Examples with ParameterPanelFX qupath.lib.gui.dialogs.ParameterPanelFX used on opensource projects

Example 6 with ParameterPanelFX

use of qupath.lib.gui.dialogs.ParameterPanelFX in project qupath by qupath.

the class ClassifierBuilderPane method initializeBuildPanel.

private void initializeBuildPanel() {
    Button btnUpdateClassifier = new Button("Build & Apply");
    btnUpdateClassifier.setTooltip(new Tooltip("Build classifier & apply to objects in the current image"));
    tbAutoUpdate.setTooltip(new Tooltip("Automatically update the classification when changes are made to the data - only recommended if the classifier is fast & the amount of training data is small"));
    tbAutoUpdate.setOnAction(e -> {
        if (!tbAutoUpdate.isDisabled() && tbAutoUpdate.isSelected())
            updateClassification(true);
    });
    panelUpdate = new ParameterPanelFX(paramsUpdate);
    // panelUpdate.getPane().setPadding(new Insets(0, 10, 0, 10));
    comboClassifiers.setOnAction(e -> {
        maybeUpdate();
        // WekaClassifierBuilder builder = (WekaClassifierBuilder)comboClassifiers.getSelectedItem();
        // We can't auto-update if we don't have a valid (non-advanced) classifier builder
        // cbAutoUpdate.setEnabled(builder != null && builder.getClassifierClass() != null);
        classifier = (T) comboClassifiers.getSelectionModel().getSelectedItem();
        // Enable/disable edit button
        if (btnEdit != null)
            btnEdit.setDisable(!(classifier instanceof Parameterizable));
        tbAutoUpdate.setDisable(classifier == null || !classifier.supportsAutoUpdate());
    });
    // Make panel to create a classifier
    GridPane panelClassifierType = new GridPane();
    panelClassifierType.add(new Label("Classifier type: "), 0, 0);
    panelClassifierType.add(comboClassifiers, 1, 0);
    comboClassifiers.setMaxWidth(Double.MAX_VALUE);
    comboClassifiers.setTooltip(new Tooltip("Choose classifier type"));
    GridPane.setHgrow(comboClassifiers, Priority.ALWAYS);
    panelClassifierType.setHgap(5);
    panelClassifierType.setVgap(5);
    // Add in options button
    btnEdit = new Button("Edit");
    btnEdit.setTooltip(new Tooltip("Edit advanced classifier options"));
    btnEdit.setDisable(!(classifier instanceof Parameterizable));
    btnEdit.setOnAction(e -> {
        if (!(classifier instanceof Parameterizable)) {
            Dialogs.showErrorMessage("Classifier settings", "No options available for selected classifier!");
            return;
        }
        Parameterizable parameterizable = (Parameterizable) classifier;
        ParameterPanelFX panel = new ParameterPanelFX(parameterizable.getParameterList());
        // JDialog dialog = new JDialog(qupath.getFrame(), "Classifier settings", ModalityType.APPLICATION_MODAL);
        BorderPane pane = new BorderPane();
        pane.setCenter(panel.getPane());
        Button btnRun = new Button("Rebuild classifier");
        btnRun.setOnAction(e2 -> updateClassification(true));
        pane.setBottom(btnRun);
        Dialogs.showMessageDialog("Classifier settings", pane);
    });
    panelClassifierType.add(btnEdit, 2, 0);
    panelClassifierType.add(tbAutoUpdate, 3, 0);
    panelClassifierType.add(btnUpdateClassifier, 4, 0);
    panelClassifierType.setPadding(new Insets(10, 10, 10, 10));
    // Make feature panel
    GridPane panelFeatures = new GridPane();
    Button btnFeatures = new Button("Select...");
    btnFeatures.setTooltip(new Tooltip("Select features to use for classification - this is required before any classifier can be made"));
    btnFeatures.setOnAction(e -> {
        qupath.submitShortTask(() -> featurePanel.ensureMeasurementsUpdated());
        Dialogs.showMessageDialog("Select Features", featurePanel.getPanel());
        updateSelectedFeaturesLabel();
    });
    Button btnUseAllFeatures = new Button("Use all");
    btnUseAllFeatures.setTooltip(new Tooltip("Update feature list to use all available features"));
