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

Example 1 with QuPathViewerPlus

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

the class QuPathGUI method setViewerPopupMenu.

private void setViewerPopupMenu(final QuPathViewerPlus viewer) {
    final ContextMenu popup = new ContextMenu();
    MenuItem miAddRow = new MenuItem("Add row");
    miAddRow.setOnAction(e -> viewerManager.addRow(viewer));
    MenuItem miAddColumn = new MenuItem("Add column");
    miAddColumn.setOnAction(e -> viewerManager.addColumn(viewer));
    MenuItem miRemoveRow = new MenuItem("Remove row");
    miRemoveRow.setOnAction(e -> viewerManager.removeViewerRow(viewer));
    MenuItem miRemoveColumn = new MenuItem("Remove column");
    miRemoveColumn.setOnAction(e -> viewerManager.removeViewerColumn(viewer));
    MenuItem miCloseViewer = new MenuItem("Close viewer");
    miCloseViewer.setOnAction(e -> {
        viewerManager.closeViewer(viewer);
    // viewerManager.removeViewer(viewer);
    });
    MenuItem miResizeGrid = new MenuItem("Reset grid size");
    miResizeGrid.setOnAction(e -> {
        viewerManager.resetGridSize();
    });
    MenuItem miToggleSync = ActionTools.createCheckMenuItem(defaultActions.TOGGLE_SYNCHRONIZE_VIEWERS, null);
    MenuItem miMatchResolutions = ActionTools.createMenuItem(defaultActions.MATCH_VIEWER_RESOLUTIONS);
    Menu menuMultiview = MenuTools.createMenu("Multi-view", miToggleSync, miMatchResolutions, miCloseViewer, null, miResizeGrid, null, // null,
    miAddRow, miAddColumn, null, miRemoveRow, miRemoveColumn);
    Menu menuView = MenuTools.createMenu("Display", ActionTools.createCheckMenuItem(defaultActions.SHOW_ANALYSIS_PANE, null), defaultActions.BRIGHTNESS_CONTRAST, null, ActionTools.createAction(() -> Commands.setViewerDownsample(viewer, 0.25), "400%"), ActionTools.createAction(() -> Commands.setViewerDownsample(viewer, 1), "100%"), ActionTools.createAction(() -> Commands.setViewerDownsample(viewer, 2), "50%"), ActionTools.createAction(() -> Commands.setViewerDownsample(viewer, 10), "10%"), ActionTools.createAction(() -> Commands.setViewerDownsample(viewer, 100), "1%"));
    ToggleGroup groupTools = new ToggleGroup();
    Menu menuTools = MenuTools.createMenu("Set tool", ActionTools.createCheckMenuItem(defaultActions.MOVE_TOOL, groupTools), ActionTools.createCheckMenuItem(defaultActions.RECTANGLE_TOOL, groupTools), ActionTools.createCheckMenuItem(defaultActions.ELLIPSE_TOOL, groupTools), ActionTools.createCheckMenuItem(defaultActions.LINE_TOOL, groupTools), ActionTools.createCheckMenuItem(defaultActions.POLYGON_TOOL, groupTools), ActionTools.createCheckMenuItem(defaultActions.POLYLINE_TOOL, groupTools), ActionTools.createCheckMenuItem(defaultActions.BRUSH_TOOL, groupTools), ActionTools.createCheckMenuItem(defaultActions.POINTS_TOOL, groupTools), null, ActionTools.createCheckMenuItem(defaultActions.SELECTION_MODE));
    // Handle awkward 'TMA core missing' option
    CheckMenuItem miTMAValid = new CheckMenuItem("Set core valid");
    miTMAValid.setOnAction(e -> setTMACoreMissing(viewer.getHierarchy(), false));
    CheckMenuItem miTMAMissing = new CheckMenuItem("Set core missing");
    miTMAMissing.setOnAction(e -> setTMACoreMissing(viewer.getHierarchy(), true));
    Menu menuTMA = new Menu("TMA");
    MenuTools.addMenuItems(menuTMA, miTMAValid, miTMAMissing, null, defaultActions.TMA_ADD_NOTE, null, MenuTools.createMenu("Add", createImageDataAction(imageData -> TMACommands.promptToAddRowBeforeSelected(imageData), "Add TMA row before"), createImageDataAction(imageData -> TMACommands.promptToAddRowAfterSelected(imageData), "Add TMA row after"), createImageDataAction(imageData -> TMACommands.promptToAddColumnBeforeSelected(imageData), "Add TMA column before"), createImageDataAction(imageData -> TMACommands.promptToAddColumnAfterSelected(imageData), "Add TMA column after")), MenuTools.createMenu("Remove", createImageDataAction(imageData -> TMACommands.promptToDeleteTMAGridRow(imageData), "Remove TMA row"), createImageDataAction(imageData -> TMACommands.promptToDeleteTMAGridColumn(imageData), "column")));
    // Create an empty placeholder menu
    Menu menuSetClass = MenuTools.createMenu("Set class");
    // CheckMenuItem miTMAValid = new CheckMenuItem("Set core valid");
    // miTMAValid.setOnAction(e -> setTMACoreMissing(viewer.getHierarchy(), false));
    // CheckMenuItem miTMAMissing = new CheckMenuItem("Set core missing");
    // miTMAMissing.setOnAction(e -> setTMACoreMissing(viewer.getHierarchy(), true));
