List of usage examples for javafx.scene.layout BorderPane BorderPane
public BorderPane()
From source file:org.jevis.jeconfig.JEConfig.java
/** * Build an new JEConfig Login and main frame/stage * * @param primaryStage/*from w w w .j a va 2 s .com*/ */ //AITBilal - Login private void initGUI(Stage primaryStage) { Scene scene; LoginGlass login = new LoginGlass(primaryStage); AnchorPane jeconfigRoot = new AnchorPane(); AnchorPane.setTopAnchor(jeconfigRoot, 0.0); AnchorPane.setRightAnchor(jeconfigRoot, 0.0); AnchorPane.setLeftAnchor(jeconfigRoot, 0.0); AnchorPane.setBottomAnchor(jeconfigRoot, 0.0); // jeconfigRoot.setStyle("-fx-background-color: white;"); // jeconfigRoot.getChildren().setAll(new Label("sodfhsdhdsofhdshdsfdshfjf")); Screen screen = Screen.getPrimary(); Rectangle2D bounds = screen.getVisualBounds(); // @AITBilal - Main frame elemente wird aufgerufen nachdem man sich eingeloggt hat. login.getLoginStatus().addListener(new ChangeListener<Boolean>() { @Override public void changed(ObservableValue<? extends Boolean> observable, Boolean oldValue, Boolean newValue) { if (newValue) { System.out.println("after request"); _mainDS = login.getDataSource(); ds = _mainDS; Platform.runLater(new Runnable() { @Override public void run() { FadeTransition ft = new FadeTransition(Duration.millis(1500), login); ft.setFromValue(1.0); ft.setToValue(0); ft.setCycleCount(1); ft.play(); } }); JEConfig.PROGRAMM_INFO.setJEVisAPI(ds.getInfo()); JEConfig.PROGRAMM_INFO.addLibrary(org.jevis.commons.application.Info.INFO); JEConfig.PROGRAMM_INFO.addLibrary(org.jevis.application.Info.INFO); preLodedClasses = login.getAllClasses(); preLodedRootObjects = login.getRootObjects(); PluginManager pMan = new PluginManager(ds); //@AITBilal - Toolbar fr save, newB, delete, sep1, form GlobalToolBar toolbar = new GlobalToolBar(pMan); pMan.addPluginsByUserSetting(null); // StackPane root = new StackPane(); // root.setId("mainpane"); BorderPane border = new BorderPane(); VBox vbox = new VBox(); vbox.getChildren().addAll(new TopMenu(), toolbar.ToolBarFactory()); border.setTop(vbox); //@AITBilal - Alle Plugins Inhalt fr JEConfig (Resources... | System | Attribute) border.setCenter(pMan.getView()); Statusbar statusBar = new Statusbar(ds); border.setBottom(statusBar); System.out.println("show welcome"); //Disable GUI is StatusBar note an disconnect border.disableProperty().bind(statusBar.connectedProperty.not()); Platform.runLater(new Runnable() { @Override public void run() { AnchorPane.setTopAnchor(border, 0.0); AnchorPane.setRightAnchor(border, 0.0); AnchorPane.setLeftAnchor(border, 0.0); AnchorPane.setBottomAnchor(border, 0.0); jeconfigRoot.getChildren().setAll(border); // try { // WelcomePage welcome = new WelcomePage(primaryStage, new URI("http://coffee-project.eu/")); // WelcomePage welcome = new WelcomePage(primaryStage, new URI("http://openjevis.org/projects/openjevis/wiki/JEConfig3#JEConfig-Version-3")); // Task<Void> showWelcome = new Task<Void>() { // @Override // protected Void call() throws Exception { try { WelcomePage welcome = new WelcomePage(primaryStage, _config.getWelcomeURL()); } catch (URISyntaxException ex) { Logger.getLogger(JEConfig.class.getName()).log(Level.SEVERE, null, ex); } catch (MalformedURLException ex) { Logger.getLogger(JEConfig.class.getName()).log(Level.SEVERE, null, ex); } // return null; // } // }; // new Thread(showWelcome).start(); // WelcomePage welcome = new WelcomePage(primaryStage, _config.getWelcomeURL()); // } catch (URISyntaxException ex) { // Logger.getLogger(JEConfig.class.getName()).log(Level.SEVERE, null, ex); // } catch (MalformedURLException ex) { // Logger.getLogger(JEConfig.class.getName()).log(Level.SEVERE, null, ex); // } } }); } } }); AnchorPane.setTopAnchor(login, 0.0); AnchorPane.setRightAnchor(login, 0.0); AnchorPane.setLeftAnchor(login, 0.0); AnchorPane.setBottomAnchor(login, 0.0); //@AITBilal - Login Dialog scene = new Scene(jeconfigRoot, bounds.getWidth(), bounds.getHeight()); scene.getStylesheets().add("/styles/Styles.css"); primaryStage.getIcons().add(getImage("1393354629_Config-Tools.png")); primaryStage.setTitle("JEConfig"); primaryStage.setScene(scene); maximize(primaryStage); primaryStage.show(); // Platform.runLater(new Runnable() { // @Override // public void run() { //@AITBilal - Inhalt bzw. die Elemente von LoginDialog jeconfigRoot.getChildren().setAll(login); // } // }); primaryStage.onCloseRequestProperty().addListener(new ChangeListener<EventHandler<WindowEvent>>() { @Override public void changed(ObservableValue<? extends EventHandler<WindowEvent>> ov, EventHandler<WindowEvent> t, EventHandler<WindowEvent> t1) { try { System.out.println("Disconnect"); ds.disconnect(); } catch (JEVisException ex) { Logger.getLogger(JEConfig.class.getName()).log(Level.SEVERE, null, ex); } } }); }
From source file:ca.wumbo.doommanager.client.controller.file.DoomFileController.java
