Examples with ProjectImageEntry qupath.lib.projects.ProjectImageEntry used on opensource projects

Example 1 with ProjectImageEntry

use of qupath.lib.projects.ProjectImageEntry in project qupath by qupath.

the class ProjectImportImagesCommand method promptToImportImages.

/**
 * Prompt to import images to the current project.
 *
 * @param qupath QuPath instance, used to access the current project and stage
 * @param builder if not null, this will be used to create the servers. If null, a combobox will be shown to choose an installed builder.
 * @param defaultPaths URIs to use to prepopulate the list
 * @return
 */
static List<ProjectImageEntry<BufferedImage>> promptToImportImages(QuPathGUI qupath, ImageServerBuilder<BufferedImage> builder, String... defaultPaths) {
    var project = qupath.getProject();
    if (project == null) {
        Dialogs.showNoProjectError(commandName);
        return Collections.emptyList();
    }
    ListView<String> listView = new ListView<>();
    listView.setPrefWidth(480);
    listView.setMinHeight(100);
    listView.getItems().addAll(defaultPaths);
    listView.setPlaceholder(new Label("Drag & drop image or project files for import, \nor choose from the options below"));
    Button btnFile = new Button("Choose files");
    btnFile.setOnAction(e -> loadFromFileChooser(listView.getItems()));
    Button btnURL = new Button("Input URL");
    btnURL.setOnAction(e -> loadFromSingleURL(listView.getItems()));
    Button btnClipboard = new Button("From clipboard");
    btnClipboard.setOnAction(e -> loadFromClipboard(listView.getItems()));
    Button btnFileList = new Button("From path list");
    btnFileList.setOnAction(e -> loadFromTextFile(listView.getItems()));
    TitledPane paneList = new TitledPane("Image paths", listView);
    paneList.setCollapsible(false);
    BorderPane paneImages = new BorderPane();
    class BuilderListCell extends ListCell<ImageServerBuilder<BufferedImage>> {