    btnUseAllFeatures.setOnAction(e -> selectAllFeatures());
    panelFeatures.add(labelSelectedFeatures, 0, 0);
    GridPane.setHgrow(labelSelectedFeatures, Priority.ALWAYS);
    labelSelectedFeatures.setMaxWidth(Double.MAX_VALUE);
    // labelSelectedFeatures.setTextAlignment(TextAlignment.CENTER);
    // labelSelectedFeatures.setAlignment(Pos.CENTER);
    panelFeatures.add(btnFeatures, 1, 0);
    panelFeatures.add(btnUseAllFeatures, 2, 0);
    panelFeatures.setHgap(5);
    // Multi-image stuff
    GridPane panelSouth = new GridPane();
    // Tooltip.install(btnResetTrainingObjects, new Tooltip("Reset all the retained objects, so that the classifier only uses the training objects from the current image"));
    miResetTrainingObjects.setOnAction(e -> {
        if (retainedObjectsMap == null || retainedObjectsMap.isEmpty())
            return;
        int nObjects = retainedObjectsMap.countRetainedObjects();
        String message = nObjects == 1 ? "Remove one retained object from classifier training?" : "Remove " + nObjects + " retained objects from classifier training?";
        if (Dialogs.showYesNoDialog("Remove retained objects", message)) {
            retainedObjectsMap.clear();
            updateRetainedObjectsLabel();
        }
    });
    final String trainingExtension = "qptrain";
    miLoadTrainingObjects.setOnAction(e -> {
        File fileTraining = Dialogs.promptForFile("Load objects", null, trainingExtension, new String[] { trainingExtension });
        if (fileTraining == null)
            return;
        if (!loadRetainedObjects(fileTraining)) {
            Dialogs.showErrorMessage("Load training objects", "There was an error loading training objects from \n" + fileTraining);
        }
    });
    // btnSaveTrainingObjects.setTooltip(new Tooltip("Load training objects saved in a previous session"));
    miSaveTrainingObjects.setOnAction(e -> {
        File fileTraining = Dialogs.promptToSaveFile("Save objects", null, null, trainingExtension, trainingExtension);
        if (fileTraining == null)
            return;
        if (!saveRetainedObjects(fileTraining)) {
            Dialogs.showErrorMessage("Save training objects", "There was an error saving training objects to \n" + fileTraining);
        }
    });
    // btnSaveTrainingObjects.setTooltip(new Tooltip("Save training objects for reloading in another session"));
    miExportTrainingFeatures.setOnAction(e -> {
        File fileTraining = Dialogs.promptToSaveFile("Export features", null, null, "Text file", "txt");
        if (fileTraining == null)
            return;
        if (!exportTrainingFeatures(fileTraining)) {
            Dialogs.showErrorMessage("Export features", "There was an exporting the training features to \n" + fileTraining);
        }
    });
    // btnExportTrainingFeatures.setTooltip(new Tooltip("Export training features to a text file (e.g. for analysis elsewhere"));
    // btnRebuildTrainingFromProject.setTooltip(new Tooltip("Load training objects from all images in the project to use these to create a single classifier"));
    miRebuildTrainingFromProject.setOnAction(e -> {
        loadAllTrainingSamplesForProject();
    });
    miClassifyAllImagesInProject.setOnAction(e -> {
        classifyAllImagesInProject();
    });
    miCrossValidateAcrossImages.setOnAction(e -> {
        crossValidateAcrossImages();
    });
    labelRetainedObjects.setTooltip(new Tooltip("The total number of objects last used for training - including from other images not currently open"));
    // labelRetainedObjects.setAlignment(Pos.CENTER);
    labelRetainedObjects.setMaxWidth(Double.MAX_VALUE);
    // labelRetainedObjects.setPadding(new Insets(5, 5, 5, 5));
    panelSouth.add(labelRetainedObjects, 0, 0);
    GridPane.setHgrow(labelRetainedObjects, Priority.ALWAYS);
    // panelSouth.setStyle("-fx-background-color: red;");
    MenuItem miShowTrainingObjectMatrix = new MenuItem("Show training object counts");