/** * This is to be called when the user clicks on a new row, which means the * GUI should be updated by disposing of whatever is on the right (if it's * possible), and adding in the new view. * /* w w w . ja va 2s . c o m*/ * @param oldTreeItem * The old tree item (null is allowed). * * @param newTreeItem * The new tree item (null is allowed). */ private void updateGUIFromEntrySelection(TreeItem<Entry> oldTreeItem, TreeItem<Entry> newTreeItem) { // We only care if a click causes a change in entries. if (oldTreeItem != newTreeItem) { // Check if we haven't saved yet, and if not... prompt the user. // TODO // If we're changing to a new entry, time to load a new Pane. if (newTreeItem != null) { // Load the new Node based on what the entry is, and place it on the right. EntryControllable entryControllable = newTreeItem.getValue().getNewController(); entryControllable.setEntry(newTreeItem.getValue()); // Clean up the right pane to assist the garbage collector. // TODO // Insert the root pane at the center. rightBorderPane.setCenter(entryControllable.getRootPane()); } else { // If we're going to null, we should clear last element placed in the pane with a blank pane. rightBorderPane.setCenter(new BorderPane()); } } }
From source file:qupath.lib.gui.panels.classify.RandomTrainingRegionSelector.java
private void createDialog() { dialog = new Stage(); dialog.initOwner(qupath.getStage()); dialog.setTitle("Training sample selector"); pointCreator = new RandomPointCreator(); for (PathClass pathClass : pathClassListModel) { if (pathClass != null && pathClass.getName() != null) pointCreator.addPathClass(pathClass, KeyCode.getKeyCode(pathClass.getName().toUpperCase().substring(0, 1))); // pointCreator.addPathClass(pathClass, KeyStroke.getKeyStroke(new pathClass.getName().toLowerCase().charAt(0), 0).getKeyCode()); }/*from www .jav a 2s.c om*/ // PathClass tumourClass = PathClassFactory.getDefaultPathClass(PathClasses.TUMOR); // PathClass stromaClass = PathClassFactory.getDefaultPathClass(PathClasses.STROMA); // pointCreator.addPathClass(tumourClass, KeyCode.T); // pointCreator.addPathClass(stromaClass, KeyCode.S); QuPathViewer viewer = qupath.getViewer(); pointCreator.registerViewer(viewer); // Adapt to changing active viewers ImageDataChangeListener<BufferedImage> listener = new ImageDataChangeListener<BufferedImage>() { @Override public void imageDataChanged(ImageDataWrapper<BufferedImage> source, ImageData<BufferedImage> imageDataOld, ImageData<BufferedImage> imageDataNew) { if (pointCreator != null) { QuPathViewer viewer = qupath.getViewer(); pointCreator.registerViewer(viewer); updateObjectCache(viewer); } refreshList(); updateLabel(); } }; qupath.addImageDataChangeListener(listener); // Remove listeners for cleanup dialog.setOnCloseRequest(e -> { pointCreator.deregisterViewer(); qupath.removeImageDataChangeListener(listener); dialog.setOnCloseRequest(null); dialog = null; // Re-enable mode switching qupath.setModeSwitchingEnabled(true); }); ParameterPanelFX paramPanel = new ParameterPanelFX(params); paramPanel.getPane().setPadding(new Insets(2, 5, 5, 5)); list = new ListView<PathClass>(pathClassListModel); list.setPrefSize(400, 200); // TODO: ADD A SENSIBLE RENDERER! // For now, this is simply duplicated from PathAnnotationPanel list.setCellFactory(new Callback<ListView<PathClass>, ListCell<PathClass>>() { @Override public ListCell<PathClass> call(ListView<PathClass> p) { ListCell<PathClass> cell = new ListCell<PathClass>() { @Override protected void updateItem(PathClass value, boolean bln) { super.updateItem(value, bln); int size = 10; if (value == null) { setText(null); setGraphic(null); } else if (value.getName() == null) { setText("None"); setGraphic(new Rectangle(size, size, ColorToolsFX.getCachedColor(0, 0, 0, 0))); } else { setText(value.getName()); setGraphic(new Rectangle(size, size, ColorToolsFX.getPathClassColor(value))); } } }; return cell; } }); // list.setCellRenderer(new PathClassListCellRendererPoints()); list.setTooltip(new Tooltip("Available classes")); labelCount = new Label(); labelCount.setTextAlignment(TextAlignment.CENTER); labelCount.setPadding(new Insets(5, 0, 5, 0)); BorderPane panelTop = new BorderPane(); panelTop.setTop(paramPanel.getPane()); panelTop.setCenter(list); panelTop.setBottom(labelCount); labelCount.prefWidthProperty().bind(panelTop.widthProperty()); updateLabel(); // panelButtons.add(new JButton(new UndoAction("Undo"))); Action actionAdd = new Action("Add to class", e -> { if (list == null || pointCreator == null) return; PathClass pathClass = list.getSelectionModel().getSelectedItem(); pointCreator.addPoint(pathClass); }); Action actionSkip = new Action("Skip", e -> { if (pointCreator != null) pointCreator.addPoint(null); }); GridPane panelButtons = PanelToolsFX.createColumnGridControls(ActionUtils.createButton(actionAdd), ActionUtils.createButton(actionSkip)); BorderPane pane = new BorderPane(); pane.setCenter(panelTop); pane.setBottom(panelButtons); pane.setPadding(new Insets(10, 10, 10, 10)); Scene scene = new Scene(pane); dialog.setScene(scene); }
From source file:Main.java
