Example usage for javafx.util Callback Callback

List of usage examples for javafx.util Callback Callback

Introduction

In this page you can find the example usage for javafx.util Callback Callback.

Prototype

Callback

Source Link

Usage

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();
            }
        }
    });

}