Examples with HistogramDisplay qupath.lib.gui.charts.HistogramDisplay used on opensource projects

Example 1 with HistogramDisplay

use of qupath.lib.gui.charts.HistogramDisplay in project qupath by qupath.

the class TMASummaryViewer method initialize.

private void initialize() {
    model = new TMATableModel();
    groupByIDProperty.addListener((v, o, n) -> refreshTableData());
    MenuBar menuBar = new MenuBar();
    Menu menuFile = new Menu("File");
    MenuItem miOpen = new MenuItem("Open...");
    miOpen.setAccelerator(new KeyCodeCombination(KeyCode.O, KeyCombination.SHORTCUT_DOWN));
    miOpen.setOnAction(e -> {
        File file = Dialogs.getChooser(stage).promptForFile(null, null, "TMA data files", new String[] { "qptma" });
        if (file == null)
            return;
        setInputFile(file);
    });
    MenuItem miSave = new MenuItem("Save As...");
    miSave.setAccelerator(new KeyCodeCombination(KeyCode.S, KeyCombination.SHORTCUT_DOWN, KeyCombination.SHIFT_DOWN));
    miSave.setOnAction(e -> SummaryMeasurementTableCommand.saveTableModel(model, null, Collections.emptyList()));
    MenuItem miImportFromImage = new MenuItem("Import from current image...");
    miImportFromImage.setAccelerator(new KeyCodeCombination(KeyCode.I, KeyCombination.SHORTCUT_DOWN, KeyCombination.SHIFT_DOWN));
    miImportFromImage.setOnAction(e -> setTMAEntriesFromOpenImage());
    MenuItem miImportFromProject = new MenuItem("Import from current project... (experimental)");
    miImportFromProject.setAccelerator(new KeyCodeCombination(KeyCode.P, KeyCombination.SHORTCUT_DOWN, KeyCombination.SHIFT_DOWN));
    miImportFromProject.setOnAction(e -> setTMAEntriesFromOpenProject());
    MenuItem miImportClipboard = new MenuItem("Import from clipboard...");
    miImportClipboard.setOnAction(e -> {
        String text = Clipboard.getSystemClipboard().getString();
        if (text == null) {
            Dialogs.showErrorMessage("Import scores", "Clipboard is empty!");
            return;
        }
        int n = importScores(text);
        if (n > 0) {
            setTMAEntries(new ArrayList<>(entriesBase));
        }
        Dialogs.showMessageDialog("Import scores", "Number of scores imported: " + n);
    });
    Menu menuEdit = new Menu("Edit");
    MenuItem miCopy = new MenuItem("Copy table to clipboard");
    miCopy.setOnAction(e -> {
        SummaryMeasurementTableCommand.copyTableContentsToClipboard(model, Collections.emptyList());
    });
    combinedPredicate.addListener((v, o, n) -> {
        // We want any other changes triggered by this to have happened,
        // so that the data has already been updated
        Platform.runLater(() -> handleTableContentChange());
    });
    // Reset the scores for missing cores - this ensures they will be NaN and not influence subsequent results
    MenuItem miResetMissingScores = new MenuItem("Reset scores for missing cores");
    miResetMissingScores.setOnAction(e -> {
        int changes = 0;
        for (TMAEntry entry : entriesBase) {
            if (!entry.isMissing())
                continue;
            boolean changed = false;
            for (String m : entry.getMeasurementNames().toArray(new String[0])) {
                if (!TMASummaryEntry.isSurvivalColumn(m) && !Double.isNaN(entry.getMeasurementAsDouble(m))) {
                    entry.putMeasurement(m, null);
                    changed = true;
                }
