List of usage examples for javafx.util Callback Callback
Callback
From source file:de.bayern.gdi.gui.Controller.java
private void loadDownloadConfig(DownloadConfig conf) { String dataset = conf.getDataset(); if (dataset != null) { boolean datasetAvailable = false; List<ItemModel> datasets = serviceTypeChooser.getItems(); for (ItemModel iItem : datasets) { if (isFeatureTypeToSelect(iItem, conf)) { serviceTypeChooser.getSelectionModel().select(iItem); datasetAvailable = true; }//from www . j av a2s . co m } if (!datasetAvailable) { MiscItemModel errorItem = new MiscItemModel(); errorItem.setDataset(dataset); errorItem.setItem(conf.getDataset()); setStatusTextUI(I18n.format("gui.dataset-not-available")); serviceTypeChooser.getItems().add(errorItem); serviceTypeChooser.getSelectionModel().select(errorItem); } } serviceTypeChooser.setCellFactory(new Callback<ListView<ItemModel>, ListCell<ItemModel>>() { @Override public ListCell<ItemModel> call(ListView<ItemModel> list) { return new CellTypes.ItemCell(); } }); atomVariationChooser.setCellFactory(new Callback<ListView<ItemModel>, ListCell<ItemModel>>() { @Override public ListCell<ItemModel> call(ListView<ItemModel> list) { return new CellTypes.ItemCell(); } }); referenceSystemChooser.setCellFactory(new Callback<ListView<CRSModel>, ListCell<CRSModel>>() { @Override public ListCell<CRSModel> call(ListView<CRSModel> list) { return new CellTypes.CRSCell() { }; } }); dataFormatChooser.setCellFactory(new Callback<ListView<OutputFormatModel>, ListCell<OutputFormatModel>>() { @Override public ListCell<OutputFormatModel> call(ListView<OutputFormatModel> list) { return new CellTypes.StringCell(); } }); loadGUIComponents(); }
From source file:io.bitsquare.gui.main.funds.withdrawal.WithdrawalView.java
private void setAddressColumnCellFactory() { addressColumn/*from ww w.j a va 2 s. c o m*/ .setCellValueFactory((addressListItem) -> new ReadOnlyObjectWrapper<>(addressListItem.getValue())); addressColumn.setCellFactory( new Callback<TableColumn<WithdrawalListItem, WithdrawalListItem>, TableCell<WithdrawalListItem, WithdrawalListItem>>() { @Override public TableCell<WithdrawalListItem, WithdrawalListItem> call( TableColumn<WithdrawalListItem, WithdrawalListItem> column) { return new TableCell<WithdrawalListItem, WithdrawalListItem>() { private HyperlinkWithIcon hyperlinkWithIcon; @Override public void updateItem(final WithdrawalListItem item, boolean empty) { super.updateItem(item, empty); if (item != null && !empty) { String address = item.getAddressString(); hyperlinkWithIcon = new HyperlinkWithIcon(address, AwesomeIcon.EXTERNAL_LINK); hyperlinkWithIcon.setOnAction(event -> openBlockExplorer(item)); hyperlinkWithIcon.setTooltip(new Tooltip( "Open external blockchain explorer for " + "address: " + address)); setGraphic(hyperlinkWithIcon); } else { setGraphic(null); if (hyperlinkWithIcon != null) hyperlinkWithIcon.setOnAction(null); } } }; } }); }
From source file:io.bitsquare.gui.main.funds.withdrawal.WithdrawalView.java
private void setBalanceColumnCellFactory() { balanceColumn// w ww . j a v a 2 s . com .setCellValueFactory((addressListItem) -> new ReadOnlyObjectWrapper<>(addressListItem.getValue())); balanceColumn.setCellFactory( new Callback<TableColumn<WithdrawalListItem, WithdrawalListItem>, TableCell<WithdrawalListItem, WithdrawalListItem>>() { @Override public TableCell<WithdrawalListItem, WithdrawalListItem> call( TableColumn<WithdrawalListItem, WithdrawalListItem> column) { return new TableCell<WithdrawalListItem, WithdrawalListItem>() { @Override public void updateItem(final WithdrawalListItem item, boolean empty) { super.updateItem(item, empty); setGraphic((item != null && !empty) ? item.getBalanceLabel() : null); } }; } }); }
From source file:io.bitsquare.gui.main.funds.withdrawal.WithdrawalView.java
private void setSelectColumnCellFactory() { selectColumn/*from ww w . j a v a 2s . co m*/ .setCellValueFactory((addressListItem) -> new ReadOnlyObjectWrapper<>(addressListItem.getValue())); selectColumn.setCellFactory( new Callback<TableColumn<WithdrawalListItem, WithdrawalListItem>, TableCell<WithdrawalListItem, WithdrawalListItem>>() { @Override public TableCell<WithdrawalListItem, WithdrawalListItem> call( TableColumn<WithdrawalListItem, WithdrawalListItem> column) { return new TableCell<WithdrawalListItem, WithdrawalListItem>() { CheckBox checkBox; @Override public void updateItem(final WithdrawalListItem item, boolean empty) { super.updateItem(item, empty); if (item != null && !empty) { if (checkBox == null) { checkBox = new CheckBox(); checkBox.setOnAction(e -> selectForWithdrawal(item, checkBox.isSelected())); setGraphic(checkBox); } } else { setGraphic(null); if (checkBox != null) { checkBox.setOnAction(null); checkBox = null; } } } }; } }); }
