Examples with QuPathViewer qupath.lib.gui.viewer.QuPathViewer used on opensource projects

Example 6 with QuPathViewer

use of qupath.lib.gui.viewer.QuPathViewer 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 QuPathViewer

use of qupath.lib.gui.viewer.QuPathViewer in project qupath by qupath.

the class PathClassifierPane method runClassifier.

void runClassifier() {
    QuPathViewer viewer = viewerValue.getValue();
    if (viewer == null)
        return;
    ImageData<BufferedImage> imageData = viewer.getImageData();
    if (classifier == null || imageData == null || !classifier.isValid())
        return;
    Collection<PathObject> pathObjects = imageData.getHierarchy().getDetectionObjects();
    var availableFeatures = PathClassifierTools.getAvailableFeatures(pathObjects);
    var requiredFeatures = classifier.getRequiredMeasurements();
    String missingFeatures = requiredFeatures.stream().filter(p -> !availableFeatures.contains(p)).collect(Collectors.joining("\n\t"));
    if (!missingFeatures.isEmpty())
        logger.warn("Detection objects are missing the following feature(s):\n\t" + missingFeatures + "\nWill proceed with classification anyway..");
    // SwingUtilities.getRoot(viewer).setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
    try {
        PathClassifierTools.runClassifier(imageData.getHierarchy(), classifier);
        // Log the classifier
        if (pathClassifier != null) {
            imageData.getHistoryWorkflow().addStep(new RunSavedClassifierWorkflowStep(pathClassifier));
        }
    } catch (Exception e) {
        e.printStackTrace();
    } finally {
        // SwingUtilities.getRoot(viewer).setCursor(cursor);
        // Update displayed list - names may have changed - and classifier summary
        updateClassifierSummary();
    }
}

Example 8 with QuPathViewer

use of qupath.lib.gui.viewer.QuPathViewer in project qupath by qupath.

the class ScreenshotCommand method run.

@Override
public void run() {
    QuPathViewer viewer = qupath.getViewer();
    if (viewer == null)
        return;
    BufferedImage img = GuiTools.makeSnapshot(qupath, GuiTools.SnapshotType.VIEWER);
    // Try to start up & display ImageJ
    ImageJ ij = IJExtension.getImageJInstance();
    if (ij != null)
        ij.setVisible(true);
    String name = "QuPath screenshot";
    if (viewer.getServer() != null)
        name = WindowManager.getUniqueName("Screenshot - " + ServerTools.getDisplayableImageName(viewer.getServer()));
    ImagePlus imp = new ImagePlus(name, img);
    double pixelWidth = getDisplayedPixelWidthMicrons(viewer);
    double pixelHeight = getDisplayedPixelHeightMicrons(viewer);
    if (!Double.isNaN(pixelWidth + pixelHeight)) {
        Calibration cal = imp.getCalibration();
        cal.pixelWidth = pixelWidth;
        cal.pixelHeight = pixelHeight;
        cal.setUnit("um");
    // // TODO: Set the screenshot origin, if no rotations have been applied
    // cal.xOrigin = -viewer.componentXtoImageX(0) / viewer.getDownsampleFactor();
    // cal.yOrigin = -viewer.componentYtoImageY(0) / viewer.getDownsampleFactor();
    }
    // TODO: Put image path into screenshot images - so they can also be used as whole slide images later
    // Make sure we aren't in batch mode, so that image will display
    Interpreter.batchMode = false;
    SwingUtilities.invokeLater(() -> imp.show());
}

Example 9 with QuPathViewer

use of qupath.lib.gui.viewer.QuPathViewer in project qupath by qupath.

the class UndoRedoManager method hierarchyChanged.

@Override
public void hierarchyChanged(PathObjectHierarchyEvent event) {
    // Try to avoid calling too often
    if (undoingOrRedoing || event.isChanging() || maxUndoHierarchySize.get() <= 0 || event.getChangedObjects().stream().allMatch(p -> p instanceof ParallelTileObject))
        return;
    // *Potentially* we might have the same hierarchy in multiple viewers
    // Since we don't have the viewer stored in the event, check to see what viewers are impacted
    QuPathViewer[] viewers = map.keySet().toArray(new QuPathViewer[map.size()]);
    PathObjectHierarchy hierarchy = event.getHierarchy();
    int maxSize = maxUndoHierarchySize.get();
    boolean sizeOK = hierarchy.nObjects() <= maxSize;
    for (QuPathViewer viewer : viewers) {
        if (viewer.getHierarchy() == hierarchy) {
            SerializableUndoRedoStack<PathObjectHierarchy> undoRedo = map.get(viewer);
            // If the size is ok, register the change for potential undo-ing
            if (sizeOK) {
                if (undoRedo == null)
                    map.put(viewer, new SerializableUndoRedoStack<>(hierarchy));
                else
                    undoRedo.addLatest(hierarchy, maxUndoLevels.get());
            } else {
                // If the hierarchy is too big turn off undo/redo
                map.put(viewer, (SerializableUndoRedoStack<PathObjectHierarchy>) null);
            }
        }
    }
    refreshProperties();
}

Example 10 with QuPathViewer

use of qupath.lib.gui.viewer.QuPathViewer in project qupath by qupath.

the class BrightnessContrastCommand method changed.

@Override
public void changed(ObservableValue<? extends ImageData<BufferedImage>> source, ImageData<BufferedImage> imageDataOld, ImageData<BufferedImage> imageDataNew) {
    // TODO: Consider different viewers but same ImageData
    if (imageDataOld == imageDataNew)
        return;
    QuPathViewer viewerNew = qupath.getViewer();
    if (viewer != viewerNew) {
        if (viewer != null)
            viewer.getView().removeEventHandler(KeyEvent.KEY_TYPED, keyListener);
        if (viewerNew != null)
            viewerNew.getView().addEventHandler(KeyEvent.KEY_TYPED, keyListener);
        viewer = viewerNew;
    }
    if (imageDisplay != null) {
        showGrayscale.unbindBidirectional(imageDisplay.useGrayscaleLutProperty());
        imageDisplay.useGrayscaleLutProperty().unbindBidirectional(showGrayscale);
    }
    imageDisplay = viewer == null ? null : viewer.getImageDisplay();
    if (imageDataOld != null)
        imageDataOld.removePropertyChangeListener(this);
    if (imageDataNew != null)
        imageDataNew.addPropertyChangeListener(this);
    updateTable();
    // updateHistogramMap();
    // Update if we aren't currently initializing
    updateHistogram();
    updateSliders();
}