    miShowTrainingObjectMatrix.setOnAction(e -> {
        updateRetainedObjectsMap();
        showRetainedTrainingMap(retainedObjectsMap);
    });
    ContextMenu context = new ContextMenu();
    context.getItems().addAll(miLoadTrainingObjects, miSaveTrainingObjects, miRebuildTrainingFromProject, new SeparatorMenuItem(), miShowTrainingObjectMatrix, miResetTrainingObjects, new SeparatorMenuItem(), miExportTrainingFeatures, miCrossValidateAcrossImages, miClassifyAllImagesInProject);
    context.setOnShowing(e -> {
        boolean hasRetainedObjects = !retainedObjectsMap.isEmpty();
        boolean hasAnyObjects = hasRetainedObjects || (getHierarchy() != null && !getHierarchy().isEmpty());
        miResetTrainingObjects.setDisable(!hasRetainedObjects);
        miCrossValidateAcrossImages.setDisable(!hasRetainedObjects);
        miSaveTrainingObjects.setDisable(!hasAnyObjects);
        miExportTrainingFeatures.setDisable(!hasAnyObjects);
        miRebuildTrainingFromProject.setVisible(qupath.getProject() != null);
        miClassifyAllImagesInProject.setVisible(qupath.getProject() != null);
    });
    Button buttonMore = new Button("More...");
    buttonMore.setOnMouseClicked(e -> {
        context.show(buttonMore, e.getScreenX(), e.getScreenY());
    });
    panelSouth.add(buttonMore, 1, 0);
    // panelSouth.setBottom(panelRetainingButtons);
    updateRetainedObjectsLabel();
    // TitledPane multiImage = new TitledPane("Multi-image training", panelSouth);
    // labelRetainedObjects.prefWidthProperty().bind(multiImage.widthProperty());
    // panelClassifier.getChildren().add(multiImage);
    // panelSouth.add(panelRetaining, BorderLayout.NORTH);
    // panelSouth.add(btnSaveClassifier, BorderLayout.SOUTH);
    // panelFeatures.setStyle("-fx-background-color: blue;");
    GridPane paneAdvancedMain = new GridPane();
    paneAdvancedMain.add(panelFeatures, 0, 0);
    paneAdvancedMain.add(panelSouth, 0, 1);
    paneAdvancedMain.add(panelUpdate.getPane(), 0, 2);
    paneAdvancedMain.setVgap(5);
    panelUpdate.getPane().setMaxWidth(Double.MAX_VALUE);
    GridPane.setHgrow(panelFeatures, Priority.ALWAYS);
    GridPane.setHgrow(panelSouth, Priority.ALWAYS);
    GridPane.setHgrow(panelUpdate.getPane(), Priority.ALWAYS);
    // panelUpdate.getPane().setStyle("-fx-background-color: green;");
    TitledPane paneAdvanced = new TitledPane("Advanced options", paneAdvancedMain);
    paneAdvanced.setMaxWidth(Double.MAX_VALUE);
    paneAdvanced.setExpanded(false);
    // Really, I should probably just use a CSS stylesheet somewhere... here is an inelegant way to change things...
    Platform.runLater(() -> {
        try {
            paneAdvanced.lookup(".title").setStyle("-fx-background-color: transparent");
            paneAdvanced.lookup(".title").setEffect(null);
            paneAdvanced.lookup(".content").setStyle("-fx-border-color: null");
        } catch (Exception e) {
            logger.error("Error setting Advanced options pane style", e);
        }
    });
    panelClassifierType.add(paneAdvanced, 0, 1, 6, 1);
    progressIndicator.setVisible(false);
    progressIndicator.setPrefSize(30, 30);
    panelClassifierType.add(progressIndicator, 5, 0, 1, 1);
    // panelClassifierType.add(panelUpdate.getPane(), 0, 1, 4, 1);
    GridPane.setHgrow(panelUpdate.getPane(), Priority.ALWAYS);
    GridPane.setHgrow(paneAdvanced, Priority.ALWAYS);
    // btnUpdateClassifier.setMaxWidth(Double.MAX_VALUE);
    // panelClassifierType.add(btnUpdateClassifier, 0, 2, 3, 1);
    panelClassifier.getChildren().add(new TitledPane("Classifier", panelClassifierType));
    panelIntensities.intensityFeatureProperty().addListener((v, o, n) -> updateIntensityPanelCallback());
    panelIntensities.addThresholdParameterChangeListener((p, k, a) -> updateIntensityPanelCallback());
    panelClassifier.getChildren().add(new TitledPane("Intensity", panelIntensities.getPane()));
    btnUpdateClassifier.setOnAction(e -> updateClassification(true));
}