From source file:com.chart.SwingChart.java
/** * Series edition// w ww. j a va 2s. c o m * @param series Series to edit */ void editSeries(final Series series) { String[] style = series.getStyle().split(";"); String strColor = "black"; final TextField editWidth = new TextField(); String tempS = "null"; for (String e : style) { if (e.contains("color: ")) { strColor = e.replace("color: ", ""); } else if (e.contains("width: ")) { editWidth.setText(e.replace("width: ", "")); } else if (e.contains("shape: ")) { tempS = e.replace("shape: ", ""); } } final String symbol = tempS; final List<SeriesShape> symbolList = new ArrayList<>(); final ObservableList<SeriesShape> symbolListModel; final ListView<SeriesShape> comboSymbol = new ListView(); symbolList.add(new SeriesShape("null", javafx.scene.paint.Color.web(strColor))); symbolList.add(new SeriesShape("rectangle", javafx.scene.paint.Color.web(strColor))); symbolList.add(new SeriesShape("circle", javafx.scene.paint.Color.web(strColor))); symbolList.add(new SeriesShape("triangle", javafx.scene.paint.Color.web(strColor))); symbolList.add(new SeriesShape("crux", javafx.scene.paint.Color.web(strColor))); symbolList.add(new SeriesShape("diamond", javafx.scene.paint.Color.web(strColor))); symbolList.add(new SeriesShape("empty rectangle", javafx.scene.paint.Color.web(strColor))); symbolList.add(new SeriesShape("empty circle", javafx.scene.paint.Color.web(strColor))); symbolList.add(new SeriesShape("empty triangle", javafx.scene.paint.Color.web(strColor))); symbolList.add(new SeriesShape("empty diamond", javafx.scene.paint.Color.web(strColor))); symbolListModel = FXCollections.observableList(symbolList); comboSymbol.setItems(symbolListModel); comboSymbol.setCellFactory(new Callback<ListView<SeriesShape>, ListCell<SeriesShape>>() { @Override public ListCell<SeriesShape> call(ListView<SeriesShape> p) { ListCell<SeriesShape> cell = new ListCell<SeriesShape>() { @Override protected void updateItem(SeriesShape t, boolean bln) { super.updateItem(t, bln); if (t != null) { setText(""); setGraphic(t.getShapeGraphic()); } } }; return cell; } }); for (SeriesShape smb : symbolListModel) { if (smb.getName().equals(symbol)) { comboSymbol.getSelectionModel().select(smb); } } final ColorPicker colorPicker = new ColorPicker(javafx.scene.paint.Color.web(strColor)); colorPicker.setOnAction((ActionEvent t) -> { String sc = colorPicker.getValue().toString(); symbolListModel.clear(); symbolListModel.add(new SeriesShape("null", javafx.scene.paint.Color.web(sc))); symbolListModel.add(new SeriesShape("rectangle", javafx.scene.paint.Color.web(sc))); symbolListModel.add(new SeriesShape("circle", javafx.scene.paint.Color.web(sc))); symbolListModel.add(new SeriesShape("triangle", javafx.scene.paint.Color.web(sc))); symbolListModel.add(new SeriesShape("crux", javafx.scene.paint.Color.web(sc))); symbolListModel.add(new SeriesShape("diamond", javafx.scene.paint.Color.web(sc))); symbolListModel.add(new SeriesShape("empty rectangle", javafx.scene.paint.Color.web(sc))); symbolListModel.add(new SeriesShape("empty circle", javafx.scene.paint.Color.web(sc))); symbolListModel.add(new SeriesShape("empty triangle", javafx.scene.paint.Color.web(sc))); symbolListModel.add(new SeriesShape("empty diamond", javafx.scene.paint.Color.web(sc))); comboSymbol.setItems(symbolListModel); for (SeriesShape smb : symbolListModel) { if (smb.getName().equals(symbol)) { comboSymbol.getSelectionModel().select(smb); } } }); GridPane grid = new GridPane(); grid.setHgap(10); grid.setVgap(10); grid.setPadding(new Insets(0, 10, 0, 10)); grid.add(new Label("Series"), 0, 0); grid.add(new Label(series.getKey().toString()), 1, 0); grid.add(new Label("Color"), 0, 1); grid.add(colorPicker, 1, 1); grid.add(new Label("Width"), 0, 2); grid.add(editWidth, 1, 2); grid.add(new Label("Shape"), 0, 3); grid.add(comboSymbol, 1, 3); new PseudoModalDialog(skeleton, grid, true) { @Override public boolean validation() { String strColor = colorPicker.getValue().toString(); String strWidth = editWidth.getText(); double dWidth = Double.valueOf(strWidth); String strSimbolo = "null"; SeriesShape simb = new SeriesShape(comboSymbol.getSelectionModel().getSelectedItem().toString(), javafx.scene.paint.Color.web(strColor)); XYItemRenderer