    Menu menuCells = MenuTools.createMenu("Cells", ActionTools.createCheckMenuItem(defaultActions.SHOW_CELL_BOUNDARIES_AND_NUCLEI, null), ActionTools.createCheckMenuItem(defaultActions.SHOW_CELL_NUCLEI, null), ActionTools.createCheckMenuItem(defaultActions.SHOW_CELL_BOUNDARIES, null), ActionTools.createCheckMenuItem(defaultActions.SHOW_CELL_CENTROIDS, null));
    MenuItem miClearSelectedObjects = new MenuItem("Delete object");
    miClearSelectedObjects.setOnAction(e -> {
        PathObjectHierarchy hierarchy = viewer.getHierarchy();
        if (hierarchy == null)
            return;
        if (hierarchy.getSelectionModel().singleSelection()) {
            GuiTools.promptToRemoveSelectedObject(hierarchy.getSelectionModel().getSelectedObject(), hierarchy);
        } else {
            GuiTools.promptToClearAllSelectedObjects(viewer.getImageData());
        }
    });
    // Create a standard annotations menu
    Menu menuAnnotations = GuiTools.populateAnnotationsMenu(this, new Menu("Annotations"));
    SeparatorMenuItem topSeparator = new SeparatorMenuItem();
    popup.setOnShowing(e -> {
        // Check if we have any cells
        ImageData<?> imageData = viewer.getImageData();
        if (imageData == null)
            menuCells.setVisible(false);
        else
            menuCells.setVisible(!imageData.getHierarchy().getDetectionObjects().isEmpty());
        // Check what to show for TMA cores or annotations
        Collection<PathObject> selectedObjects = viewer.getAllSelectedObjects();
        PathObject pathObject = viewer.getSelectedObject();
        menuTMA.setVisible(false);
        if (pathObject instanceof TMACoreObject) {
            boolean isMissing = ((TMACoreObject) pathObject).isMissing();
            miTMAValid.setSelected(!isMissing);
            miTMAMissing.setSelected(isMissing);
            menuTMA.setVisible(true);
        }
        // Add clear objects option if we have more than one non-TMA object
        if (imageData == null || imageData.getHierarchy().getSelectionModel().noSelection() || imageData.getHierarchy().getSelectionModel().getSelectedObject() instanceof TMACoreObject)
            miClearSelectedObjects.setVisible(false);
        else {
            if (imageData.getHierarchy().getSelectionModel().singleSelection()) {
                miClearSelectedObjects.setText("Delete object");
                miClearSelectedObjects.setVisible(true);
            } else {
                miClearSelectedObjects.setText("Delete objects");
                miClearSelectedObjects.setVisible(true);
            }
        }
        boolean hasAnnotations = pathObject instanceof PathAnnotationObject || (!selectedObjects.isEmpty() && selectedObjects.stream().allMatch(p -> p.isAnnotation()));
        updateSetAnnotationPathClassMenu(menuSetClass, viewer);
        menuAnnotations.setVisible(hasAnnotations);
        topSeparator.setVisible(hasAnnotations || pathObject instanceof TMACoreObject);
        // Occasionally, the newly-visible top part of a popup menu can have the wrong size?
        popup.setWidth(popup.getPrefWidth());
    });
    // popup.add(menuClassify);
    popup.getItems().addAll(miClearSelectedObjects, menuTMA, menuSetClass, menuAnnotations, topSeparator, menuMultiview, menuCells, menuView, menuTools);
    popup.setAutoHide(true);
    // Enable circle pop-up for quick classification on right-click
    CirclePopupMenu circlePopup = new CirclePopupMenu(viewer.getView(), null);
    viewer.getView().addEventHandler(MouseEvent.MOUSE_PRESSED, e -> {
        if ((e.isPopupTrigger() || e.isSecondaryButtonDown()) && e.isShiftDown() && !getAvailablePathClasses().isEmpty()) {
            circlePopup.setAnimationDuration(Duration.millis(200));
            updateSetAnnotationPathClassMenu(circlePopup, viewer);
            circlePopup.show(e.getScreenX(), e.getScreenY());
            e.consume();
            return;
        } else if (circlePopup.isShown())
            circlePopup.hide();
        if (e.isPopupTrigger() || e.isSecondaryButtonDown()) {
            popup.show(viewer.getView().getScene().getWindow(), e.getScreenX(), e.getScreenY());
            e.consume();
        }
    });
// // It's necessary to make the Window the owner, since otherwise the context menu does not disappear when clicking elsewhere on the viewer
// viewer.getView().setOnContextMenuRequested(e -> {
// popup.show(viewer.getView().getScene().getWindow(), e.getScreenX(), e.getScreenY());
// //			popup.show(viewer.getView(), e.getScreenX(), e.getScreenY());
// });
}