        @Override
        protected void updateItem(ImageServerBuilder<BufferedImage> item, boolean empty) {
            super.updateItem(item, empty);
            if (empty) {
                setText(null);
            } else {
                if (item == null)
                    setText("Default (let QuPath decide)");
                else
                    setText(item.getName());
            }
        }
    }
    boolean requestBuilder = builder == null;
    ComboBox<ImageServerBuilder<BufferedImage>> comboBuilder = new ComboBox<>();
    Label labelBuilder = new Label("Image provider");
    if (requestBuilder) {
        comboBuilder.setCellFactory(p -> new BuilderListCell());
        comboBuilder.setButtonCell(new BuilderListCell());
        List<ImageServerBuilder<BufferedImage>> availableBuilders = new ArrayList<>(ImageServerProvider.getInstalledImageServerBuilders(BufferedImage.class));
        if (!availableBuilders.contains(null))
            availableBuilders.add(0, null);
        comboBuilder.getItems().setAll(availableBuilders);
        comboBuilder.getSelectionModel().selectFirst();
        labelBuilder.setLabelFor(comboBuilder);
        labelBuilder.setMinWidth(Label.USE_PREF_SIZE);
    }
    ComboBox<ImageType> comboType = new ComboBox<>();
    comboType.getItems().setAll(ImageType.values());
    Label labelType = new Label("Set image type");
    labelType.setLabelFor(comboType);
    labelType.setMinWidth(Label.USE_PREF_SIZE);
    ComboBox<Rotation> comboRotate = new ComboBox<>();
    comboRotate.getItems().setAll(Rotation.values());
    Label labelRotate = new Label("Rotate image");
    labelRotate.setLabelFor(comboRotate);
    labelRotate.setMinWidth(Label.USE_PREF_SIZE);
    TextField tfArgs = new TextField();
    Label labelArgs = new Label("Optional args");
    labelArgs.setLabelFor(tfArgs);
    labelArgs.setMinWidth(Label.USE_PREF_SIZE);
    CheckBox cbPyramidalize = new CheckBox("Auto-generate pyramids");
    cbPyramidalize.setSelected(pyramidalizeProperty.get());
    CheckBox cbImportObjects = new CheckBox("Import objects");
    cbImportObjects.setSelected(importObjectsProperty.get());
    PaneTools.setMaxWidth(Double.MAX_VALUE, comboBuilder, comboType, comboRotate, cbPyramidalize, cbImportObjects, tfArgs);
    PaneTools.setFillWidth(Boolean.TRUE, comboBuilder, comboType, comboRotate, cbPyramidalize, cbImportObjects, tfArgs);
    PaneTools.setHGrowPriority(Priority.ALWAYS, comboBuilder, comboType, comboRotate, cbPyramidalize, cbImportObjects, tfArgs);
    GridPane paneType = new GridPane();
    paneType.setPadding(new Insets(5));
    paneType.setHgap(5);
    paneType.setVgap(5);
    int row = 0;
    if (requestBuilder)
        PaneTools.addGridRow(paneType, row++, 0, "Specify the library used to open images", labelBuilder, comboBuilder);
    PaneTools.addGridRow(paneType, row++, 0, "Specify the default image type for all images being imported (required for analysis, can be changed later under the 'Image' tab)", labelType, comboType);
    PaneTools.addGridRow(paneType, row++, 0, "Optionally rotate images on import", labelRotate, comboRotate);
    PaneTools.addGridRow(paneType, row++, 0, "Optionally pass reader-specific arguments to the image provider.\nUsually this should just be left empty.", labelArgs, tfArgs);
    PaneTools.addGridRow(paneType, row++, 0, "Dynamically create image pyramids for large, single-resolution images", cbPyramidalize, cbPyramidalize);
    PaneTools.addGridRow(paneType, row++, 0, "Read and import objects (e.g. annotations) from the image file, if possible", cbImportObjects, cbImportObjects);
    paneImages.setCenter(paneList);
    paneImages.setBottom(paneType);
    // TilePane paneButtons = new TilePane();
    // paneButtons.getChildren().addAll(btnFile, btnURL, btnClipboard, btnFileList);
    GridPane paneButtons = PaneTools.createColumnGridControls(btnFile, btnURL, btnClipboard, btnFileList);
    paneButtons.setHgap(5);
    paneButtons.setPadding(new Insets(5));
    BorderPane pane = new BorderPane();
    pane.setCenter(paneImages);
    pane.setBottom(paneButtons);
    // Support drag & drop for files
    pane.setOnDragOver(e -> {
        e.acceptTransferModes(TransferMode.COPY);
        e.consume();
    });
    pane.setOnDragDropped(e -> {
        Dragboard dragboard = e.getDragboard();
        if (dragboard.hasFiles()) {
            logger.trace("Files dragged onto project import dialog");
            try {
                var paths = dragboard.getFiles().stream().filter(f -> f.isFile() && !f.isHidden()).map(f -> f.getAbsolutePath()).collect(Collectors.toList());
                paths.removeAll(listView.getItems());
                if (!paths.isEmpty())
                    listView.getItems().addAll(paths);
            } catch (Exception ex) {
                Dialogs.showErrorMessage("Drag & Drop", ex);
            }
        }
        e.setDropCompleted(true);
        e.consume();
    });
    Dialog<ButtonType> dialog = new Dialog<>();
    dialog.setResizable(true);
    dialog.initOwner(qupath.getStage());
    dialog.setTitle("Import images to project");
    ButtonType typeImport = new ButtonType("Import", ButtonData.OK_DONE);
    dialog.getDialogPane().getButtonTypes().addAll(typeImport, ButtonType.CANCEL);
    ScrollPane scroll = new ScrollPane(pane);
    scroll.setFitToHeight(true);
    scroll.setFitToWidth(true);
    dialog.getDialogPane().setContent(scroll);
    Optional<ButtonType> result = dialog.showAndWait();
    if (!result.isPresent() || result.get() != typeImport)
        return Collections.emptyList();
    // // Do the actual import
    // List<String> pathSucceeded = new ArrayList<>();
    // List<String> pathFailed = new ArrayList<>();
    // for (String path : listView.getItems()) {
    // if (qupath.getProject().addImage(path.trim()))
    // pathSucceeded.add(path);
    // else
    // pathFailed.add(path);
    // }
    ImageType type = comboType.getValue();
    Rotation rotation = comboRotate.getValue();
    boolean pyramidalize = cbPyramidalize.isSelected();
    boolean importObjects = cbImportObjects.isSelected();
    pyramidalizeProperty.set(pyramidalize);
    importObjectsProperty.set(importObjects);
    ImageServerBuilder<BufferedImage> requestedBuilder = requestBuilder ? comboBuilder.getSelectionModel().getSelectedItem() : builder;
    List<String> argsList = new ArrayList<>();
    String argsString = tfArgs.getText();
    // TODO: Use a smarter approach to splitting! Currently we support so few arguments that splitting on spaces should be ok... for now.
    String[] argsSplit = argsString == null || argsString.isBlank() ? new String[0] : argsString.split(" ");
    for (var a : argsSplit) {
        argsList.add(a);
    }
    if (rotation != null && rotation != Rotation.ROTATE_NONE) {
        argsList.add("--rotate");
        argsList.add(rotation.toString());
    }
    if (!argsList.isEmpty())
        logger.debug("Args: [{}]", argsList.stream().collect(Collectors.joining(", ")));
    String[] args = argsList.toArray(String[]::new);
    List<String> pathSucceeded = new ArrayList<>();
    List<String> pathFailed = new ArrayList<>();
    List<ProjectImageEntry<BufferedImage>> entries = new ArrayList<>();
    Task<Collection<ProjectImageEntry<BufferedImage>>> worker = new Task<>() {