            }
            if (changed)
                changes++;
        }
        if (changes == 0) {
            logger.info("No changes made when resetting scores for missing cores!");
            return;
        }
        logger.info("{} change(s) made when resetting scores for missing cores!", changes);
        table.refresh();
        updateSurvivalCurves();
        if (scatterPane != null)
            scatterPane.updateChart();
        if (histogramDisplay != null)
            histogramDisplay.refreshHistogram();
    });
    menuEdit.getItems().add(miResetMissingScores);
    MenuTools.addMenuItems(menuFile, miOpen, miSave, null, miImportClipboard, null, miImportFromImage, miImportFromProject);
    menuBar.getMenus().add(menuFile);
    menuEdit.getItems().add(miCopy);
    menuBar.getMenus().add(menuEdit);
    menuFile.setOnShowing(e -> {
        boolean imageDataAvailable = QuPathGUI.getInstance() != null && QuPathGUI.getInstance().getImageData() != null && QuPathGUI.getInstance().getImageData().getHierarchy().getTMAGrid() != null;
        miImportFromImage.setDisable(!imageDataAvailable);
        boolean projectAvailable = QuPathGUI.getInstance() != null && QuPathGUI.getInstance().getProject() != null && !QuPathGUI.getInstance().getProject().getImageList().isEmpty();
        miImportFromProject.setDisable(!projectAvailable);
    });
    // Double-clicking previously used for comments... but conflicts with tree table expansion
    // table.setOnMouseClicked(e -> {
    // if (!e.isPopupTrigger() && e.getClickCount() > 1)
    // promptForComment();
    // });
    table.setPlaceholder(new Text("Drag TMA data folder onto window, or choose File -> Open"));
    table.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);
    BorderPane pane = new BorderPane();
    pane.setTop(menuBar);
    menuBar.useSystemMenuBarProperty().bindBidirectional(PathPrefs.useSystemMenubarProperty());
    // menuBar.setUseSystemMenuBar(true);
    // Create options
    ToolBar toolbar = new ToolBar();
    Label labelMeasurementMethod = new Label("Combination method");
    labelMeasurementMethod.setLabelFor(comboMeasurementMethod);
    labelMeasurementMethod.setTooltip(new Tooltip("Method whereby measurements for multiple cores with the same " + TMACoreObject.KEY_UNIQUE_ID + " will be combined"));
    CheckBox cbHidePane = new CheckBox("Hide pane");
    cbHidePane.setSelected(hidePaneProperty.get());
    cbHidePane.selectedProperty().bindBidirectional(hidePaneProperty);
    CheckBox cbGroupByID = new CheckBox("Group by ID");
    entriesBase.addListener((Change<? extends TMAEntry> event) -> {
        if (!event.getList().stream().anyMatch(e -> e.getMetadataValue(TMACoreObject.KEY_UNIQUE_ID) != null)) {
            cbGroupByID.setSelected(false);
            cbGroupByID.setDisable(true);
        } else {
            cbGroupByID.setDisable(false);
        }
    });
    cbGroupByID.setSelected(groupByIDProperty.get());
    cbGroupByID.selectedProperty().bindBidirectional(groupByIDProperty);
    CheckBox cbUseSelected = new CheckBox("Use selection only");
    cbUseSelected.selectedProperty().bindBidirectional(useSelectedProperty);
    CheckBox cbSkipMissing = new CheckBox("Hide missing cores");
    cbSkipMissing.selectedProperty().bindBidirectional(skipMissingCoresProperty);
    skipMissingCoresProperty.addListener((v, o, n) -> {
        table.refresh();
        updateSurvivalCurves();