renderer = (XYItemRenderer) plot.getRenderer(series.getAxisIndex()); renderer.setSeriesPaint(series.getSeriesIndex(), scene2awtColor(colorPicker.getValue())); try { if (Double.valueOf(strWidth) > 0) { ((XYLineAndShapeRenderer) renderer).setSeriesLinesVisible(series.getSeriesIndex(), true); renderer.setSeriesStroke(series.getSeriesIndex(), new BasicStroke(Integer.valueOf(strWidth))); } else { ((XYLineAndShapeRenderer) renderer).setSeriesLinesVisible(series.getSeriesIndex(), false); } } catch (NumberFormatException ex) { } if (simb.getName().contains("null")) { ((XYLineAndShapeRenderer) renderer).setSeriesShapesVisible(series.getSeriesIndex(), false); renderer.setSeriesShape(series.getSeriesIndex(), null); } else { ((XYLineAndShapeRenderer) renderer).setSeriesShapesVisible(series.getSeriesIndex(), true); renderer.setSeriesShape(series.getSeriesIndex(), simb.getShapeAWT()); if (simb.getName().contains("empty")) { ((XYLineAndShapeRenderer) renderer).setSeriesShapesFilled(series.getSeriesIndex(), false); } else { ((XYLineAndShapeRenderer) renderer).setSeriesShapesFilled(series.getSeriesIndex(), true); } } series.setStyle( "color: " + strColor + ";width: " + editWidth.getText() + ";shape: " + strSimbolo + ";"); for (Node le : legendFrame.getChildren()) { if (le instanceof LegendAxis) { for (Node nn : ((LegendAxis) le).getChildren()) { if (nn instanceof Label) { if (((Label) nn).getText().equals(series.getKey().toString())) { ((Label) nn).setGraphic(simb.getShapeGraphic()); } } } } } return true; } }.show(); }
From source file:com.rvantwisk.cnctools.controllers.CNCToolsController.java
@FXML // This method is called by the FXMLLoader when initialization is complete void initialize() { assert addMillTask != null : "fx:id=\"addMillTask\" was not injected: check your FXML file 'CNCTools.fxml'."; assert btnMoveTaskDown != null : "fx:id=\"btnMoveTaskDown\" was not injected: check your FXML file 'CNCTools.fxml'."; assert btnMoveTaskUp != null : "fx:id=\"btnMoveTaskUp\" was not injected: check your FXML file 'CNCTools.fxml'."; assert btnPostProcessor != null : "fx:id=\"btnPostProcessor\" was not injected: check your FXML file 'CNCTools.fxml'."; assert btnView != null : "fx:id=\"btnView\" was not injected: check your FXML file 'CNCTools.fxml'."; assert deleteProject != null : "fx:id=\"deleteProject\" was not injected: check your FXML file 'CNCTools.fxml'."; assert descriptionValue != null : "fx:id=\"descriptionValue\" was not injected: check your FXML file 'CNCTools.fxml'."; assert details != null : "fx:id=\"details\" was not injected: check your FXML file 'CNCTools.fxml'."; assert displayedIssueLabel != null : "fx:id=\"displayedIssueLabel\" was not injected: check your FXML file 'CNCTools.fxml'."; assert editMilltask != null : "fx:id=\"editMilltask\" was not injected: check your FXML file 'CNCTools.fxml'."; assert generateGCode != null : "fx:id=\"generateGCode\" was not injected: check your FXML file 'CNCTools.fxml'."; //assert millTaskDescription != null : "fx:id=\"millTaskDescription\" was not injected: check your FXML file 'CNCTools.fxml'."; //assert millTaskName != null : "fx:id=\"millTaskName\" was not injected: check your FXML file 'CNCTools.fxml'."; //assert millTaskOperation != null : "fx:id=\"millTaskOperation\" was not injected: check your FXML file 'CNCTools.fxml'."; assert milltaskEnabled != null : "fx:id=\"milltaskEnabled\" was not injected: check your FXML file 'CNCTools.fxml'."; assert removeMilltask != null : "fx:id=\"removeMilltask\" was not injected: check your FXML file 'CNCTools.fxml'."; assert tbl_millTasks != null : "fx:id=\"tbl_millTasks\" was not injected: check your FXML file 'CNCTools.fxml'."; assert v_projectList != null : "fx:id=\"v_projectList\" was not injected: check your FXML file 'CNCTools.fxml'."; v_projectList.setItems(projectModel.projectsProperty()); projectModel.loadPostProcessors();//from www . j a v a 2 s . c o m if (projectModel.postProcessorsProperty().size() == 0) { addDefaultPostprocessorSet(); projectModel.savePostProcessors(); MonologFX dialog = new MonologFX(MonologFX.Type.INFO); dialog.setTitleText("Postprocessor defaults loaded"); dialog.setMessage("No Post Processors where found, a new a new post processor set has been created."); dialog.show(); } projectModel.loadToolsFromDB(); if (projectModel.toolDBProperty().size() == 0) { addDefaultToolSet(); projectModel.saveToolDB(); MonologFX dialog = new