@Override public void start(Stage stage) { BorderPane root = new BorderPane(); Pane parentContainer = new Pane(); parentContainer.setPrefSize(500, 500); parentContainer.setPickOnBounds(false); //Pane parent = new Pane(); Group parent = new Group(); boundsLayoutNode = parent;/*from w ww . ja v a 2 s.c o m*/ //parent.setPrefSize(300, 200); parent.setLayoutX(200); parent.setLayoutY(200); parent.setStyle("-fx-background-color:white;"); parent.getChildren().addAll(new Group(localXAxisGroup, localYAxisGroup), new Group(parentXAxisGroup, parentYAxisGroup), new Group(parentBoundsRect, PARENT_BOUNDS_PATH_CIRCLE), new Group(localBoundsRect, LOCAL_BOUNDS_PATH_CIRCLE), new Group(layoutBoundsRect, LAYOUT_BOUNDS_PATH_CIRCLE), new Group(mainRect)); parentContainer.getChildren().addAll(parent); VBox transformsControls = getTransformationControls(); VBox resultsControls = getResultsControls(); BorderPane nestedPane = new BorderPane(); nestedPane.setCenter(parentContainer); nestedPane.setBottom(resultsControls); //nestedPane.setTop(printDataTextArea); //printDataTextArea.setPrefColumnCount(40); //printDataTextArea.setPrefRowCount(3); root.setCenter(nestedPane); root.setRight(transformsControls); //root.setBottom(resultsControls); //root.setCenter(parentContainer); // Attach event handlers attachEventHandlers(); Scene scene = new Scene(root); //, 600, 400); stage.setScene(scene); stage.setTitle("Bounds of a Node"); Rectangle2D visualBounds = Screen.getPrimary().getVisualBounds(); stage.setX(visualBounds.getMinX()); stage.setY(visualBounds.getMinY()); stage.setWidth(visualBounds.getWidth()); stage.setHeight(visualBounds.getHeight()); stage.show(); // Make sure everything is in sync relayout(); }
From source file:org.jevis.jeconfig.JEConfig.java
/** * Build an new JEConfig Login and main frame/stage * * @param primaryStage//from w w w .jav a 2s. com */ //@AITBilal - Dieses Method wird nirgendwo aufgerufen! private void buildGUI(Stage primaryStage) { try { LoginDialog loginD = new LoginDialog(); // ds = loginD.showSQL(primaryStage, _config.get<LoginIcon()); ds = loginD.showSQL(primaryStage);//Default // ds = loginD.showSQL(primaryStage, _config.getLoginIcon(), _config.getEnabledSSL(), _config.getShowServer(), _config.getDefaultServer());//KAUST // ds = loginD.showSQL(primaryStage, _config.getLoginIcon(), _config.getEnabledSSL(), _config.getShowServer(), _config.getDefaultServer());//Coffee // while (ds == null) { // Thread.sleep(100); // } // if (ds == null) { // System.exit(0); // } // System.exit(1); // ds = new JEVisDataSourceSQL("192.168.2.55", "3306", "jevis", "jevis", "jevistest", "Sys Admin", "jevis"); // ds.connect("Sys Admin", "jevis"); } catch (Exception ex) { Logger.getLogger(JEConfig.class.getName()).log(Level.SEVERE, null, ex); ExceptionDialog dia = new ExceptionDialog(); dia.show(primaryStage, "Error", "Could not connect to Server", ex, PROGRAMM_INFO); } _mainDS = ds; JEConfig.PROGRAMM_INFO.setJEVisAPI(ds.getInfo()); JEConfig.PROGRAMM_INFO.addLibrary(org.jevis.commons.application.Info.INFO); JEConfig.PROGRAMM_INFO.addLibrary(org.jevis.application.Info.INFO); PluginManager pMan = new PluginManager(ds); GlobalToolBar toolbar = new GlobalToolBar(pMan); pMan.addPluginsByUserSetting(null); StackPane root = new StackPane(); root.setId("mainpane"); BorderPane border = new BorderPane(); VBox vbox = new VBox(); vbox.getChildren().addAll(new TopMenu(), toolbar.ToolBarFactory()); border.setTop(vbox); border.setCenter(pMan.getView()); Statusbar statusBar = new Statusbar(ds); border.setBottom(statusBar); root.getChildren().addAll(border); Scene scene = new Scene(root, 300, 250); scene.getStylesheets().add("/styles/Styles.css"); primaryStage.getIcons().add(getImage("1393354629_Config-Tools.png")); primaryStage.setTitle("JEConfig"); primaryStage.setScene(scene); maximize(primaryStage); primaryStage.show(); try { // WelcomePage welcome = new WelcomePage(primaryStage, new URI("http://coffee-project.eu/")); // WelcomePage welcome = new WelcomePage(primaryStage, new URI("http://openjevis.org/projects/openjevis/wiki/JEConfig3#JEConfig-Version-3")); WelcomePage welcome = new WelcomePage(primaryStage, _config.getWelcomeURL()); } catch (URISyntaxException ex) { Logger.getLogger(JEConfig.class.getName()).log(Level.SEVERE, null, ex); } catch (MalformedURLException ex) { Logger.getLogger(JEConfig.class.getName()).log(Level.SEVERE, null, ex); } //Disable GUI is StatusBar note an disconnect root.disableProperty().bind(statusBar.connectedProperty.not()); primaryStage.onCloseRequestProperty().addListener(new ChangeListener<EventHandler<WindowEvent>>() { @Override public void changed(ObservableValue<? extends EventHandler<WindowEvent>> ov, EventHandler<WindowEvent> t, EventHandler<WindowEvent> t1) { try { System.out.println("Disconnect"); ds.disconnect(); } catch (JEVisException ex) { Logger.getLogger(JEConfig.class.getName()).log(Level.SEVERE, null, ex); } } }); }
From source file:qupath.lib.gui.tma.TMASummaryViewer.java
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 -> {//from w w w .j a v a2 s . com File file = QuPathGUI.getDialogHelper(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) { DisplayHelpers.showErrorMessage("Import scores", "Clipboard is empty!"); return; } int n = importScores(text); if (n > 0) { setTMAEntries(new ArrayList<>(entriesBase)); } DisplayHelpers.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); QuPathGUI.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.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(MeasurementCombinationMethod.values()); comboMeasurementMethod.getSelectionModel().select(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())); // row.itemProperty().addListener((v, o, n) -> { // if (n == null || n instanceof TMASummaryEntry || row.isSelected()) // row.setStyle(""); // else if (n.isMissing()) // row.setStyle("-fx-background-color:rgb(225,225,232)"); // else // row.setStyle("-fx-background-color:rgb(240,240,245)"); // }); 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.getEntries().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; } }); }
From source file:UI.MainStageController.java