        if (histogramDisplay != null)
            histogramDisplay.refreshHistogram();
        updateSurvivalCurves();
        if (scatterPane != null)
            scatterPane.updateChart();
    });
    toolbar.getItems().addAll(labelMeasurementMethod, comboMeasurementMethod, new Separator(Orientation.VERTICAL), cbHidePane, new Separator(Orientation.VERTICAL), cbGroupByID, new Separator(Orientation.VERTICAL), cbUseSelected, new Separator(Orientation.VERTICAL), cbSkipMissing);
    comboMeasurementMethod.getItems().addAll(TMAEntries.MeasurementCombinationMethod.values());
    comboMeasurementMethod.getSelectionModel().select(TMAEntries.MeasurementCombinationMethod.MEDIAN);
    selectedMeasurementCombinationProperty.addListener((v, o, n) -> table.refresh());
    ContextMenu popup = new ContextMenu();
    MenuItem miSetMissing = new MenuItem("Set missing");
    miSetMissing.setOnAction(e -> setSelectedMissingStatus(true));
    MenuItem miSetAvailable = new MenuItem("Set available");
    miSetAvailable.setOnAction(e -> setSelectedMissingStatus(false));
    MenuItem miExpand = new MenuItem("Expand all");
    miExpand.setOnAction(e -> {
        if (table.getRoot() == null)
            return;
        for (TreeItem<?> item : table.getRoot().getChildren()) {
            item.setExpanded(true);
        }
    });
    MenuItem miCollapse = new MenuItem("Collapse all");
    miCollapse.setOnAction(e -> {
        if (table.getRoot() == null)
            return;
        for (TreeItem<?> item : table.getRoot().getChildren()) {
            item.setExpanded(false);
        }
    });
    popup.getItems().addAll(miSetMissing, miSetAvailable, new SeparatorMenuItem(), miExpand, miCollapse);
    table.setContextMenu(popup);
    table.setRowFactory(e -> {
        TreeTableRow<TMAEntry> row = new TreeTableRow<>();
        // // Make rows invisible if they don't pass the predicate
        // row.visibleProperty().bind(Bindings.createBooleanBinding(() -> {
        // TMAEntry entry = row.getItem();
        // if (entry == null || (entry.isMissing() && skipMissingCoresProperty.get()))
        // return false;
        // return entries.getPredicate() == null || entries.getPredicate().test(entry);
        // },
        // skipMissingCoresProperty,
        // entries.predicateProperty()));
        // Style rows according to what they contain
        row.styleProperty().bind(Bindings.createStringBinding(() -> {
            if (row.isSelected())
                return "";
            TMAEntry entry = row.getItem();
            if (entry == null || entry instanceof TMASummaryEntry)
                return "";
            else if (entry.isMissing())
                return "-fx-background-color:rgb(225,225,232)";
            else
                return "-fx-background-color:rgb(240,240,245)";
        }, row.itemProperty(), row.selectedProperty()));
        // });
        return row;
    });
    BorderPane paneTable = new BorderPane();
    paneTable.setTop(toolbar);
    paneTable.setCenter(table);
    MasterDetailPane mdTablePane = new MasterDetailPane(Side.RIGHT, paneTable, createSidePane(), true);
    mdTablePane.showDetailNodeProperty().bind(Bindings.createBooleanBinding(() -> !hidePaneProperty.get() && !entriesBase.isEmpty(), hidePaneProperty, entriesBase));
    mdTablePane.setDividerPosition(2.0 / 3.0);
    pane.setCenter(mdTablePane);
    model.getItems().addListener(new ListChangeListener<TMAEntry>() {