MonologFX(MonologFX.Type.INFO); dialog.setTitleText("Tools defaults loaded"); dialog.setMessage("No tools where found, a new a new toolset has been created."); dialog.show(); } projectModel.loadProjectsFromDB(); if (projectModel.projectsProperty().size() == 0) { addProjectDefaults(); projectModel.saveProjects(); MonologFX dialog = new MonologFX(MonologFX.Type.INFO); dialog.setTitleText("Project defaults loaded"); dialog.setMessage( "No project was found, a new template project was created. Feel free to delete or modify"); dialog.show(); } deleteProject.disableProperty().bind(v_projectList.getSelectionModel().selectedItemProperty().isNull()); btnPostProcessor.disableProperty().bind(v_projectList.getSelectionModel().selectedItemProperty().isNull()); btnView.disableProperty().bind(v_projectList.getSelectionModel().selectedItemProperty().isNull()); removeMilltask.disableProperty().bind(tbl_millTasks.getSelectionModel().selectedItemProperty().isNull()); addMillTask.disableProperty().bind(v_projectList.getSelectionModel().selectedItemProperty().isNull()); editMilltask.disableProperty().bind(tbl_millTasks.getSelectionModel().selectedItemProperty().isNull()); generateGCode.disableProperty().bind(v_projectList.getSelectionModel().selectedItemProperty().isNull()); // Update description when project changes by means of databinding v_projectList.getSelectionModel().selectedItemProperty().addListener(new ChangeListener<Project>() { @Override public void changed(ObservableValue<? extends Project> observable, Project oldValue, Project newValue) { if (oldValue != null) { descriptionValue.textProperty().unbindBidirectional(oldValue.descriptionProperty()); } if (projectModel.projectsProperty().size() == 0) { tbl_millTasks.getItems().clear(); } else { tbl_millTasks.setItems(newValue.millTasksProperty()); descriptionValue.textProperty().bindBidirectional(newValue.descriptionProperty()); } } }); // Enable/Disable up/Down arrows tbl_millTasks.getSelectionModel().selectedItemProperty().addListener(new ChangeListener<TaskRunnable>() { @Override public void changed(ObservableValue<? extends TaskRunnable> observable, TaskRunnable o, TaskRunnable o2) { if (o2 != null) { final int index = tbl_millTasks.getSelectionModel().getSelectedIndex(); btnMoveTaskUp.setDisable(index == 0 ? true : false); btnMoveTaskDown.setDisable((index + 1) == tbl_millTasks.getItems().size() ? true : false); } else { btnMoveTaskUp.setDisable(true); btnMoveTaskDown.setDisable(true); } } }); btnMoveTaskUp.setDisable(true); btnMoveTaskDown.setDisable(true); // Set text in ListView v_projectList.setCellFactory(new Callback<ListView<Project>, ListCell<Project>>() { @Override public ListCell<Project> call(ListView<Project> p) { ListCell<Project> cell = new ListCell<Project>() { @Override protected void updateItem(Project t, boolean bln) { super.updateItem(t, bln); if (t != null) { setText(t.nameProperty().getValue()); } else { setText(null); } } }; return cell; } }); // checkbox renderer for milltasks milltaskEnabled.setCellFactory( new Callback<TableColumn<TaskRunnable, Boolean>, TableCell<TaskRunnable, Boolean>>() { @Override public TableCell<TaskRunnable, Boolean> call(TableColumn<TaskRunnable, Boolean> p) { CheckBoxTableCell<TaskRunnable, Boolean> cell = new CheckBoxTableCell<>(); cell.setEditable(true); cell.setAlignment(Pos.CENTER); return cell; } }); tbl_millTasks.setEditable(true); // Save DB on exit getDialog().setOnHidden(new EventHandler<WindowEvent>() { public void handle(WindowEvent we) { save(null); } }); }
From source file:de.bayern.gdi.gui.Controller.java
private void loadWfsSimple() { ObservableList<Node> children = simpleWFSContainer.getChildren(); Map<String, String> parameters = downloadConfig.getParams(); for (Node node : children) { if (node instanceof HBox) { HBox hb = (HBox) node;/* www . j av a2s . c o m*/ Node n1 = hb.getChildren().get(0); Node n2 = hb.getChildren().get(1); if (n1 instanceof Label && n2 instanceof TextField) { Label paramLabel = (Label) n1; TextField paramBox = (TextField) n2; String targetValue = parameters.get(paramLabel.getText()); if (targetValue != null) { paramBox.setText(targetValue); } } if (n2 instanceof ComboBox) { ComboBox<OutputFormatModel> cb = (ComboBox<OutputFormatModel>) n2; cb.setCellFactory(new Callback<ListView<OutputFormatModel>, ListCell<OutputFormatModel>>() { @Override public ListCell<OutputFormatModel> call(ListView<OutputFormatModel> list) { return new CellTypes.StringCell(); } }); cb.setOnAction(event -> { if (cb.getValue().isAvailable()) { cb.setStyle(FX_BORDER_COLOR_NULL); } else { cb.setStyle(FX_BORDER_COLOR_RED); } }); boolean formatAvailable = false; for (OutputFormatModel i : cb.getItems()) { if (i.getItem().equals(downloadConfig.getOutputFormat())) { cb.getSelectionModel().select(i); formatAvailable = true; } } if (!formatAvailable) { String format = downloadConfig.getOutputFormat(); OutputFormatModel m = new OutputFormatModel(); m.setItem(format); m.setAvailable(false); cb.getItems().add(m); cb.getSelectionModel().select(m); } if (cb.getValue().isAvailable()) { cb.setStyle(FX_BORDER_COLOR_NULL); } else { cb.setStyle(FX_BORDER_COLOR_RED); } } } } }