Example 7 with ParameterPanelFX

use of qupath.lib.gui.dialogs.ParameterPanelFX in project qupath by qupath.

the class PathIntensityClassifierPane method initialize.

private void initialize() {
    panelHistogram = new HistogramPanelFX();
    panelHistogram.setShowTickLabels(false);
    panelHistogram.getChart().getXAxis().setVisible(false);
    panelHistogram.getChart().getXAxis().setTickMarkVisible(false);
    panelHistogram.getChart().getYAxis().setVisible(false);
    panelHistogram.getChart().getYAxis().setTickMarkVisible(false);
    panelHistogram.getChart().setMinHeight(10);
    panelHistogram.getChart().setMinWidth(10);
    panelHistogram.getChart().setVisible(false);
    panelHistogram.getChart().setAnimated(false);
    thresholdWrapper = new ThresholdedChartWrapper(panelHistogram.getChart());
    comboIntensities = new ComboBox<>();
    comboIntensities.setOnAction(e -> {
        String selected = comboIntensities.getSelectionModel().getSelectedItem();
        logger.trace("Intensities selected: {}", selected);
        updateIntensityHistogram();
    });
    comboIntensities.setTooltip(new Tooltip("Select an intensity feature for thresholding, e.g. to sub-classify objects according to levels of positive staining"));
    double threshold_1 = 0.2;
    double threshold_2 = 0.4;
    double threshold_3 = 0.6;
    paramsIntensity = new ParameterList().addDoubleParameter("threshold_1", "Threshold 1+", threshold_1, null, 0, 1.5, "Set first intensity threshold, if required (lowest)").addDoubleParameter("threshold_2", "Threshold 2+", threshold_2, null, 0, 1.5, "Set second intensity threshold, if required (intermediate)").addDoubleParameter("threshold_3", "Threshold 3+", threshold_3, null, 0, 1.5, "Set third intensity threshold, if required (highest)").addBooleanParameter("single_threshold", "Use single threshold", false, "Use only the first intensity threshold to separate positive & negative objects");
    pane.add(new Label("Intensity feature: "), 0, 0);
    pane.add(comboIntensities, 1, 0);
    comboIntensities.setMaxWidth(Double.MAX_VALUE);
    GridPane.setHgrow(comboIntensities, Priority.ALWAYS);
    this.panelParameters = new ParameterPanelFX(paramsIntensity);
    this.panelParameters.addParameterChangeListener(new ParameterChangeListener() {

        @Override
        public void parameterChanged(ParameterList parameterList, String key, boolean isAdjusting) {
            if ("single_threshold".equals(key)) {
                boolean single = paramsIntensity.getBooleanParameterValue("single_threshold");
                panelParameters.setParameterEnabled("threshold_2", !single);
                panelParameters.setParameterEnabled("threshold_3", !single);
            }
            updateHistogramThresholdLines();
        }
    });
    // pane.add(panelParameters.getPane(), 0, 1, 2, 1);
    // GridPane.setFillWidth(panelParameters.getPane(), Boolean.FALSE);
    // 
    // pane.add(thresholdWrapper.getPane(), 2, 1, 1, 1);
    // //		thresholdWrapper.getPane().setMinSize(10, 10);
    // //		GridPane.setHgrow(thresholdWrapper.getPane(), Priority.ALWAYS);
    // GridPane.setFillHeight(thresholdWrapper.getPane(), Boolean.TRUE);
    BorderPane paneBorder = new BorderPane();
    paneBorder.setLeft(panelParameters.getPane());
    paneBorder.setCenter(thresholdWrapper.getPane());
    pane.add(paneBorder, 0, 1, 2, 1);
    pane.setVgap(5);
    pane.setHgap(5);
// if (addTitle)
// setBorder(BorderFactory.createTitledBorder("Intensity feature"));
}

Example 8 with ParameterPanelFX

use of qupath.lib.gui.dialogs.ParameterPanelFX in project qupath by qupath.

the class QuPathGUI method showSetupDialog.