        @Override
        public void onChanged(ListChangeListener.Change<? extends TMAEntry> c) {
            if (histogramDisplay != null)
                histogramDisplay.refreshHistogram();
            updateSurvivalCurves();
            if (scatterPane != null)
                scatterPane.updateChart();
        }
    });
    Label labelPredicate = new Label();
    labelPredicate.setPadding(new Insets(5, 5, 5, 5));
    labelPredicate.setAlignment(Pos.CENTER);
    // labelPredicate.setStyle("-fx-background-color: rgba(20, 120, 20, 0.15);");
    labelPredicate.setStyle("-fx-background-color: rgba(120, 20, 20, 0.15);");
    labelPredicate.textProperty().addListener((v, o, n) -> {
        if (n.trim().length() > 0)
            pane.setBottom(labelPredicate);
        else
            pane.setBottom(null);
    });
    labelPredicate.setMaxWidth(Double.MAX_VALUE);
    labelPredicate.setMaxHeight(labelPredicate.getPrefHeight());
    labelPredicate.setTextAlignment(TextAlignment.CENTER);
    predicateMeasurements.addListener((v, o, n) -> {
        if (n == null)
            labelPredicate.setText("");
        else if (n instanceof TablePredicate) {
            TablePredicate tp = (TablePredicate) n;
            if (tp.getOriginalCommand().trim().isEmpty())
                labelPredicate.setText("");
            else
                labelPredicate.setText("Predicate: " + tp.getOriginalCommand());
        } else
            labelPredicate.setText("Predicate: " + n.toString());
    });
    // predicate.set(new TablePredicate("\"Tumor\" > 100"));
    scene = new Scene(pane);
    scene.addEventHandler(KeyEvent.KEY_PRESSED, e -> {
        KeyCode code = e.getCode();
        if ((code == KeyCode.SPACE || code == KeyCode.ENTER) && entrySelected != null) {
            promptForComment();
            return;
        }
    });
}

