Examples with ObservableMeasurementTableData qupath.lib.gui.measure.ObservableMeasurementTableData used on opensource projects

Example 6 with ObservableMeasurementTableData

use of qupath.lib.gui.measure.ObservableMeasurementTableData in project qupath by qupath.

the class SummaryMeasurementTableCommand method showTable.

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

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

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

Example 7 with ObservableMeasurementTableData

use of qupath.lib.gui.measure.ObservableMeasurementTableData in project qupath by qupath.

the class MeasurementExportCommand method createAndShowDialog.

private void createAndShowDialog() {
    project = qupath.getProject();
    if (project == null) {
        Dialogs.showNoProjectError("Export measurements");
        return;
    }
    BorderPane mainPane = new BorderPane();
    BorderPane imageEntryPane = new BorderPane();
    GridPane optionPane = new GridPane();
    optionPane.setHgap(5.0);
    optionPane.setVgap(5.0);
    // TOP PANE (SELECT PROJECT ENTRY FOR EXPORT)
    project = qupath.getProject();
    pathObjectCombo = new ComboBox<>();
    separatorCombo = new ComboBox<>();
    includeCombo = new CheckComboBox<String>();
    String sameImageWarning = "A selected image is open in the viewer!\nData should be saved before exporting.";
    var listSelectionView = ProjectDialogs.createImageChoicePane(qupath, project.getImageList(), previousImages, sameImageWarning);
    // BOTTOM PANE (OPTIONS)
    int row = 0;
    Label pathOutputLabel = new Label("Output file");
    var btnChooseFile = new Button("Choose");
    btnChooseFile.setOnAction(e -> {
        String extSelected = separatorCombo.getSelectionModel().getSelectedItem();
        String ext = extSelected.equals("Tab (.tsv)") ? ".tsv" : ".csv";
        String extDesc = ext.equals(".tsv") ? "TSV (Tab delimited)" : "CSV (Comma delimited)";
        File pathOut = Dialogs.promptToSaveFile("Output file", Projects.getBaseDirectory(project), "measurements" + ext, extDesc, ext);
        if (pathOut != null) {
            if (pathOut.isDirectory())
                pathOut = new File(pathOut.getAbsolutePath() + File.separator + "measurements" + ext);
            outputText.setText(pathOut.getAbsolutePath());
        }
    });
    pathOutputLabel.setLabelFor(outputText);
    PaneTools.addGridRow(optionPane, row++, 0, "Choose output file", pathOutputLabel, outputText, outputText, btnChooseFile, btnChooseFile);
    outputText.setMaxWidth(Double.MAX_VALUE);
    btnChooseFile.setMaxWidth(Double.MAX_VALUE);
    Label pathObjectLabel = new Label("Export type");
    pathObjectLabel.setLabelFor(pathObjectCombo);
    pathObjectCombo.getItems().setAll("Image", "Annotations", "Detections", "Cells", "TMA cores");
    pathObjectCombo.getSelectionModel().selectFirst();
    pathObjectCombo.valueProperty().addListener((v, o, n) -> {
        if (n != null)
            setType(n);
    });
    PaneTools.addGridRow(optionPane, row++, 0, "Choose the export type", pathObjectLabel, pathObjectCombo, pathObjectCombo, pathObjectCombo, pathObjectCombo);
    Label separatorLabel = new Label("Separator");
    separatorLabel.setLabelFor(separatorCombo);
    separatorCombo.getItems().setAll("Tab (.tsv)", "Comma (.csv)", "Semicolon (.csv)");
    separatorCombo.getSelectionModel().selectFirst();
    PaneTools.addGridRow(optionPane, row++, 0, "Choose a value separator", separatorLabel, separatorCombo, separatorCombo, separatorCombo, separatorCombo);
    Label includeLabel = new Label("Columns to include (Optional)");
    includeLabel.setLabelFor(includeCombo);
    GuiTools.installSelectAllOrNoneMenu(includeCombo);
    Button btnPopulateColumns = new Button("Populate\t");
    ProgressIndicator progressIndicator = new ProgressIndicator();
    progressIndicator.setPrefSize(20, 20);
    progressIndicator.setMinSize(20, 20);
    progressIndicator.setOpacity(0);
    Button btnResetColumns = new Button("Reset");
    PaneTools.addGridRow(optionPane, row++, 0, "Choose the specific column(s) to include (default: all)", includeLabel, includeCombo, btnPopulateColumns, progressIndicator, btnResetColumns);
    btnPopulateColumns.setOnAction(e -> {
        includeCombo.setDisable(true);
        Set<String> allColumnsForCombo = Collections.synchronizedSet(new LinkedHashSet<>());
        setType(pathObjectCombo.getSelectionModel().getSelectedItem());
        for (int i = 0; i < ProjectDialogs.getTargetItems(listSelectionView).size(); i++) {
            ProjectImageEntry<BufferedImage> entry = ProjectDialogs.getTargetItems(listSelectionView).get(i);
            int updatedEntries = i;
            executor.submit(() -> {
                try {
                    progressIndicator.setOpacity(100);
                    ImageData<?> imageData = entry.readImageData();
                    ObservableMeasurementTableData model = new ObservableMeasurementTableData();
                    model.setImageData(imageData, imageData == null ? Collections.emptyList() : imageData.getHierarchy().getObjects(null, type));
                    allColumnsForCombo.addAll(model.getAllNames());
                    imageData.getServer().close();
                    if (updatedEntries == ProjectDialogs.getTargetItems(listSelectionView).size() - 1) {
                        Platform.runLater(() -> {
                            allColumnsForCombo.removeIf(n -> n == null);