/**
 * Show a dialog requesting setup parameters
 *
 * @return
 */
public boolean showSetupDialog() {
    // Show a setup message
    Dialog<ButtonType> dialog = new Dialog<>();
    dialog.setTitle("QuPath setup");
    dialog.initOwner(getStage());
    // Try to get an image to display
    Image img = loadIcon(128);
    BorderPane pane = new BorderPane();
    if (img != null) {
        StackPane imagePane = new StackPane(new ImageView(img));
        imagePane.setPadding(new Insets(10, 10, 10, 10));
        pane.setLeft(imagePane);
    }
    Map<String, Locale> localeMap = Arrays.stream(Locale.getAvailableLocales()).collect(Collectors.toMap(l -> l.getDisplayName(Locale.US), l -> l));
    localeMap.remove("");
    List<String> localeList = new ArrayList<>(localeMap.keySet());
    Collections.sort(localeList);
    long maxMemoryMB = Runtime.getRuntime().maxMemory() / 1024 / 1024;
    String maxMemoryString = String.format("Current maximum memory is %.2f GB.", maxMemoryMB / 1024.0);
    boolean canSetMemory = PathPrefs.hasJavaPreferences();
    ParameterList paramsSetup = new ParameterList().addTitleParameter("Memory");
    double originalMaxMemory = Math.ceil(maxMemoryMB / 1024.0);
    if (canSetMemory) {
        paramsSetup.addEmptyParameter("Set the maximum memory used by QuPath.");
        // .addEmptyParameter(maxMemoryString);
        boolean lowMemory = maxMemoryMB < 1024 * 6;
        if (lowMemory) {
            paramsSetup.addEmptyParameter("It is suggested to increase the memory limit to approximately\nhalf of the RAM available on your computer.");
        }
        paramsSetup.addDoubleParameter("maxMemoryGB", "Maximum memory", originalMaxMemory, "GB", "Set the maximum memory for Java.\n" + "Note that some commands (e.g. pixel classification) may still use more memory when needed,\n" + "so this value should generally not exceed half the total memory available on the system.");
    } else {
        paramsSetup.addEmptyParameter(maxMemoryString).addEmptyParameter("Sorry, I can't access the config file needed to change the max memory.\n" + "See the QuPath installation instructions for more details.");
    }
    paramsSetup.addTitleParameter("Region").addEmptyParameter("Set the region for QuPath to use for displaying numbers and messages.\n" + "Note: It is *highly recommended* to keep the default (English, US) region settings.\n" + "Support for regions that use different number formatting (e.g. commas as decimal marks)\n" + "is still experimental, and may give unexpected results.").addChoiceParameter("localeFormatting", "Numbers & dates", Locale.getDefault(Category.FORMAT).getDisplayName(), localeList, "Choose region settings used to format numbers and dates").addTitleParameter("Updates").addBooleanParameter("checkForUpdates", "Check for updates on startup (recommended)", PathPrefs.doAutoUpdateCheckProperty().get(), "Specify whether to automatically prompt to download the latest QuPath on startup (required internet connection)");
    ParameterPanelFX parameterPanel = new ParameterPanelFX(paramsSetup);
    pane.setCenter(parameterPanel.getPane());
    Label labelMemory;
    if (canSetMemory) {
        labelMemory = new Label("You will need to restart QuPath for memory changes to take effect");
        labelMemory.setStyle("-fx-font-weight: bold;");
        labelMemory.setMaxWidth(Double.MAX_VALUE);
        labelMemory.setAlignment(Pos.CENTER);
        labelMemory.setFont(Font.font("Arial"));
        labelMemory.setPadding(new Insets(10, 10, 10, 10));
        pane.setBottom(labelMemory);
    }
    // dialog.initStyle(StageStyle.UNDECORATED);
    dialog.getDialogPane().setContent(pane);
    dialog.getDialogPane().getButtonTypes().setAll(ButtonType.APPLY, ButtonType.CANCEL);
    Optional<ButtonType> result = dialog.showAndWait();
    if (!result.isPresent() || !ButtonType.APPLY.equals(result.get()))
        return false;
    Locale localeFormatting = localeMap.get(paramsSetup.getChoiceParameterValue("localeFormatting"));
    // Locale localeDisplay = localeMap.get(paramsSetup.getChoiceParameterValue("localeDisplay"));
    PathPrefs.defaultLocaleFormatProperty().set(localeFormatting);
    // PathPrefs.defaultLocaleDisplayProperty().set(localeDisplay);
    PathPrefs.doAutoUpdateCheckProperty().set(paramsSetup.getBooleanParameterValue("checkForUpdates"));
    if (canSetMemory && paramsSetup.containsKey("maxMemoryGB")) {
        int maxMemorySpecifiedMB = (int) (Math.round(paramsSetup.getDoubleParameterValue("maxMemoryGB") * 1024));
        if (maxMemorySpecifiedMB >= 1024) {
            PathPrefs.maxMemoryMBProperty().set(maxMemorySpecifiedMB);
        } else {
            if (maxMemorySpecifiedMB >= 0)
                Dialogs.showErrorNotification("Max memory setting", "Specified maximum memory setting too low - it must be at least 1 GB");
            else
                logger.warn("Requested max memory must be at least 1 GB - specified value {} will be ignored", paramsSetup.getDoubleParameterValue("maxMemoryGB"));
        // PathPrefs.maxMemoryMBProperty().set(-1);
        }
    }
    // Try to update display
    if (getStage() != null && getStage().isShowing())
        updateListsAndTables(getStage().getScene().getRoot());
    return true;
}