Example 2 with HistogramDisplay

use of qupath.lib.gui.charts.HistogramDisplay in project qupath by qupath.

the class SummaryMeasurementTableCommand method showTable.

/**
 * Show a measurement table for the specified image data.
 * @param imageData the image data
 * @param type the object type to show
 */
public void showTable(ImageData<BufferedImage> imageData, Class<? extends PathObject> type) {
    if (imageData == null) {
        Dialogs.showNoImageError("Show measurement table");
        return;
    }
    final PathObjectHierarchy hierarchy = imageData.getHierarchy();
    ObservableMeasurementTableData model = new ObservableMeasurementTableData();
    model.setImageData(imageData, imageData == null ? Collections.emptyList() : imageData.getHierarchy().getObjects(null, type));
    SplitPane splitPane = new SplitPane();
    HistogramDisplay histogramDisplay = new HistogramDisplay(model, true);
    // table.setTableMenuButtonVisible(true);
    TableView<PathObject> table = new TableView<>();
    table.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);
    table.getSelectionModel().getSelectedItems().addListener(new ListChangeListener<PathObject>() {

        @Override
        public void onChanged(ListChangeListener.Change<? extends PathObject> c) {
            synchronizeSelectionModelToTable(hierarchy, c, table);
        }
    });
    StringProperty displayedName = new SimpleStringProperty(ServerTools.getDisplayableImageName(imageData.getServer()));
    var title = Bindings.createStringBinding(() -> {
        if (type == null)
            return "Results " + displayedName.get();
        else
            return PathObjectTools.getSuitableName(type, false) + " results - " + displayedName.get();
    }, displayedName);
    // Handle double-click as a way to center on a ROI
    // var enter = new KeyCodeCombination(KeyCode.ENTER);
    table.setRowFactory(params -> {
        var row = new TableRow<PathObject>();
        row.setOnMouseClicked(e -> {
            if (e.getClickCount() == 2) {
                maybeCenterROI(row.getItem());
            }
        });
        // });
        return row;
    });
    // Create columns according to the table model
    // for (int i = 0; i < model.getColumnCount(); i++) {
    // // Add string column
    // if (model.getColumnClass(i).equals(String.class)) {
    // TableColumn<PathObject, String> col = null;
    // col = new TableColumn<>(model.getColumnName(i));
    // col.setCellValueFactory(new Callback<CellDataFeatures<PathObject, String>, ObservableValue<String>>() {
    // public ObservableValue<String> call(CellDataFeatures<PathObject, String> val) {
    // return new SimpleStringProperty(val.getValue().getDisplayedName());
    // }
    // });
    // col.setCellFactory(column -> new BasicTableCell<String>());
    // table.getColumns().add(col);
    // }
    // }
    boolean tmaCoreList = TMACoreObject.class.isAssignableFrom(type);
    // Add TMA core columns, if suitable
    if (tmaCoreList) {
        TableColumn<PathObject, ROI> col = new TableColumn<>("Image");
        col.setCellValueFactory(val -> new SimpleObjectProperty<>(val.getValue().getROI()));
        double maxWidth = maxDimForTMACore;
        double padding = 10;
        col.setCellFactory(column -> new TMACoreTableCell(table, imageData.getServer(), maxWidth, padding));
        col.widthProperty().addListener((v, o, n) -> table.refresh());
        col.setMaxWidth(maxWidth + padding * 2);
        table.getColumns().add(col);
        // While here, make sure we have fewer bins - don't usually have all that many cores
        histogramDisplay.setNumBins(10);
    }
    // Create numeric columns
    for (String columnName : model.getAllNames()) {
        // Add column
        if (model.isStringMeasurement(columnName)) {
            TableColumn<PathObject, String> col = new TableColumn<>(columnName);
            col.setCellValueFactory(column -> model.createStringMeasurement(column.getValue(), column.getTableColumn().getText()));
            col.setCellFactory(column -> new BasicTableCell<>());
            table.getColumns().add(col);
        } else {
            TableColumn<PathObject, Number> col = new TableColumn<>(columnName);
            col.setCellValueFactory(column -> model.createNumericMeasurement(column.getValue(), column.getTableColumn().getText()));
            col.setCellFactory(column -> new NumericTableCell<PathObject>(histogramDisplay));
            table.getColumns().add(col);
        }
    }
    // Set the PathObjects - need to deal with sorting, since a FilteredList won't handle it directly
    SortedList<PathObject> items = new SortedList<>(model.getItems());
    items.comparatorProperty().bind(table.comparatorProperty());
    table.setItems(items);
    List<ButtonBase> buttons = new ArrayList<>();
    ToggleButton btnHistogram = new ToggleButton("Show histograms");
    btnHistogram.selectedProperty().addListener((v, o, n) -> {
        if (n) {
            Pane paneHistograms = histogramDisplay.getPane();