        @Override
        protected Collection<ProjectImageEntry<BufferedImage>> call() throws Exception {
            AtomicLong counter = new AtomicLong(0L);
            List<String> items = new ArrayList<>(listView.getItems());
            updateMessage("Checking for compatible image readers...");
            // Limit the size of the thread pool
            // The previous use of a cached thread pool caused trouble when importing may large, non-pyramidal images
            var pool = Executors.newFixedThreadPool(ThreadTools.getParallelism(), ThreadTools.createThreadFactory("project-import", true));
            // var pool = Executors.newCachedThreadPool(ThreadTools.createThreadFactory("project-import", true));
            List<Future<List<ServerBuilder<BufferedImage>>>> results = new ArrayList<>();
            List<ProjectImageEntry<BufferedImage>> projectImages = new ArrayList<>();
            for (var item : items) {
                // Try to load items from a project if possible
                if (item.toLowerCase().endsWith(ProjectIO.DEFAULT_PROJECT_EXTENSION)) {
                    try {
                        var tempProject = ProjectIO.loadProject(GeneralTools.toURI(item), BufferedImage.class);
                        projectImages.addAll(tempProject.getImageList());
                    } catch (Exception e) {
                        logger.error("Unable to add images from {} ({})", item, e.getLocalizedMessage());
                    }
                    continue;
                }
                results.add(pool.submit(() -> {
                    try {
                        var uri = GeneralTools.toURI(item);
                        UriImageSupport<BufferedImage> support;
                        if (requestedBuilder == null)
                            support = ImageServers.getImageSupport(uri, args);
                        else
                            support = ImageServers.getImageSupport(requestedBuilder, uri, args);
                        if (support != null)
                            return support.getBuilders();
                    } catch (Exception e) {
                        logger.error("Unable to add {}");
                        logger.error(e.getLocalizedMessage(), e);
                    }
                    return new ArrayList<ServerBuilder<BufferedImage>>();
                }));
            }
            List<ProjectImageEntry<BufferedImage>> failures = Collections.synchronizedList(new ArrayList<>());
            // If we have projects, try adding images from these first
            if (!projectImages.isEmpty()) {
                if (projectImages.size() == 1)
                    updateMessage("Importing 1 image from existing projects");
                else
                    updateMessage("Importing " + projectImages.size() + " images from existing projects");
                for (var temp : projectImages) {
                    try {
                        project.addDuplicate(temp, true);
                    } catch (Exception e) {
                        failures.add(temp);
                    }
                }
            }
            // If we have 'standard' image paths, use these next
            List<ServerBuilder<BufferedImage>> builders = new ArrayList<>();
            for (var result : results) {
                try {
                    builders.addAll(result.get());
                } catch (ExecutionException e) {
                    logger.error("Execution exception importing image", e);
                }
            }
            long max = builders.size();
            if (!builders.isEmpty()) {
                if (max == 1)
                    updateMessage("Adding 1 image to project");
                else
                    updateMessage("Adding " + max + " images to project");
                // Add everything in order first
                List<ProjectImageEntry<BufferedImage>> entries = new ArrayList<>();
                for (var builder : builders) {
                    // if (rotation != null && rotation != Rotation.ROTATE_NONE)
                    // builder = RotatedImageServer.getRotatedBuilder(builder, rotation);
                    // if (swapRedBlue)
                    // builder = RearrangeRGBImageServer.getSwapRedBlueBuilder(builder);
                    entries.add(project.addImage(builder));
                }
                // Initialize (the slow bit)
                int n = builders.size();
                for (var entry : entries) {
                    pool.submit(() -> {
                        try {
                            initializeEntry(entry, type, pyramidalize, importObjects);
                        } catch (Exception e) {
                            failures.add(entry);
                            logger.warn("Exception adding " + entry, e);
                        } finally {
                            long i = counter.incrementAndGet();
                            updateProgress(i, max);
                            String name = entry.getImageName();
                            if (name != null) {
                                updateMessage("Added " + i + "/" + n + " - " + name);
                            }
                        }
                    });
                }
            }
            pool.shutdown();
            try {
                pool.awaitTermination(60, TimeUnit.MINUTES);
            } catch (Exception e) {
                logger.error("Exception waiting for project import to complete: " + e.getLocalizedMessage(), e);
            }
            if (!failures.isEmpty()) {
                String message;
                if (failures.size() == 1)
                    message = "Failed to load one image.";
                else
                    message = "Failed to load " + failures.size() + " images.";
                if (requestedBuilder != null)
                    message += "\nThe image type might not be supported by '" + requestedBuilder.getName() + "'";
                Dialogs.showErrorMessage("Import images", message);
                var toRemove = failures.stream().filter(p -> project.getImageList().contains(p)).collect(Collectors.toList());
                project.removeAllImages(toRemove, true);
            }
            // Now save changes
            project.syncChanges();
            // builders.parallelStream().forEach(builder -> {
            // //				builders.parallelStream().forEach(builder -> {
            // try (var server =  builder.build()) {
            // var entry = addSingleImageToProject(project, server);
            // updateMessage("Added " + entry.getImageName());
            // } catch (Exception e) {
            // logger.warn("Exception adding " + builder, e);
            // } finally {
            // updateProgress(counter.incrementAndGet(), max);
            // }
            // });
            updateProgress(max, max);
            return entries;
        }
    };
    ProgressDialog progress = new ProgressDialog(worker);
    progress.setTitle("Project import");
    qupath.submitShortTask(worker);
    progress.showAndWait();
    try {
        project.syncChanges();
    } catch (IOException e1) {
        Dialogs.showErrorMessage("Sync project", e1);
    }
    qupath.refreshProject();
    StringBuilder sb = new StringBuilder();
    if (!pathSucceeded.isEmpty()) {
        sb.append("Successfully imported " + pathSucceeded.size() + " paths:\n");
        for (String path : pathSucceeded) sb.append("\t" + path + "\n");
        sb.append("\n");
        qupath.refreshProject();
        ProjectBrowser.syncProject(qupath.getProject());
    }
    if (!pathFailed.isEmpty()) {
        sb.append("Unable to import " + pathFailed.size() + " paths:\n");
        for (String path : pathFailed) sb.append("\t" + path + "\n");
        sb.append("\n");
        TextArea textArea = new TextArea();
        textArea.setText(sb.toString());
        if (pathSucceeded.isEmpty())
            Dialogs.showErrorMessage(commandName, textArea);
        else
            Dialogs.showMessageDialog(commandName, textArea);
    }
    // TODO: Add failed and successful paths to pathFailed/pathSucceeded, so the line below prints something
    if (sb.length() > 0)
        logger.info(sb.toString());
    return entries;
}