From source file:editeurpanovisu.EquiCubeDialogController.java
/** * * @param strTypeTransf/*from www . j a v a 2 s .c o m*/ * @throws Exception Exceptions */ public void afficheFenetre(String strTypeTransf) throws Exception { lvListeFichier.getItems().clear(); stTransformations = new Stage(StageStyle.UTILITY); apTransformations = new AnchorPane(); stTransformations.initModality(Modality.APPLICATION_MODAL); stTransformations.setResizable(true); apTransformations.setStyle("-fx-background-color : #ff0000;"); VBox vbFenetre = new VBox(); HBox hbChoix = new HBox(); Pane paneChoixFichier = new Pane(); btnAjouteFichiers = new Button("Ajouter des Fichiers"); paneChoixTypeFichier = new Pane(); Label lblType = new Label("Type des Fichiers de sortie"); rbJpeg = new RadioButton("JPEG (.jpg)"); rbBmp = new RadioButton("BMP (.bmp)"); rbTiff = new RadioButton("TIFF (.tif)"); cbSharpen = new CheckBox("Masque de nettet"); cbSharpen.setSelected(EditeurPanovisu.isbNetteteTransf()); slSharpen = new Slider(0, 2, EditeurPanovisu.getNiveauNetteteTransf()); lblSharpen = new Label(); double lbl = (Math.round(EditeurPanovisu.getNiveauNetteteTransf() * 20.d) / 20.d); lblSharpen.setText(lbl + ""); slSharpen.setDisable(!EditeurPanovisu.isbNetteteTransf()); lblSharpen.setDisable(!EditeurPanovisu.isbNetteteTransf()); Pane paneboutons = new Pane(); btnAnnuler = new Button("Fermer la fentre"); btnValider = new Button("Lancer le traitement"); strTypeTransformation = strTypeTransf; Image imgTransf; if (strTypeTransf.equals(EquiCubeDialogController.EQUI2CUBE)) { stTransformations.setTitle("Transformation d'quirectangulaire en faces de cube"); imgTransf = new Image( "file:" + EditeurPanovisu.getStrRepertAppli() + File.separator + "images/equi2cube.png"); } else { stTransformations.setTitle("Transformation de faces de cube en quirectangulaire"); imgTransf = new Image( "file:" + EditeurPanovisu.getStrRepertAppli() + File.separator + "images/cube2equi.png"); } ImageView ivTypeTransfert = new ImageView(imgTransf); ivTypeTransfert.setLayoutX(35); ivTypeTransfert.setLayoutY(280); paneChoixTypeFichier.getChildren().add(ivTypeTransfert); apTransformations.setPrefHeight(EditeurPanovisu.getHauteurE2C()); apTransformations.setPrefWidth(EditeurPanovisu.getLargeurE2C()); paneChoixFichier.setPrefHeight(350); paneChoixFichier.setPrefWidth(410); paneChoixFichier.setStyle("-fx-background-color: #d0d0d0; -fx-border-color: #bbb;"); paneChoixTypeFichier.setPrefHeight(350); paneChoixTypeFichier.setPrefWidth(180); paneChoixTypeFichier.setStyle("-fx-background-color: #d0d0d0; -fx-border-color: #bbb;"); hbChoix.getChildren().addAll(paneChoixFichier, paneChoixTypeFichier); vbFenetre.setPrefHeight(400); vbFenetre.setPrefWidth(600); apTransformations.getChildren().add(vbFenetre); hbChoix.setPrefHeight(350); hbChoix.setPrefWidth(600); hbChoix.setStyle("-fx-background-color: #d0d0d0;"); paneboutons.setPrefHeight(50); paneboutons.setPrefWidth(600); paneboutons.setStyle("-fx-background-color: #d0d0d0;"); vbFenetre.setStyle("-fx-background-color: #d0d0d0;"); btnAnnuler.setLayoutX(296); btnAnnuler.setLayoutY(10); btnValider.setLayoutX(433); btnValider.setLayoutY(10); lvListeFichier.setPrefHeight(290); lvListeFichier.setPrefWidth(380); lvListeFichier.setEditable(true); lvListeFichier.setLayoutX(14); lvListeFichier.setLayoutY(14); btnAjouteFichiers.setLayoutX(259); btnAjouteFichiers.setLayoutY(319); paneChoixFichier.getChildren().addAll(lvListeFichier, btnAjouteFichiers); if (strTypeTransf.equals(EquiCubeDialogController.EQUI2CUBE)) { lblDragDropE2C = new Label(rbLocalisation.getString("transformation.dragDropE2C")); } else { lblDragDropE2C = new