            splitPane.getItems().add(paneHistograms);
        } else if (histogramDisplay != null)
            splitPane.getItems().remove(histogramDisplay.getPane());
    });
    buttons.add(btnHistogram);
    // Button btnScatterplot = new Button("Show scatterplots");
    // btnScatterplot.setOnAction(e -> {
    // SwingUtilities.invokeLater(() -> {
    // JDialog dialog = new ScatterplotDisplay(null, "Scatterplots: " + displayedName, model).getDialog();
    // dialog.setLocationRelativeTo(null);
    // dialog.setVisible(true);
    // });
    // });
    // buttons.add(btnScatterplot);
    Button btnCopy = new Button("Copy to clipboard");
    btnCopy.setOnAction(e -> {
        // TODO: Deal with repetition immediately below...
        Set<String> excludeColumns = new HashSet<>();
        for (TableColumn<?, ?> col : table.getColumns()) {
            if (!col.isVisible())
                excludeColumns.add(col.getText());
        }
        copyTableContentsToClipboard(model, excludeColumns);
    });
    buttons.add(btnCopy);
    Button btnSave = new Button("Save");
    btnSave.setOnAction(e -> {
        Set<String> excludeColumns = new HashSet<>();
        for (TableColumn<?, ?> col : table.getColumns()) {
            if (!col.isVisible())
                excludeColumns.add(col.getText());
        }
        File fileOutput = promptForOutputFile();
        if (fileOutput == null)
            return;
        if (saveTableModel(model, fileOutput, excludeColumns)) {
            WorkflowStep step;
            String includeColumns;
            if (excludeColumns.isEmpty())
                includeColumns = "";
            else {
                List<String> includeColumnList = new ArrayList<>(model.getAllNames());
                includeColumnList.removeAll(excludeColumns);
                includeColumns = ", " + includeColumnList.stream().map(s -> "'" + s + "'").collect(Collectors.joining(", "));
            }
            String path = qupath.getProject() == null ? fileOutput.toURI().getPath() : fileOutput.getParentFile().toURI().getPath();
            if (type == TMACoreObject.class) {
                step = new DefaultScriptableWorkflowStep("Save TMA measurements", String.format("saveTMAMeasurements('%s'%s)", path, includeColumns));
            } else if (type == PathAnnotationObject.class) {
                step = new DefaultScriptableWorkflowStep("Save annotation measurements", String.format("saveAnnotationMeasurements('%s\'%s)", path, includeColumns));
            } else if (type == PathDetectionObject.class) {
                step = new DefaultScriptableWorkflowStep("Save detection measurements", String.format("saveDetectionMeasurements('%s'%s)", path, includeColumns));
            } else {
                step = new DefaultScriptableWorkflowStep("Save measurements", String.format("saveMeasurements('%s', %s%s)", path, type == null ? null : type.getName(), includeColumns));
            }
            imageData.getHistoryWorkflow().addStep(step);
        }
    });
    buttons.add(btnSave);
    Stage frame = new Stage();
    frame.initOwner(qupath.getStage());
    frame.titleProperty().bind(title);
    BorderPane paneTable = new BorderPane();
    paneTable.setCenter(table);
    // Add text field to filter visible columns
    TextField tfColumnFilter = new TextField();
    GridPane paneFilter = new GridPane();
    paneFilter.add(new Label("Column filter"), 0, 0);
    paneFilter.add(tfColumnFilter, 1, 0);
    GridPane.setHgrow(tfColumnFilter, Priority.ALWAYS);
    paneFilter.setHgap(5);
    if (tmaCoreList) {
        CheckBox cbHideMissing = new CheckBox("Hide missing cores");
        paneFilter.add(cbHideMissing, 2, 0);
        cbHideMissing.selectedProperty().addListener((v, o, n) -> {
            if (n) {
                model.setPredicate(p -> (!(p instanceof TMACoreObject)) || !((TMACoreObject) p).isMissing());
            } else
                model.setPredicate(null);
        });
        cbHideMissing.setSelected(true);
    }
    paneFilter.setPadding(new Insets(2, 5, 2, 5));
    paneTable.setBottom(paneFilter);
    StringProperty columnFilter = tfColumnFilter.textProperty();
    columnFilter.addListener((v, o, n) -> {
        String val = n.toLowerCase().trim();
        if (val.isEmpty()) {
            for (TableColumn<?, ?> col : table.getColumns()) {
                if (!col.isVisible())
                    col.setVisible(true);
            }
            return;
        }
        for (TableColumn<?, ?> col : table.getColumns()) {
            col.setVisible(col.getText().toLowerCase().contains(val));
        }
    });
    BorderPane pane = new BorderPane();
    // pane.setCenter(table);
    splitPane.getItems().add(paneTable);
    pane.setCenter(splitPane);
    GridPane panelButtons = PaneTools.createColumnGridControls(buttons.toArray(new ButtonBase[0]));
    pane.setBottom(panelButtons);
    PathObjectHierarchyListener listener = new PathObjectHierarchyListener() {