Example 2 with QuPathViewerPlus

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

the class QuPathGUI method initializeMainComponent.

private BorderPane initializeMainComponent() {
    pane = new BorderPane();
    // Create a reasonably-sized viewer
    QuPathViewerPlus viewer = new QuPathViewerPlus(null, imageRegionStore, overlayOptions, viewerDisplayOptions);
    // Add analysis panel & viewer to split pane
    viewerManager = new MultiviewManager(viewer);
    viewerProperty.bind(viewerManager.activeViewerProperty());
    // Now that we have a viewer, we can create an undo/redo manager
    undoRedoManager = new UndoRedoManager(this);
    // TODO: MOVE INITIALIZING MANAGERS ELSEWHERE
    actions.addAll(new Menus(this).getActions());
    // Add a recent projects menu
    getMenu("File", true).getItems().add(1, createRecentProjectsMenu());
    // analysisPanel = createAnalysisPanel();
    initializeAnalysisPanel();
    analysisPanel.setMinWidth(300);
    analysisPanel.setPrefWidth(400);
    splitPane.setMinWidth(analysisPanel.getMinWidth() + 200);
    splitPane.setPrefWidth(analysisPanel.getPrefWidth() + 200);
    SplitPane.setResizableWithParent(analysisPanel, Boolean.FALSE);
    // paneCommands.setRight(cbPin);
    mainViewerPane = CommandFinderTools.createCommandFinderPane(this, viewerManager.getNode(), CommandFinderTools.commandBarDisplayProperty());
    // paneViewer.setTop(tfCommands);
    // paneViewer.setCenter(viewerManager.getNode());
    splitPane.getItems().addAll(analysisPanel, mainViewerPane);
    // splitPane.getItems().addAll(viewerManager.getComponent());
    SplitPane.setResizableWithParent(viewerManager.getNode(), Boolean.TRUE);
    pane.setCenter(splitPane);
    toolbar = new ToolBarComponent(this);
    pane.setTop(toolbar.getToolBar());
    setAnalysisPaneVisible(showAnalysisPane.get());
    showAnalysisPane.addListener((v, o, n) -> setAnalysisPaneVisible(n));
    // setInitialLocationAndMagnification(getViewer());
    // Prepare the viewer
    setupViewer(viewerManager.getActiveViewer());
    // Ensure the mode is set
    // Ensure actions are set appropriately
    selectedToolProperty.addListener((v, o, n) -> {
        Action action = toolActions.get(n);
        if (action != null)
            action.setSelected(true);
        activateTools(getViewer());
        if (n == PathTools.POINTS)
            defaultActions.COUNTING_PANEL.handle(null);
        updateCursor();
    });
    setSelectedTool(getSelectedTool());
    return pane;
}

