) {
                    updateResults(imp.getCurrentSlice());
                }
            }
        };
        ImagePlus.addImageListener(listener);
    } else {
        listener = null;
    }
    final NonBlockingGenericDialog gd = new NonBlockingGenericDialog(title);
    gd.addMessage("View the example source image");
    gd.addChoice("Template", names, settings.getTemplate());
    gd.addCheckbox("Close_on_exit", settings.getClose());
    gd.hideCancelButton();
    templateImage = true;
    gd.addDialogListener(this::dialogItemChanged);
    // Show the first template
    final String template = ((Choice) (gd.getChoices().get(0))).getSelectedItem();
    showTemplateImage(template);
    gd.addHelp(HelpUrls.getUrl("template-manager-show-images"));
    gd.showDialog();
    // There is no cancel so read the settings.
    settings.setTemplate(gd.getNextChoice());
    settings.setClose(gd.getNextBoolean());
    // This is null safe so always do this
    ImagePlus.removeImageListener(listener);
    if (settings.getClose()) {
        if (imp != null) {
            imp.close();
        }
        closeResults();
        closeInfo();
    }
}

Example 2 with ImageAdapter

use of uk.ac.sussex.gdsc.core.ij.ImageAdapter 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;
}

Example 3 with ImageAdapter

use of uk.ac.sussex.gdsc.core.ij.ImageAdapter in project GDSC-SMLM by aherbert.

the class SpotAnalysis method run.

@Override
public void run(String arg) {
    SmlmUsageTracker.recordPlugin(this.getClass(), arg);
    if (WindowManager.getImageCount() == 0) {
        IJ.showMessage(PLUGIN_TITLE, "No images opened.");
        return;
    }
    final Frame frame = instance.get();
    if ("add".equals(arg)) {
        if (frame != null) {
            ((SpotAnalysis) frame).addFrame();
        }
        return;
    }
    if (frame != null) {
        frame.toFront();
        return;
    }
    instance.set(this);
    IJ.register(SpotAnalysis.class);
    WindowManager.addWindow(this);
    ImagePlus.addImageListener(new ImageAdapter() {

        @Override
        public void imageUpdated(ImagePlus imp) {
            SpotAnalysis.this.imageUpdated(imp);
        }
    });
    createFrame();
    setup();
    addKeyListener(new KeyAdapter() {

        @Override
        public void keyTyped(KeyEvent event) {
            switch(event.getKeyChar()) {
                case 'a':
                    addFrame();
                    break;
                case ',':
                    rawImp.setSlice(rawImp.getSlice() + 1);
                    break;
                case '.':
                    rawImp.setSlice(rawImp.getSlice() - 1);
                    break;
                default:
                    break;
            }
        }
    });
    pack();
    final Point loc = Prefs.getLocation(OPT_LOCATION);
    if (loc != null) {
        setLocation(loc);
    } else {
        GUI.center(this);
    }
    if (IJ.isMacOSX()) {
        setResizable(false);
    }
    setVisible(true);
    // Install shortcut for adding a slice
    final String command = "Spot Analysis (Add)";
    final String shortcut = "6";
    final String plugin = "ij.plugin.Hotkeys(" + "\"" + command + "\")";
    Menus.installPlugin(plugin, Menus.SHORTCUTS_MENU, "*" + command, shortcut, IJ.getInstance());
}

Example 4 with ImageAdapter

use of uk.ac.sussex.gdsc.core.ij.ImageAdapter in project GDSC-SMLM by aherbert.

the class SmoothImage method setup.

@Override
public int setup(String arg, ImagePlus imp) {
    if ("final".equals(arg)) {
        imp.updateAndDraw();
        return DONE;
    }
    SmlmUsageTracker.recordPlugin(this.getClass(), arg);
    if (imp == null) {
        IJ.noImage();
        return DONE;
    }
    final Roi roi = imp.getRoi();
    if (roi != null && roi.getType() != Roi.RECTANGLE) {
        IJ.error("Rectangular ROI required");
        return DONE;
    }
    // Support simultaneous contrast adjustment by saving the min/max
    // only when in the preview.
    imageId = imp.getID();
    saveMinMax(imp);
    ImagePlus.addImageListener(new ImageAdapter() {

        @Override
        public void imageUpdated(ImagePlus imp) {
            // Only when the dialog is open
            if (imp.getID() == imageId && dialogVisible) {
                saveMinMax(imp);
            }
        }
    });
    return FLAGS;
}