        @Override
        public void hierarchyChanged(PathObjectHierarchyEvent event) {
            if (event.isChanging())
                return;
            if (!Platform.isFxApplicationThread()) {
                Platform.runLater(() -> hierarchyChanged(event));
                return;
            }
            if (imageData != null)
                displayedName.set(ServerTools.getDisplayableImageName(imageData.getServer()));
            model.refreshEntries();
            table.refresh();
            if (histogramDisplay != null)
                histogramDisplay.refreshHistogram();
        }
    };
    QuPathViewer viewer = qupath.getViewer();
    TableViewerListener tableViewerListener = new TableViewerListener(viewer, table);
    frame.setOnShowing(e -> {
        hierarchy.addPathObjectListener(listener);
        viewer.addViewerListener(tableViewerListener);
    });
    frame.setOnHiding(e -> {
        hierarchy.removePathObjectListener(listener);
        viewer.removeViewerListener(tableViewerListener);
    });
    Scene scene = new Scene(pane, 600, 500);
    frame.setScene(scene);
    frame.show();
    // Add ability to remove entries from table
    ContextMenu menu = new ContextMenu();
    Menu menuLimitClasses = new Menu("Show classes");
    menu.setOnShowing(e -> {
        Set<PathClass> representedClasses = model.getBackingListEntries().stream().map(p -> p.getPathClass() == null ? null : p.getPathClass().getBaseClass()).collect(Collectors.toCollection(() -> new HashSet<>()));
        representedClasses.remove(null);
        if (representedClasses.isEmpty()) {
            menuLimitClasses.setVisible(false);
        } else {
            menuLimitClasses.setVisible(true);
        }
        menuLimitClasses.getItems().clear();
        List<PathClass> sortedClasses = new ArrayList<>(representedClasses);
        Collections.sort(sortedClasses);
        MenuItem miClass = new MenuItem("All");
        miClass.setOnAction(e2 -> {
            model.setPredicate(null);
            histogramDisplay.refreshHistogram();
        });
        menuLimitClasses.getItems().add(miClass);
        for (PathClass pathClass : sortedClasses) {
            miClass = new MenuItem(pathClass.getName());
            miClass.setOnAction(e2 -> {
                model.setPredicate(p -> pathClass.isAncestorOf(p.getPathClass()));
                histogramDisplay.refreshHistogram();
            });
            menuLimitClasses.getItems().add(miClass);
        }
    });
    if (type != TMACoreObject.class) {
        menu.getItems().add(menuLimitClasses);
        table.setContextMenu(menu);
    }
}