/** * shows the correlation table in the analysis view *//* www.j a v a 2 s . c om*/ @FXML private void displayCorrelationTable() { //Delete whatever's been in the table before TableView<String[]> analysisTable = new TableView<>(); //We want to display correlations and p-Values of every node combination double[][] correlationMatrix = AnalysisData.getCorrelationMatrix().getData(); double[][] pValueMatrix = AnalysisData.getPValueMatrix().getData(); LinkedList<TaxonNode> taxonList = SampleComparison.getUnifiedTaxonList(LoadedData.getSamplesToAnalyze(), AnalysisData.getLevelOfAnalysis()); //Table will consist of strings String[][] tableValues = new String[correlationMatrix.length][correlationMatrix[0].length + 1]; //Add the values as formatted strings for (int i = 0; i < tableValues.length; i++) { tableValues[i][0] = taxonList.get(i).getName(); for (int j = 1; j < tableValues[0].length; j++) { tableValues[i][j] = String.format("%.3f", correlationMatrix[i][j - 1]).replace(",", ".") + "\n(" + String.format("%.2f", pValueMatrix[i][j - 1]).replace(",", ".") + ")"; } } for (int i = 0; i < tableValues[0].length; i++) { String columnTitle; if (i > 0) { columnTitle = taxonList.get(i - 1).getName(); } else { columnTitle = ""; } TableColumn<String[], String> column = new TableColumn<>(columnTitle); final int columnIndex = i; column.setCellValueFactory(cellData -> { String[] row = cellData.getValue(); return new SimpleStringProperty(row[columnIndex]); }); analysisTable.getColumns().add(column); //First column contains taxon names and should be italic if (i == 0) column.setStyle("-fx-font-style:italic;"); } for (int i = 0; i < tableValues.length; i++) { analysisTable.getItems().add(tableValues[i]); } //Display table on a new stage Stage tableStage = new Stage(); tableStage.setTitle("Correlation Table"); BorderPane tablePane = new BorderPane(); Button exportCorrelationsButton = new Button("Save correlation table to CSV"); Button exportPValuesButton = new Button("Save p-value table to CSV"); exportCorrelationsButton.setOnAction(e -> exportTableToCSV(tableValues, false)); exportPValuesButton.setOnAction(e -> exportTableToCSV(tableValues, true)); HBox exportBox = new HBox(exportCorrelationsButton, exportPValuesButton); exportBox.setPadding(new Insets(10)); exportBox.setSpacing(10); tablePane.setTop(exportBox); tablePane.setCenter(analysisTable); Scene tableScene = new Scene(tablePane); tableStage.setScene(tableScene); tableStage.show(); }
From source file:com.core.meka.SOMController.java
private void initPopovers() { patronesEntrenamientoPopover = new PopOver(); StackPane pane = new StackPane(); BorderPane b = new BorderPane(); b.setPadding(new Insets(10, 20, 10, 20)); VBox vbox = new VBox(); Label title = new Label("Configuracion correcta"); Label content = new Label("Aqui un ejemplo de configuracion"); Label content1 = new Label("de patrones de entrenamiento de dimension 2"); content.setPadding(new Insets(5, 0, 0, 0)); content1.setPadding(new Insets(5, 0, 0, 0)); content.setWrapText(true);//from ww w . j av a 2 s . c om vbox.getChildren().addAll(title, content, content1, new ImageView(new Image("/img/config1.png"))); b.setCenter(vbox); patronesEntrenamientoPopover.setContentNode(b); }
From source file:qupath.lib.gui.tma.TMASummaryViewer.java
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);//from w w w. j ava2 s. c o m 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; }
From source file:qupath.lib.gui.panels.survival.KaplanMeierDisplay.java
@SuppressWarnings("unchecked") private void generatePlot() { KaplanMeierDisplay.ScoreData newScoreData = scoreData; // If we have a hierarchy, update the scores with the most recent data if (hierarchy != null) { List<TMACoreObject> cores = PathObjectTools.getTMACoreObjects(hierarchy, false); double[] survival = new double[cores.size()]; boolean[] censored = new boolean[cores.size()]; double[] scores = new double[cores.size()]; // // Optionally sort by scores... helps a bit when debugging e.g. p-values, Hazard ratios etc. // cores.sort((c1, c2) -> Double.compare(c1.getMeasurementList().getMeasurementValue(scoreColumn), c2.getMeasurementList().getMeasurementValue(scoreColumn))); // scoreColumn = "Positive %"; // scoreColumn = "RoughScore"; for (int i = 0; i < cores.size(); i++) { TMACoreObject core = cores.get(i); MeasurementList ml = core.getMeasurementList(); survival[i] = core.getMeasurementList().getMeasurementValue(survivalColumn); double censoredValue = core.getMeasurementList().getMeasurementValue(censoredColumn); boolean hasCensoredValue = !Double.isNaN(censoredValue) && (censoredValue == 0 || censoredValue == 1); censored[i] = censoredValue != 0; if (!hasCensoredValue) { // If we don't have a censored value, ensure we mask out everything else scores[i] = Double.NaN; survival[i] = Double.NaN; } else if (ml.containsNamedMeasurement(scoreColumn)) // Get the score if we can scores[i] = ml.getMeasurementValue(scoreColumn); else { // // Try to compute score if we need to // Map<String, Number> map = ROIMeaningfulMeasurements.getPathClassSummaryMeasurements(core.getChildObjects(), true); // Number value = map.get(scoreColumn); // if (value == null) scores[i] = Double.NaN; // else // scores[i] = value.doubleValue(); }/* www.ja v a2s. c om*/ } // Mask out any scores that don't have associated survival data for (int i = 0; i < survival.length; i++) { if (Double.isNaN(survival[i])) scores[i] = Double.NaN; } newScoreData = new ScoreData(scores, survival, censored); } if (newScoreData == null || newScoreData.scores.length == 0) return; // KaplanMeier kmHigh = new KaplanMeier("Above threshold"); // KaplanMeier kmLow = new KaplanMeier("Below threshold"); double[] quartiles = StatisticsHelper.getQuartiles(newScoreData.scores); double q1 = quartiles[0]; double median = quartiles[1]; double q3 = quartiles[2]; double[] thresholds; if (params != null) { Object thresholdMethod = params.getChoiceParameterValue("scoreThresholdMethod"); if (thresholdMethod.equals("Median")) { // panelParams.setNumericParameterValue("scoreThreshold", median); // ((DoubleParameter)params.getParameters().get("scoreThreshold")).setValue(median); // TODO: UPDATE DIALOG! thresholds = new double[] { median }; } else if (thresholdMethod.equals("Tertiles")) { // ((DoubleParameter)params.getParameters().get("scoreThreshold")).setValue(median); // TODO: UPDATE DIALOG! thresholds = StatisticsHelper.getTertiles(newScoreData.scores); } else if (thresholdMethod.equals("Quartiles")) { // ((DoubleParameter)params.getParameters().get("scoreThreshold")).setValue(median); // TODO: UPDATE DIALOG! thresholds = new double[] { q1, median, q3 }; } else if (thresholdMethod.equals("Manual (1)")) { thresholds = new double[] { params.getDoubleParameterValue("threshold1") }; } else if (thresholdMethod.equals("Manual (2)")) { thresholds = new double[] { params.getDoubleParameterValue("threshold1"), params.getDoubleParameterValue("threshold2") }; } else //if (thresholdMethod.equals("Manual (3)")) { thresholds = new double[] { params.getDoubleParameterValue("threshold1"), params.getDoubleParameterValue("threshold2"), params.getDoubleParameterValue("threshold3") }; } else thresholds = new double[] { median }; double minVal = Double.POSITIVE_INFINITY; double maxVal = Double.NEGATIVE_INFINITY; int numNonNaN = 0; for (double d : newScoreData.scores) { if (Double.isNaN(d)) continue; if (d < minVal) minVal = d; if (d > maxVal) maxVal = d; numNonNaN++; } boolean scoresValid = maxVal > minVal; // If not this, we don't have valid scores that we can work with double maxTimePoint = 0; for (double d : newScoreData.survival) { if (Double.isNaN(d)) continue; if (d > maxTimePoint) maxTimePoint = d; } if (panelParams != null && maxTimePoint > ((IntParameter) params.getParameters().get("censorTimePoints")).getUpperBound()) { panelParams.setNumericParameterValueRange("censorTimePoints", 0, Math.ceil(maxTimePoint)); } // Optionally censor at specified time double censorThreshold = params == null ? maxTimePoint : params.getIntParameterValue("censorTimePoints"); // Compute log-rank p-values for *all* possible thresholds // Simultaneously determine the threshold that yields the lowest p-value, // resolving ties in favour of a more even split between high/low numbers of events boolean pValuesChanged = false; if (calculateAllPValues) { if (!(pValues != null && pValueThresholds != null && newScoreData.equals(scoreData) && censorThreshold == lastPValueCensorThreshold)) { Map<Double, Double> mapLogRank = new TreeMap<>(); Set<Double> setObserved = new HashSet<>(); for (int i = 0; i < newScoreData.scores.length; i++) { Double d = newScoreData.scores[i]; boolean observed = !newScoreData.censored[i] && newScoreData.survival[i] < censorThreshold; if (observed) setObserved.add(d); if (mapLogRank.containsKey(d)) continue; List<KaplanMeierData> kmsTemp = splitByThresholds(newScoreData, new double[] { d }, censorThreshold, false); // if (kmsTemp.get(1).nObserved() == 0 || kmsTemp.get(1).nObserved() == 0) // continue; LogRankResult test = LogRankTest.computeLogRankTest(kmsTemp.get(0), kmsTemp.get(1)); double pValue = test.getPValue(); // double pValue = test.hazardRatio < 1 ? test.hazardRatio : 1.0/test.hazardRatio; // Checking usefulness of Hazard ratios... if (!Double.isFinite(pValue)) continue; // if (!Double.isFinite(test.getHazardRatio())) { //// continue; // pValue = Double.NaN; // } mapLogRank.put(d, pValue); } pValueThresholds = new double[mapLogRank.size()]; pValues = new double[mapLogRank.size()]; pValueThresholdsObserved = new boolean[mapLogRank.size()]; int count = 0; for (Entry<Double, Double> entry : mapLogRank.entrySet()) { pValueThresholds[count] = entry.getKey(); pValues[count] = entry.getValue(); if (setObserved.contains(entry.getKey())) pValueThresholdsObserved[count] = true; count++; } // Find the longest 'significant' stretch int maxSigCount = 0; int maxSigInd = -1; int sigCurrent = 0; int[] sigCount = new int[pValues.length]; for (int i = 0; i < pValues.length; i++) { if (pValues[i] < 0.05) { sigCurrent++; sigCount[i] = sigCurrent; if (sigCurrent > maxSigCount) { maxSigCount = sigCurrent; maxSigInd = i; } } else sigCurrent = 0; } if (maxSigCount == 0) { logger.info("No p-values < 0.05"); } else { double minThresh = maxSigInd - maxSigCount < 0 ? pValueThresholds[0] - 0.0000001 : pValueThresholds[maxSigInd - maxSigCount]; double maxThresh = pValueThresholds[maxSigInd]; int nBetween = 0; int nBetweenObserved = 0; for (int i = 0; i < newScoreData.scores.length; i++) { if (newScoreData.scores[i] > minThresh && newScoreData.scores[i] <= maxThresh) { nBetween++; if (newScoreData.survival[i] < censorThreshold && !newScoreData.censored[i]) nBetweenObserved++; } } logger.info("Longest stretch of p-values < 0.05: {} - {} ({} entries, {} observed)", minThresh, maxThresh, nBetween, nBetweenObserved); } pValuesSmoothed = new double[pValues.length]; Arrays.fill(pValuesSmoothed, Double.NaN); int n = (pValues.length / 20) * 2 + 1; logger.info("Smoothing log-rank test p-values by " + n); for (int i = n / 2; i < pValues.length - n / 2; i++) { double sum = 0; for (int k = i - n / 2; k < i - n / 2 + n; k++) { sum += pValues[k]; } pValuesSmoothed[i] = sum / n; } // for (int i = 0; i < pValues.length; i++) { // double sum = 0; // for (int k = Math.max(0, i-n/2); k < Math.min(pValues.length, i-n/2+n); k++) { // sum += pValues[k]; // } // pValuesSmoothed[i] = sum/n; // } // pValues = pValuesSmoothed; lastPValueCensorThreshold = censorThreshold; pValuesChanged = true; } } else { lastPValueCensorThreshold = Double.NaN; pValueThresholds = null; pValues = null; } // if (params != null && !Double.isNaN(bestThreshold) && (params.getChoiceParameterValue("scoreThresholdMethod").equals("Lowest p-value"))) if (params != null && (params.getChoiceParameterValue("scoreThresholdMethod").equals("Lowest p-value"))) { int bestIdx = -1; double bestPValue = Double.POSITIVE_INFINITY; for (int i = pValueThresholds.length / 10; i < pValueThresholds.length * 9 / 10; i++) { if (pValues[i] < bestPValue) { bestIdx = i; bestPValue = pValues[i]; } } thresholds = bestIdx >= 0 ? new double[] { pValueThresholds[bestIdx] } : new double[0]; } else if (params != null && (params.getChoiceParameterValue("scoreThresholdMethod").equals("Lowest smoothed p-value"))) { int bestIdx = -1; double bestPValue = Double.POSITIVE_INFINITY; for (int i = pValueThresholds.length / 10; i < pValueThresholds.length * 9 / 10; i++) { if (pValuesSmoothed[i] < bestPValue) { bestIdx = i; bestPValue = pValuesSmoothed[i]; } } thresholds = bestIdx >= 0 ? new double[] { pValueThresholds[bestIdx] } : new double[0]; } // Split into different curves using the provided thresholds List<KaplanMeierData> kms = splitByThresholds(newScoreData, thresholds, censorThreshold, params != null && "Quartiles".equals(params.getChoiceParameterValue("scoreThresholdMethod"))); // for (KaplanMeier km : kms) // km.censorAtTime(censorThreshold); //// kmHigh.censorAtTime(censorThreshold); //// kmLow.censorAtTime(censorThreshold); // logger.info("High: " + kmHigh.toString()); // logger.info("Low: " + kmLow.toString()); // logger.info("Log rank comparison: {}", LogRankTest.computeLogRankTest(kmLow, kmHigh)); if (plotter == null) { plotter = new KaplanMeierChartWrapper(survivalColumn + " time"); // plotter.setBorder(BorderFactory.createTitledBorder("Survival plot")); // plotter.getCanvas().setWidth(300); // plotter.getCanvas().setHeight(300); } KaplanMeierData[] kmArray = new KaplanMeierData[kms.size()]; plotter.setKaplanMeierCurves(survivalColumn + " time", kms.toArray(kmArray)); tableModel.setSurvivalCurves(thresholds, params != null && params.getChoiceParameterValue("scoreThresholdMethod").equals("Lowest p-value"), kmArray); // Bar width determined using 'Freedman and Diaconis' rule' (but overridden if this gives < 16 bins...) double barWidth = (2 * q3 - q1) * Math.pow(numNonNaN, -1.0 / 3.0); int nBins = 100; if (!Double.isNaN(barWidth)) barWidth = (int) Math.max(16, Math.ceil((maxVal - minVal) / barWidth)); Histogram histogram = scoresValid ? new Histogram(newScoreData.scores, nBins) : null; if (histogramPanel == null) { GridPane paneHistogram = new GridPane(); histogramPanel = new HistogramPanelFX(); histogramPanel.getChart().setAnimated(false); histogramWrapper = new ThresholdedChartWrapper(histogramPanel.getChart()); for (ObservableNumberValue val : threshProperties) histogramWrapper.addThreshold(val, ColorToolsFX.getCachedColor(240, 0, 0, 128)); histogramWrapper.getPane().setPrefHeight(150); paneHistogram.add(histogramWrapper.getPane(), 0, 0); Tooltip.install(histogramPanel.getChart(), new Tooltip("Distribution of scores")); GridPane.setHgrow(histogramWrapper.getPane(), Priority.ALWAYS); GridPane.setVgrow(histogramWrapper.getPane(), Priority.ALWAYS); NumberAxis xAxis = new NumberAxis(); xAxis.setLabel("Score threshold"); NumberAxis yAxis = new NumberAxis(); yAxis.setLowerBound(0); yAxis.setUpperBound(1); yAxis.setTickUnit(0.1); yAxis.setAutoRanging(false); yAxis.setLabel("P-value"); chartPValues = new LineChart<>(xAxis, yAxis); chartPValues.setAnimated(false); chartPValues.setLegendVisible(false); // Make chart so it can be navigated ChartToolsFX.makeChartInteractive(chartPValues, xAxis, yAxis); pValuesChanged = true; Tooltip.install(chartPValues, new Tooltip( "Distribution of p-values (log-rank test) comparing low vs. high for all possible score thresholds")); // chartPValues.getYAxis().setAutoRanging(false); pValuesWrapper = new ThresholdedChartWrapper(chartPValues); for (ObservableNumberValue val : threshProperties) pValuesWrapper.addThreshold(val, ColorToolsFX.getCachedColor(240, 0, 0, 128)); pValuesWrapper.getPane().setPrefHeight(150); paneHistogram.add(pValuesWrapper.getPane(), 0, 1); GridPane.setHgrow(pValuesWrapper.getPane(), Priority.ALWAYS); GridPane.setVgrow(pValuesWrapper.getPane(), Priority.ALWAYS); ContextMenu popup = new ContextMenu(); ChartToolsFX.addChartExportMenu(chartPValues, popup); RadioMenuItem miZoomY1 = new RadioMenuItem("0-1"); miZoomY1.setOnAction(e -> { yAxis.setAutoRanging(false); yAxis.setUpperBound(1); yAxis.setTickUnit(0.2); }); RadioMenuItem miZoomY05 = new RadioMenuItem("0-0.5"); miZoomY05.setOnAction(e -> { yAxis.setAutoRanging(false); yAxis.setUpperBound(0.5); yAxis.setTickUnit(0.1); }); RadioMenuItem