Label(rbLocalisation.getString("transformation.dragDropC2E")); } lblDragDropE2C.setMinHeight(lvListeFichier.getPrefHeight()); lblDragDropE2C.setMaxHeight(lvListeFichier.getPrefHeight()); lblDragDropE2C.setMinWidth(lvListeFichier.getPrefWidth()); lblDragDropE2C.setMaxWidth(lvListeFichier.getPrefWidth()); lblDragDropE2C.setLayoutX(14); lblDragDropE2C.setLayoutY(14); lblDragDropE2C.setAlignment(Pos.CENTER); lblDragDropE2C.setTextFill(Color.web("#c9c7c7")); lblDragDropE2C.setTextAlignment(TextAlignment.CENTER); lblDragDropE2C.setWrapText(true); lblDragDropE2C.setStyle("-fx-font-size : 24px"); lblDragDropE2C.setStyle("-fx-background-color : rgba(128,128,128,0.1)"); paneChoixFichier.getChildren().add(lblDragDropE2C); lblType.setLayoutX(14); lblType.setLayoutY(14); rbBmp.setLayoutX(43); rbBmp.setLayoutY(43); rbBmp.setUserData("bmp"); if (EditeurPanovisu.getStrTypeFichierTransf().equals("bmp")) { rbBmp.setSelected(true); } rbBmp.setToggleGroup(tgTypeFichier); rbJpeg.setLayoutX(43); rbJpeg.setLayoutY(71); rbJpeg.setUserData("jpg"); if (EditeurPanovisu.getStrTypeFichierTransf().equals("jpg")) { rbJpeg.setSelected(true); } rbJpeg.setToggleGroup(tgTypeFichier); if (EditeurPanovisu.getStrTypeFichierTransf().equals("tif")) { rbTiff.setSelected(true); } rbTiff.setLayoutX(43); rbTiff.setLayoutY(99); rbTiff.setToggleGroup(tgTypeFichier); rbTiff.setUserData("tif"); tgTypeFichier.selectedToggleProperty().addListener((ov, old_toggle, new_toggle) -> { EditeurPanovisu.setStrTypeFichierTransf(tgTypeFichier.getSelectedToggle().getUserData().toString()); }); cbSharpen.setLayoutX(43); cbSharpen.setLayoutY(127); cbSharpen.selectedProperty().addListener((ov, old_val, new_val) -> { slSharpen.setDisable(!new_val); lblSharpen.setDisable(!new_val); EditeurPanovisu.setbNetteteTransf(new_val); }); slSharpen.setShowTickMarks(true); slSharpen.setShowTickLabels(true); slSharpen.setMajorTickUnit(0.5f); slSharpen.setMinorTickCount(4); slSharpen.setBlockIncrement(0.05f); slSharpen.setSnapToTicks(true); slSharpen.setLayoutX(23); slSharpen.setLayoutY(157); slSharpen.setTooltip(new Tooltip("Choisissez le niveau d'accentuation de l'image")); slSharpen.valueProperty().addListener((observableValue, oldValue, newValue) -> { if (newValue == null) { lblSharpen.setText(""); return; } DecimalFormat dfArrondi = new DecimalFormat(); dfArrondi.setMaximumFractionDigits(2); //arrondi 2 chiffres apres la virgules dfArrondi.setMinimumFractionDigits(2); dfArrondi.setDecimalSeparatorAlwaysShown(true); lblSharpen.setText(dfArrondi.format(Math.round(newValue.floatValue() * 20.f) / 20.f) + ""); EditeurPanovisu.setNiveauNetteteTransf(newValue.doubleValue()); }); slSharpen.setPrefWidth(120); lblSharpen.setLayoutX(150); lblSharpen.setLayoutY(150); lblSharpen.setMinWidth(30); lblSharpen.setMaxWidth(30); lblSharpen.setTextAlignment(TextAlignment.RIGHT); paneChoixTypeFichier.getChildren().addAll(lblType, rbBmp, rbJpeg, rbTiff, cbSharpen, slSharpen, lblSharpen); pbBarreImage.setLayoutX(40); pbBarreImage.setLayoutY(190); pbBarreImage.setStyle("-fx-accent : #0000bb"); pbBarreImage.setVisible(false); paneChoixTypeFichier.getChildren().add(pbBarreImage); pbBarreAvancement = new ProgressBar(); pbBarreAvancement.setLayoutX(40); pbBarreAvancement.setLayoutY(220); pbBarreImage.setStyle("-fx-accent : #00bb00"); paneChoixTypeFichier.getChildren().add(pbBarreAvancement); pbBarreAvancement.setVisible(false); paneboutons.getChildren().addAll(btnAnnuler, btnValider); vbFenetre.getChildren().addAll(hbChoix, paneboutons); Scene scnTransformations = new Scene(apTransformations); stTransformations.setScene(scnTransformations); stTransformations.show(); btnAnnuler.setOnAction((e) -> { annulerE2C(); }); btnValider.setOnAction((e) -> { if (!bTraitementEffectue) { validerE2C(); } }); btnAjouteFichiers.setOnAction((e) -> { lblTermine.setText(""); fileLstFichier = choixFichiers(); if (fileLstFichier != null) { if (bTraitementEffectue) { lvListeFichier.getItems().clear(); bTraitementEffectue = false; } for (File fileLstFichier1 : fileLstFichier) { String strNomFich = fileLstFichier1.getAbsolutePath(); lvListeFichier.getItems().add(strNomFich); } } }); lvListeFichier.setCellFactory(new Callback<ListView<String>, ListCell<String>>() { @Override public ListCell<String> call(ListView<String> list) { return new ListeTransformationCouleur(); } }); apTransformations.setOnDragOver((event) -> { Dragboard dbFichiersTransformation = event.getDragboard(); if (dbFichiersTransformation.hasFiles()) { event.acceptTransferModes(TransferMode.ANY); } else { event.consume(); } }); stTransformations.widthProperty().addListener((arg0, arg1, arg2) -> { EditeurPanovisu.setLargeurE2C(stTransformations.getWidth()); apTransformations.setPrefWidth(stTransformations.getWidth()); vbFenetre.setPrefWidth(stTransformations.getWidth()); btnAnnuler.setLayoutX(stTransformations.getWidth() - 314); btnValider.setLayoutX(stTransformations.getWidth() - 157); paneChoixFichier.setPrefWidth(stTransformations.getWidth() - 200); lvListeFichier.setPrefWidth(stTransformations.getWidth() - 240); lblDragDropE2C.setMinWidth(lvListeFichier.getPrefWidth()); lblDragDropE2C.setMaxWidth(lvListeFichier.getPrefWidth()); btnAjouteFichiers.setLayoutX(stTransformations.getWidth() - 341); }); stTransformations.heightProperty().addListener((arg0, arg1, arg2) -> { EditeurPanovisu.setHauteurE2C(stTransformations.getHeight()); apTransformations.setPrefHeight(stTransformations.getHeight()); vbFenetre.setPrefHeight(stTransformations.getHeight()); paneChoixFichier.setPrefHeight(stTransformations.getHeight() - 80); hbChoix.setPrefHeight(stTransformations.getHeight() - 80); lvListeFichier.setPrefHeight(stTransformations.getHeight() - 140); lblDragDropE2C.setMinHeight(lvListeFichier.getPrefHeight()); lblDragDropE2C.setMaxHeight(lvListeFichier.getPrefHeight()); btnAjouteFichiers.setLayoutY(stTransformations.getHeight() - 121); }); stTransformations.setWidth(EditeurPanovisu.getLargeurE2C()); stTransformations.setHeight(EditeurPanovisu.getHauteurE2C()); apTransformations.setOnDragDropped((event) -> { Dragboard dbFichiersTransformation = event.getDragboard(); boolean bSucces = false; File[] fileLstFich; fileLstFich = null; if (dbFichiersTransformation.hasFiles()) { lblTermine.setText(""); bSucces = true; String[] stringFichiersPath = new String[200]; int i = 0; for (File file1 : dbFichiersTransformation.getFiles()) { stringFichiersPath[i] = file1.getAbsolutePath(); i++; } int iNb = i; i = 0; boolean bAttention = false; File[] fileLstFich1 = new File[stringFichiersPath.length]; for (int j = 0; j < iNb; j++) { String strNomfich = stringFichiersPath[j]; File fileTransf = new File(strNomfich); String strExtension = strNomfich.substring(strNomfich.lastIndexOf(".") + 1, strNomfich.length()) .toLowerCase(); if (strExtension.equals("bmp") || strExtension.equals("jpg") || strExtension.equals("tif")) { if (i == 0) { strRepertFichier = fileTransf.getParent(); } Image img = null; if (strExtension != "tif") { img = new Image("file:" + fileTransf.getAbsolutePath()); } else { try { img = ReadWriteImage.readTiff(strNomfich); } catch (ImageReadException ex) { Logger.getLogger(EquiCubeDialogController.class.getName()).log(Level.SEVERE, null, ex); } catch (IOException ex) { Logger.getLogger(EquiCubeDialogController.class.getName()).log(Level.SEVERE, null, ex); } } if (strTypeTransformation.equals(EquiCubeDialogController.EQUI2CUBE)) { if (img.getWidth() == 2 * img.getHeight()) { fileLstFich1[i] = fileTransf; i++; } else { bAttention = true; } } else { if (img.getWidth() == img.getHeight()) { String strNom = fileTransf.getAbsolutePath().substring(0, fileTransf.getAbsolutePath().length() - 6); boolean bTrouve = false; for (int ik = 0; ik < i; ik++) { String strNom1 = fileLstFich1[ik].getAbsolutePath().substring(0, fileTransf.getAbsolutePath().length() - 6); if (strNom.equals(strNom1)) { bTrouve = true; } } if (!bTrouve) { fileLstFich1[i] = fileTransf; i++; } } else { bAttention = true; } } } } if (bAttention) { Alert alert = new Alert(AlertType.ERROR); alert.setTitle(rbLocalisation.getString("transformation.traiteImages")); alert.setHeaderText(null); alert.setContentText(rbLocalisation.getString("transformation.traiteImagesType")); alert.showAndWait(); } fileLstFichier = new File[i]; System.arraycopy(fileLstFich1, 0, fileLstFichier, 0, i); } if (fileLstFichier != null) { if (bTraitementEffectue) { lvListeFichier.getItems().clear(); bTraitementEffectue = false; } for (File lstFichier1 : fileLstFichier) { String nomFich = lstFichier1.getAbsolutePath(); lvListeFichier.getItems().add(nomFich); } } lblDragDropE2C.setVisible(false); event.setDropCompleted(bSucces); event.consume(); }); }
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(); }//from w w w . j a v a2 s.co m } // 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; }
From source file:org.wandora.application.gui.topicpanels.webview.WebViewPanel.java