Example 3 with HistogramDisplay

use of qupath.lib.gui.charts.HistogramDisplay in project qupath by qupath.

the class TMASummaryViewer method createSidePane.

private Pane createSidePane() {
    BorderPane pane = new BorderPane();
    TabPane tabPane = new TabPane();
    kmDisplay = new KaplanMeierDisplay(null, null, null, null);
    BorderPane paneKaplanMeier = new BorderPane();
    paneKaplanMeier.setCenter(kmDisplay.getView());
    paneKaplanMeier.setPadding(new Insets(10, 10, 10, 10));
    // comboMainMeasurement.prefWidthProperty().bind(paneKaplanMeier.widthProperty());
    comboMainMeasurement.setMaxWidth(Double.MAX_VALUE);
    comboMainMeasurement.setTooltip(new Tooltip("Measurement thresholded to create survival curves etc."));
    GridPane kmTop = new GridPane();
    kmTop.add(new Label("Score"), 0, 0);
    kmTop.add(comboMainMeasurement, 1, 0);
    kmTop.add(new Label("Survival type"), 0, 1);
    kmTop.add(comboSurvival, 1, 1);
    comboSurvival.setTooltip(new Tooltip("Specify overall or recurrence-free survival (if applicable)"));
    comboSurvival.setMaxWidth(Double.MAX_VALUE);
    GridPane.setHgrow(comboMainMeasurement, Priority.ALWAYS);
    GridPane.setHgrow(comboSurvival, Priority.ALWAYS);
    kmTop.setHgap(5);
    paneKaplanMeier.setTop(kmTop);
    // kmDisplay.setOrientation(Orientation.VERTICAL);
    histogramDisplay = new HistogramDisplay(model, false);
    comboMainMeasurement.getSelectionModel().selectedItemProperty().addListener((v, o, n) -> {
        histogramDisplay.refreshCombo();
        histogramDisplay.showHistogram(n);
        updateSurvivalCurves();
    });
    comboMeasurementMethod.getSelectionModel().selectedItemProperty().addListener((v, o, n) -> {
        histogramDisplay.refreshHistogram();
        scatterPane.updateChart();
        updateSurvivalCurves();
    });
    comboSurvival.getSelectionModel().selectedItemProperty().addListener((v, o, n) -> {
        updateSurvivalCurves();
    });
    // Create a Tab for showing images
    BorderPane paneImages = new BorderPane();
    CheckBox cbShowOverlay = new CheckBox("Show overlay");
    imageAvailability.addListener((c, v, n) -> {
        if (n == ImageAvailability.OVERLAY_ONLY)
            cbShowOverlay.setSelected(true);
        else if (n == ImageAvailability.IMAGE_ONLY)
            cbShowOverlay.setSelected(false);
        cbShowOverlay.setDisable(n != ImageAvailability.BOTH);
    });
    ListView<TMAEntry> listImages = new ListView<>();
    listImages.setCellFactory(v -> new ImageListCell(cbShowOverlay.selectedProperty(), imageCache));
    listImages.widthProperty().addListener((v, o, n) -> listImages.refresh());
    listImages.setStyle("-fx-control-inner-background-alt: -fx-control-inner-background ;");
    table.getSelectionModel().getSelectedItems().addListener((Change<? extends TreeItem<TMAEntry>> e) -> {
        List<TMAEntry> entries = new ArrayList<>();
        for (TreeItem<TMAEntry> item : e.getList()) {
            if (item.getChildren().isEmpty()) {
                if (item.getValue().hasImage() || item.getValue().hasOverlay())
                    entries.add(item.getValue());
            } else {
                for (TreeItem<TMAEntry> item2 : item.getChildren()) {
                    if (item2.getValue().hasImage() || item2.getValue().hasOverlay())
                        entries.add(item2.getValue());
                }
            }
            listImages.getItems().setAll(entries);
        }
    });
    cbShowOverlay.setAlignment(Pos.CENTER);
    cbShowOverlay.setMaxWidth(Double.MAX_VALUE);
    cbShowOverlay.setPadding(new Insets(5, 5, 5, 5));
    cbShowOverlay.selectedProperty().addListener((v, o, n) -> listImages.refresh());
    paneImages.setCenter(listImages);
    paneImages.setTop(cbShowOverlay);
    // Determine visibility based upon whether there are any images to show
    // Tab tabImages = new Tab("Images", paneImages);
    ScrollPane scrollPane = new ScrollPane(paneKaplanMeier);
    scrollPane.setFitToWidth(true);
    scrollPane.setFitToHeight(true);
    scrollPane.setVbarPolicy(ScrollBarPolicy.AS_NEEDED);
    scrollPane.setHbarPolicy(ScrollBarPolicy.AS_NEEDED);
    Tab tabSurvival = new Tab("Survival", scrollPane);
    tabPane.getTabs().addAll(new Tab("Table", getCustomizeTablePane()), // tabImages,
    new Tab("Histogram", histogramDisplay.getPane()), new Tab("Scatterplot", scatterPane.getPane()), tabSurvival);
    tabPane.setTabClosingPolicy(TabClosingPolicy.UNAVAILABLE);
    // if (imageAvailability.get() != ImageAvailability.NONE)
    // tabPane.getTabs().add(1, tabImages);
    // 
    // imageAvailability.addListener((c, v, n) -> {
    // if (n == ImageAvailability.NONE)
    // tabPane.getTabs().remove(tabImages);
    // else if (!tabPane.getTabs().contains(tabImages))
    // tabPane.getTabs().add(1, tabImages);
    // });
    // tabSurvival.visibleProperty().bind(
    // Bindings.createBooleanBinding(() -> !survivalColumns.isEmpty(), survivalColumns)
    // );
    pane.setCenter(tabPane);
    pane.setMinWidth(350);
    return pane;
}