miZoomY02 = new RadioMenuItem("0-0.2"); miZoomY02.setOnAction(e -> { yAxis.setAutoRanging(false); yAxis.setUpperBound(0.2); yAxis.setTickUnit(0.05); }); RadioMenuItem miZoomY01 = new RadioMenuItem("0-0.1"); miZoomY01.setOnAction(e -> { yAxis.setAutoRanging(false); yAxis.setUpperBound(0.1); yAxis.setTickUnit(0.05); }); RadioMenuItem miZoomY005 = new RadioMenuItem("0-0.05"); miZoomY005.setOnAction(e -> { yAxis.setAutoRanging(false); yAxis.setUpperBound(0.05); yAxis.setTickUnit(0.01); }); RadioMenuItem miZoomY001 = new RadioMenuItem("0-0.01"); miZoomY001.setOnAction(e -> { yAxis.setAutoRanging(false); yAxis.setUpperBound(0.01); yAxis.setTickUnit(0.005); }); ToggleGroup tgZoom = new ToggleGroup(); miZoomY1.setToggleGroup(tgZoom); miZoomY05.setToggleGroup(tgZoom); miZoomY02.setToggleGroup(tgZoom); miZoomY01.setToggleGroup(tgZoom); miZoomY005.setToggleGroup(tgZoom); miZoomY001.setToggleGroup(tgZoom); Menu menuZoomY = new Menu("Set y-axis range"); menuZoomY.getItems().addAll(miZoomY1, miZoomY05, miZoomY02, miZoomY01, miZoomY005, miZoomY001); MenuItem miCopyData = new MenuItem("Copy chart data"); miCopyData.setOnAction(e -> { String dataString = ChartToolsFX.getChartDataAsString(chartPValues); ClipboardContent content = new ClipboardContent(); content.putString(dataString); Clipboard.getSystemClipboard().setContent(content); }); popup.getItems().addAll(miCopyData, menuZoomY); chartPValues.setOnContextMenuRequested(e -> { popup.show(chartPValues, e.getScreenX(), e.getScreenY()); }); for (int col = 0; col < tableModel.getColumnCount(); col++) { TableColumn<Integer, String> column = new TableColumn<>(tableModel.getColumnName(col)); int colNumber = col; column.setCellValueFactory( new Callback<CellDataFeatures<Integer, String>, ObservableValue<String>>() { @Override public ObservableValue<String> call(CellDataFeatures<Integer, String> p) { return new SimpleStringProperty( (String) tableModel.getValueAt(p.getValue(), colNumber)); } }); column.setCellFactory(new Callback<TableColumn<Integer, String>, TableCell<Integer, String>>() { @Override public TableCell<Integer, String> call(TableColumn<Integer, String> param) { TableCell<Integer, String> cell = new TableCell<Integer, String>() { @Override protected void updateItem(String item, boolean empty) { super.updateItem(item, empty); setText(item); setTooltip(new Tooltip(item)); } }; return cell; } }); table.getColumns().add(column); } table.setPrefHeight(250); table.setColumnResizePolicy(TableView.CONSTRAINED_RESIZE_POLICY); table.maxHeightProperty().bind(table.prefHeightProperty()); params = new ParameterList(); // maxTimePoint = 0; // for (TMACoreObject core : hierarchy.getTMAGrid().getTMACoreList()) { // double os = core.getMeasurementList().getMeasurementValue(TMACoreObject.KEY_OVERALL_SURVIVAL); // double rfs = core.getMeasurementList().getMeasurementValue(TMACoreObject.KEY_RECURRENCE_FREE_SURVIVAL); // if (os > maxTimePoint) // maxTimePoint = os; // if (rfs > maxTimePoint) // maxTimePoint = rfs; // } params.addIntParameter("censorTimePoints", "Max censored time", (int) (censorThreshold + 0.5), null, 0, (int) Math.ceil(maxTimePoint), "Latest time point beyond which data will be censored"); // params.addChoiceParameter("scoreThresholdMethod", "Threshold method", "Manual", Arrays.asList("Manual", "Median", "Log-rank test")); if (calculateAllPValues) // Don't include "Lowest smoothed p-value" - it's not an established method and open to misinterpretation... params.addChoiceParameter("scoreThresholdMethod", "Threshold method", "Median", Arrays.asList("Manual (1)", "Manual (2)", "Manual (3)", "Median", "Tertiles", "Quartiles", "Lowest p-value")); // params.addChoiceParameter("scoreThresholdMethod", "Threshold method", "Median", Arrays.asList("Manual (1)", "Manual (2)", "Manual (3)", "Median", "Tertiles", "Quartiles", "Lowest p-value", "Lowest smoothed p-value")); else params.addChoiceParameter("scoreThresholdMethod", "Threshold method", "Median", Arrays.asList("Manual (1)", "Manual (2)", "Manual (3)", "Median", "Tertiles", "Quartiles")); params.addDoubleParameter("threshold1", "Threshold 1", thresholds.length > 0 ? thresholds[0] : (minVal + maxVal) / 2, null, "Threshold to distinguish between patient groups"); params.addDoubleParameter("threshold2", "Threshold 2", thresholds.length > 1 ? thresholds[1] : (minVal + maxVal) / 2, null, "Threshold to distinguish between patient groups"); params.addDoubleParameter("threshold3", "Threshold 3", thresholds.length > 2 ? thresholds[2] : (minVal + maxVal) / 2, null, "Threshold to distinguish between patient groups"); params.addBooleanParameter("showAtRisk", "Show at risk", plotter.getShowAtRisk(), "Show number of patients at risk below the plot"); params.addBooleanParameter("showTicks", "Show censored ticks", plotter.getShowCensoredTicks(), "Show ticks to indicate censored data"); params.addBooleanParameter("showKey", "Show key", plotter.getShowKey(), "Show key indicating display of each curve"); // params.addBooleanParameter("useColor", "Use color", plotter.getUseColor(), "Show each curve in a different color"); // params.addBooleanParameter("useStrokes", "Use strokes", plotter.getUseStrokes(), "Show each curve with a differed line stroke"); // Hide threshold parameters if threshold can't be used if (!scoresValid) { // params.setHiddenParameters(true, "scoreThresholdMethod", "scoreThreshold"); histogramPanel.getChart().setVisible(false); } panelParams = new ParameterPanelFX(params); panelParams.addParameterChangeListener(this); updateThresholdsEnabled(); for (int i = 0; i < threshProperties.length; i++) { String p = "threshold" + (i + 1); threshProperties[i].addListener((v, o, n) -> { if (interactiveThresholds()) { // Need to do a decent double check with tolerance to text field value changing while typing if (!GeneralTools.almostTheSame(params.getDoubleParameterValue(p), n.doubleValue(), 0.0001)) panelParams.setNumericParameterValue(p, n); } }); } BorderPane paneBottom = new BorderPane(); TitledPane paneOptions = new TitledPane("Options", panelParams.getPane()); // paneOptions.setCollapsible(false); Pane paneCanvas = new StackPane(); paneCanvas.getChildren().add(plotter.getCanvas()); GridPane paneLeft = new GridPane(); paneLeft.add(paneOptions, 0, 0); paneLeft.add(table, 0, 1); GridPane.setHgrow(paneOptions, Priority.ALWAYS); GridPane.setHgrow(table, Priority.ALWAYS); paneBottom.setLeft(paneLeft); paneBottom.setCenter(paneHistogram); paneMain.setCenter(paneCanvas); paneMain.setBottom(paneBottom); paneMain.setPadding(new Insets(10, 10, 10, 10)); } else if (thresholds.length > 0) { // Ensure the sliders/text fields are set sensibly if (!GeneralTools.almostTheSame(thresholds[0], params.getDoubleParameterValue("threshold1"), 0.0001)) { panelParams.setNumericParameterValue("threshold1", thresholds[0]); } if (thresholds.length > 1 && !GeneralTools.almostTheSame(thresholds[1], params.getDoubleParameterValue("threshold2"), 0.0001)) { panelParams.setNumericParameterValue("threshold2", thresholds[1]); } if (thresholds.length > 2 && !GeneralTools.almostTheSame(thresholds[2], params.getDoubleParameterValue("threshold3"), 0.0001)) { panelParams.setNumericParameterValue("threshold3", thresholds[2]); } } if (histogram != null) { histogramPanel.getHistogramData() .setAll(HistogramPanelFX.createHistogramData(histogram, false, (Color) null)); histogramPanel.getChart().getXAxis().setLabel(scoreColumn); histogramPanel.getChart().getYAxis().setLabel("Count"); ChartToolsFX.addChartExportMenu(histogramPanel.getChart(), null); // histogramWrapper.setVerticalLines(thresholds, ColorToolsFX.getCachedColor(240, 0, 0, 128)); // Deal with threshold adjustment // histogramWrapper.getThresholds().addListener((Observable o) -> generatePlot()); } if (pValues != null) { // TODO: Raise earlier where p-value calculation is if (pValuesChanged) { ObservableList<XYChart.Data<Number, Number>> data = FXCollections.observableArrayList(); for (int i = 0; i < pValueThresholds.length; i++) { double pValue = pValues[i]; if (Double.isNaN(pValue)) continue; data.add(new XYChart.Data<>(pValueThresholds[i], pValue, pValueThresholdsObserved[i])); } ObservableList<XYChart.Data<Number, Number>> dataSmoothed = null; if (pValuesSmoothed != null) { dataSmoothed = FXCollections.observableArrayList(); for (int i = 0; i < pValueThresholds.length; i++) { double pValueSmoothed = pValuesSmoothed[i]; if (Double.isNaN(pValueSmoothed)) continue; dataSmoothed.add(new XYChart.Data<>(pValueThresholds[i], pValueSmoothed)); } } // Don't bother showing the smoothed data... it tends to get in the way... // if (dataSmoothed != null) // chartPValues.getData().setAll(new XYChart.Series<>("P-values", data), new XYChart.Series<>("Smoothed P-values", dataSmoothed)); // else chartPValues.getData().setAll(new XYChart.Series<>("P-values", data)); // Add line to show 0.05 significance threshold if (pValueThresholds.length > 1) { Data<Number, Number> sigData1 = new Data<>(pValueThresholds[0], 0.05); Data<Number, Number> sigData2 = new Data<>(pValueThresholds[pValueThresholds.length - 1], 0.05); XYChart.Series<Number, Number> dataSignificant = new XYChart.Series<>("Signficance 0.05", FXCollections.observableArrayList(sigData1, sigData2)); chartPValues.getData().add(dataSignificant); sigData1.getNode().setVisible(false); sigData2.getNode().setVisible(false); } // chartPValues.getData().get(0).getNode().setVisible(true); // pValuesWrapper.clearThresholds(); for (XYChart.Data<Number, Number> dataPoint : data) { if (!Boolean.TRUE.equals(dataPoint.getExtraValue())) dataPoint.getNode().setVisible(false); } // if (dataSmoothed != null) { // for (XYChart.Data<Number, Number> dataPoint : dataSmoothed) { // dataPoint.getNode().setVisible(false); // } // chartPValues.getData().get(1).getNode().setOpacity(0.5); // } // int count = 0; // for (int i = 0; i < pValueThresholds.length; i++) { // double pValue = pValues[i]; // if (Double.isNaN(pValue)) // continue; // boolean observed = pValueThresholdsObserved[i]; //// if (observed) //// pValuesWrapper.addThreshold(new ReadOnlyDoubleWrapper(pValueThresholds[i]), Color.rgb(0, 0, 0, 0.05)); // // if (!observed) { //// StackPane pane = (StackPane)data.get(count).getNode(); //// pane.setEffect(new DropShadow()); // data.get(count).getNode().setVisible(false); // } // count++; // } } for (int i = 0; i < threshProperties.length; i++) { if (i < thresholds.length) threshProperties[i].set(thresholds[i]); else threshProperties[i].set(Double.NaN); } boolean isInteractive = interactiveThresholds(); histogramWrapper.setIsInteractive(isInteractive); pValuesWrapper.setIsInteractive(isInteractive); chartPValues.setVisible(true); } // else // chartPValues.setVisible(false); // Store values for next time scoreData = newScoreData; }