Example 3 with QuPathViewerPlus

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

the class QuPathGUI method openImageEntry.

/**
 * Open the image represented by the specified ProjectImageEntry.
 * <p>
 * If an image is currently open, this command will prompt to save any changes.
 *
 * @param entry
 * @return
 */
public boolean openImageEntry(ProjectImageEntry<BufferedImage> entry) {
    Project<BufferedImage> project = getProject();
    if (entry == null || project == null)
        return false;
    // Check if we're changing ImageData at all
    var viewer = getViewer();
    ImageData<BufferedImage> imageData = viewer.getImageData();
    if (imageData != null && project.getEntry(imageData) == entry) {
        return false;
    }
    // String path = entry.getServerPath();
    for (QuPathViewerPlus v : viewerManager.getViewers()) {
        ImageData<BufferedImage> data = v.getImageData();
        if (data != null && project.getEntry(data) == entry) {
            // if (data != null && data.getServer().getPath().equals(path)) {
            viewerManager.setActiveViewer(v);
            return true;
        }
    }
    // If the current ImageData belongs to the current project, check if there are changes to save
    if (imageData != null && project != null) {
        if (!checkSaveChanges(imageData))
            return false;
    }
    // Check if we need to rotate the image
    try {
        imageData = entry.readImageData();
        viewer.setImageData(imageData);
        // setInitialLocationAndMagnification(viewer);
        if (imageData != null && (imageData.getImageType() == null || imageData.getImageType() == ImageType.UNSET)) {
            var setType = PathPrefs.imageTypeSettingProperty().get();
            if (setType == ImageTypeSetting.AUTO_ESTIMATE || setType == ImageTypeSetting.PROMPT) {
                var type = GuiTools.estimateImageType(imageData.getServer(), imageRegionStore.getThumbnail(imageData.getServer(), 0, 0, true));
                logger.info("Image type estimated to be {}", type);
                if (setType == ImageTypeSetting.PROMPT) {
                    ImageDetailsPane.promptToSetImageType(imageData, type);
                } else {
                    imageData.setImageType(type);
                    // Don't want to retain this as a change resulting in a prompt to save the data
                    imageData.setChanged(false);
                }
            }
        }
        return true;
    } catch (Exception e) {
        Dialogs.showErrorMessage("Load ImageData", e);
        return false;
    }
}

Example 4 with QuPathViewerPlus

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

the class QuPathGUI method openSavedData.