                            includeCombo.getItems().setAll(allColumnsForCombo);
                            includeCombo.getCheckModel().clearChecks();
                            includeCombo.setDisable(false);
                        });
                        progressIndicator.setOpacity(0);
                    }
                } catch (Exception ex) {
                    logger.warn("Error loading columns for entry " + entry.getImageName() + ": " + ex.getLocalizedMessage());
                }
            });
        }
        btnResetColumns.fire();
    });
    btnPopulateColumns.disableProperty().addListener((v, o, n) -> {
        if (n != null && n == true)
            includeCombo.setDisable(true);
    });
    var targetItemBinding = Bindings.size(listSelectionView.getTargetItems()).isEqualTo(0);
    btnPopulateColumns.disableProperty().bind(targetItemBinding);
    btnResetColumns.disableProperty().bind(targetItemBinding);
    btnResetColumns.setOnAction(e -> includeCombo.getCheckModel().clearChecks());
    // Add listener to separatorCombo
    separatorCombo.getSelectionModel().selectedItemProperty().addListener((v, o, n) -> {
        if (outputText == null || n == null)
            return;
        String currentOut = outputText.getText();
        if (n.equals("Tab (.tsv)") && currentOut.endsWith(".csv"))
            outputText.setText(currentOut.replace(".csv", ".tsv"));
        else if ((n.equals("Comma (.csv)") || n.equals("Semicolon (.csv)")) && currentOut.endsWith(".tsv"))
            outputText.setText(currentOut.replace(".tsv", ".csv"));
    });
    PaneTools.getContentsOfType(optionPane, Label.class, false).forEach(e -> e.setMinWidth(160));
    PaneTools.setToExpandGridPaneWidth(outputText, pathObjectCombo, separatorCombo, includeCombo);
    btnPopulateColumns.setMinWidth(100);
    btnResetColumns.setMinWidth(75);
    dialog = Dialogs.builder().title("Export measurements").buttons(btnExport, ButtonType.CANCEL).content(mainPane).build();
    dialog.getDialogPane().setPrefSize(600, 400);
    imageEntryPane.setCenter(listSelectionView);
    // Set the disabledProperty according to (1) targetItems.size() > 0 and (2) outputText.isEmpty()
    var emptyOutputTextBinding = outputText.textProperty().isEqualTo("");
    dialog.getDialogPane().lookupButton(btnExport).disableProperty().bind(Bindings.or(emptyOutputTextBinding, targetItemBinding));
    mainPane.setTop(imageEntryPane);
    mainPane.setBottom(optionPane);
    Optional<ButtonType> result = dialog.showAndWait();
    if (!result.isPresent() || result.get() != btnExport || result.get() == ButtonType.CANCEL)
        return;
    String curExt = Files.getFileExtension(outputText.getText());
    if (curExt.equals("") || (!curExt.equals("csv") && !curExt.equals("tsv"))) {
        curExt = curExt.length() > 1 ? "." + curExt : curExt;
        String extSelected = separatorCombo.getSelectionModel().getSelectedItem();
        String ext = extSelected.equals("Tab (.tsv)") ? ".tsv" : ".csv";
        outputText.setText(outputText.getText().substring(0, outputText.getText().length() - curExt.length()) + ext);
    }
    if (new File(outputText.getText()).getParent() == null) {
        String ext = Files.getFileExtension(outputText.getText()).equals("tsv") ? ".tsv" : ".csv";
        String extDesc = ext.equals(".tsv") ? "TSV (Tab delimited)" : "CSV (Comma delimited)";
        File pathOut = Dialogs.promptToSaveFile("Output file", Projects.getBaseDirectory(project), outputText.getText(), extDesc, ext);
        if (pathOut == null)
            return;
        else
            outputText.setText(pathOut.getAbsolutePath());
    }
    var checkedItems = includeCombo.getCheckModel().getCheckedItems();
    String[] include = checkedItems.stream().collect(Collectors.toList()).toArray(new String[checkedItems.size()]);
    String separator = defSep;
    switch(separatorCombo.getSelectionModel().getSelectedItem()) {
        case "Tab (.tsv)":
            separator = "\t";
            break;
        case "Comma (.csv)":
            separator = ",";
            break;
        case "Semicolon (.csv)":
            separator = ";";
            break;
    }
    ;
    MeasurementExporter exporter;
    exporter = new MeasurementExporter().imageList(ProjectDialogs.getTargetItems(listSelectionView)).separator(separator).includeOnlyColumns(include).exportType(type);
    ExportTask worker = new ExportTask(exporter, outputText.getText());
    ProgressDialog progress = new ProgressDialog(worker);
    progress.setWidth(600);
    progress.initOwner(qupath.getStage());
    progress.setTitle("Export measurements...");
    progress.getDialogPane().setHeaderText("Export measurements");
    progress.getDialogPane().setGraphic(null);
    progress.getDialogPane().getButtonTypes().add(ButtonType.CANCEL);
    progress.getDialogPane().lookupButton(ButtonType.CANCEL).addEventFilter(ActionEvent.ACTION, e -> {
        if (Dialogs.showYesNoDialog("Cancel export", "Are you sure you want to stop the export after the current image?")) {
            worker.quietCancel();
            progress.setHeaderText("Cancelling...");
            // worker.cancel(false);
            progress.getDialogPane().lookupButton(ButtonType.CANCEL).setDisable(true);
        }
        e.consume();
    });
    // Create & run task
    runningTask.set(qupath.createSingleThreadExecutor(this).submit(worker));
    progress.show();
}