private void initFX(final JFXPanel fxPanel) { Group group = new Group(); Scene scene = new Scene(group); fxPanel.setScene(scene);//w w w. j av a2s . c o m webView = new WebView(); if (javaFXVersionInt >= 8) { webView.setScaleX(1.0); webView.setScaleY(1.0); //webView.setFitToHeight(false); //webView.setFitToWidth(false); //webView.setZoom(javafx.stage.Screen.getPrimary().getDpi() / 96); } group.getChildren().add(webView); int w = this.getWidth(); int h = this.getHeight() - 34; webView.setMinSize(w, h); webView.setMaxSize(w, h); webView.setPrefSize(w, h); // Obtain the webEngine to navigate webEngine = webView.getEngine(); webEngine.locationProperty().addListener(new ChangeListener<String>() { @Override public void changed(ObservableValue<? extends String> observable, String oldValue, final String newValue) { if (newValue.endsWith(".pdf")) { try { int a = WandoraOptionPane.showConfirmDialog(Wandora.getWandora(), "Open PDF document in external application?", "Open PDF document in external application?", WandoraOptionPane.YES_NO_OPTION); if (a == WandoraOptionPane.YES_OPTION) { Desktop dt = Desktop.getDesktop(); dt.browse(new URI(newValue)); } } catch (Exception e) { } } else { SwingUtilities.invokeLater(new Runnable() { @Override public void run() { urlTextField.setText(newValue); } }); } } }); webEngine.titleProperty().addListener(new ChangeListener<String>() { @Override public void changed(ObservableValue<? extends String> observable, String oldValue, final String newValue) { SwingUtilities.invokeLater(new Runnable() { @Override public void run() { title = newValue; } }); } }); webEngine.setOnAlert(new EventHandler<WebEvent<java.lang.String>>() { @Override public void handle(WebEvent<String> t) { if (t != null) { String str = t.getData(); if (str != null && str.length() > 0) { WandoraOptionPane.showMessageDialog(Wandora.getWandora(), str, "Javascript Alert", WandoraOptionPane.PLAIN_MESSAGE); } } } }); webEngine.setConfirmHandler(new Callback<String, Boolean>() { @Override public Boolean call(String msg) { int a = WandoraOptionPane.showConfirmDialog(Wandora.getWandora(), msg, "Javascript Alert", WandoraOptionPane.YES_NO_OPTION); return (a == WandoraOptionPane.YES_OPTION); } }); webEngine.setPromptHandler(new Callback<PromptData, String>() { @Override public String call(PromptData data) { String a = WandoraOptionPane.showInputDialog(Wandora.getWandora(), data.getMessage(), data.getDefaultValue(), "Javascript Alert", WandoraOptionPane.QUESTION_MESSAGE); return a; } }); webEngine.setCreatePopupHandler(new Callback<PopupFeatures, WebEngine>() { @Override public WebEngine call(PopupFeatures features) { if (informPopupBlocking) { WandoraOptionPane.showMessageDialog(Wandora.getWandora(), "A javascript popup has been blocked. Wandora doesn't allow javascript popups in Webview topic panel.", "Javascript popup blocked", WandoraOptionPane.PLAIN_MESSAGE); } informPopupBlocking = false; return null; } }); webEngine.setOnVisibilityChanged(new EventHandler<WebEvent<Boolean>>() { @Override public void handle(WebEvent<Boolean> t) { if (t != null) { Boolean b = t.getData(); if (informVisibilityChanges) { WandoraOptionPane.showMessageDialog(Wandora.getWandora(), "A browser window visibility change has been blocked. Wandora doesn't allow visibility changes of windows in Webview topic panel.", "Javascript visibility chnage blocked", WandoraOptionPane.PLAIN_MESSAGE); informVisibilityChanges = false; } } } }); webEngine.getLoadWorker().stateProperty().addListener(new ChangeListener<State>() { @Override public void changed(ObservableValue ov, State oldState, State newState) { if (newState == Worker.State.SCHEDULED) { //System.out.println("Scheduled!"); startLoadingAnimation(); } if (newState == Worker.State.SUCCEEDED) { Document doc = webEngine.getDocument(); try { Transformer transformer = TransformerFactory.newInstance().newTransformer(); //transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "no"); transformer.setOutputProperty(OutputKeys.METHOD, "xml"); transformer.setOutputProperty(OutputKeys.INDENT, "yes"); transformer.setOutputProperty(OutputKeys.ENCODING, "UTF-8"); transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "4"); // transformer.transform(new DOMSource(doc), new StreamResult(new OutputStreamWriter(System.out, "UTF-8"))); StringWriter stringWriter = new StringWriter(); transformer.transform(new DOMSource(doc), new StreamResult(stringWriter)); webSource = stringWriter.toString(); } catch (Exception ex) { ex.printStackTrace(); } stopLoadingAnimation(); } else if (newState == Worker.State.CANCELLED) { //System.out.println("Cancelled!"); stopLoadingAnimation(); } else if (newState == Worker.State.FAILED) { webEngine.loadContent(failedToOpenMessage); stopLoadingAnimation(); } } }); }