/**
 * Open a saved data file within a particular viewer, optionally keeping the same ImageServer as is currently open.
 * The purpose of this is to make it possible for a project (for example) to open the correct server prior to
 * opening the data file, enabling it to make use of relative path names and not have to rely on the absolute path
 * encoded within the ImageData.
 *
 * @param viewer
 * @param file
 * @param keepExistingServer if true and the viewer already has an ImageServer, then any ImageServer path recorded within the data file will be ignored
 * @param promptToSaveChanges if true, the user will be prompted to ask whether to save changes or not
 * @return
 * @throws IOException
 */
public boolean openSavedData(QuPathViewer viewer, final File file, final boolean keepExistingServer, boolean promptToSaveChanges) throws IOException {
    if (viewer == null) {
        if (getViewers().size() == 1)
            viewer = getViewer();
        else {
            Dialogs.showErrorMessage("Open saved data", "Please specify the viewer where the data should be opened!");
            return false;
        }
    }
    // First check to see if the ImageData is already open - if so, just activate the viewer
    for (QuPathViewerPlus v : viewerManager.getViewers()) {
        ImageData<?> data = v.getImageData();
        if (data != null && data.getLastSavedPath() != null && new File(data.getLastSavedPath()).equals(file)) {
            viewerManager.setActiveViewer(v);
            return true;
        }
    }
    ServerBuilder<BufferedImage> serverBuilder = null;
    ImageData<BufferedImage> imageData = viewer.getImageData();
    // If we are loading data related to the same image server, load into that - otherwise open a new image if we can find it
    try {
        serverBuilder = PathIO.extractServerBuilder(file.toPath());
    } catch (Exception e) {
        logger.warn("Unable to read server path from file: {}", e.getLocalizedMessage());
    }
    var existingBuilder = imageData == null || imageData.getServer() == null ? null : imageData.getServer().getBuilder();
    boolean sameServer = Objects.equals(existingBuilder, serverBuilder);
    // If we don't have the same server, try to check the path is valid.
    // If it isn't, then prompt to enter a new path.
    // Currently, URLs are always assumed to be valid, but files may have moved.
    // TODO: Make it possible to recover data if a stored URL ceases to be valid.
    ImageServer<BufferedImage> server = null;
    if (sameServer || (imageData != null && keepExistingServer))
        server = imageData.getServer();
    else {
        try {
            server = serverBuilder.build();
        } catch (Exception e) {
            logger.error("Unable to build server " + serverBuilder, e);
        }
        // TODO: Ideally we would use an interface like ProjectCheckUris instead
        if (server == null && serverBuilder != null) {
            var uris = serverBuilder.getURIs();
            var urisUpdated = new HashMap<URI, URI>();
            for (var uri : uris) {
                var pathUri = GeneralTools.toPath(uri);
                if (pathUri != null && Files.exists(pathUri)) {
                    urisUpdated.put(uri, uri);
                    continue;
                }
                String currentPath = pathUri == null ? uri.toString() : pathUri.toString();
                var newPath = Dialogs.promptForFilePathOrURL("Set path to missing image", currentPath, file.getParentFile(), null);
                if (newPath == null)
                    return false;
                try {
                    urisUpdated.put(uri, GeneralTools.toURI(newPath));
                } catch (URISyntaxException e) {
                    throw new IOException(e);
                }
            }
            serverBuilder = serverBuilder.updateURIs(urisUpdated);
            try {
                server = serverBuilder.build();
            } catch (Exception e) {
                logger.error("Unable to build server " + serverBuilder, e);
            }
        }
        if (server == null)
            return false;
        // 
        // Small optimization... put in a thumbnail request early in a background thread.
        // This way that it will be fetched while the image data is being read -
        // generally leading to improved performance in the viewer's setImageData method
        // (specifically the updating of the ImageDisplay, which needs a thumbnail)
        final ImageServer<BufferedImage> serverTemp = server;
        poolMultipleThreads.submit(() -> {
            imageRegionStore.getThumbnail(serverTemp, 0, 0, true);
        });
    }
    if (promptToSaveChanges && imageData != null && imageData.isChanged()) {
        if (!isReadOnly() && !promptToSaveChangesOrCancel("Save changes", imageData))
            return false;
    }
    try {
        ImageData<BufferedImage> imageData2 = PathIO.readImageData(file, imageData, server, BufferedImage.class);
        if (imageData2 != imageData) {
            viewer.setImageData(imageData2);
        }
    } catch (IOException e) {
        Dialogs.showErrorMessage("Read image data", e);
    }
    return true;
}