Example 2 with ProjectImageEntry

use of qupath.lib.projects.ProjectImageEntry in project qupath by qupath.

the class ProjectMetadataEditorCommand method showProjectMetadataEditor.

public static void showProjectMetadataEditor(Project<?> project) {
    if (project == null) {
        logger.warn("No project available!");
        return;
    }
    Set<String> metadataNameSet = new TreeSet<>();
    List<ImageEntryWrapper> entries = new ArrayList<>();
    for (ProjectImageEntry<?> entry : project.getImageList()) {
        entries.add(new ImageEntryWrapper(entry));
        metadataNameSet.addAll(entry.getMetadataKeys());
    }
    TableView<ImageEntryWrapper> table = new TableView<>();
    TableColumn<ImageEntryWrapper, String> colName = new TableColumn<>(IMAGE_NAME);
    colName.setCellValueFactory(v -> v.getValue().getNameBinding());
    table.getColumns().add(colName);
    table.setEditable(true);
    for (String metadataName : metadataNameSet) {
        TableColumn<ImageEntryWrapper, String> col = new TableColumn<>(metadataName);
        col.setCellFactory(TextFieldTableCell.<ImageEntryWrapper>forTableColumn());
        col.setOnEditCommit(e -> {
            ImageEntryWrapper entry = e.getRowValue();
            String n = e.getNewValue();
            if (n == null || n.isEmpty())
                entry.removeMetadataValue(e.getTableColumn().getText());
            else
                entry.putMetadataValue(e.getTableColumn().getText(), n);
        });
        col.setCellValueFactory(v -> v.getValue().getProperty(metadataName));
        col.setEditable(true);
        table.getColumns().add(col);
    }
    table.getItems().setAll(entries);
    table.getSelectionModel().setCellSelectionEnabled(true);
    table.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);
    // Handle deleting entries
    table.addEventHandler(KeyEvent.KEY_RELEASED, e -> {
        if (e.getCode() == KeyCode.BACK_SPACE || e.getCode() == KeyCode.DELETE) {
            var positions = table.getSelectionModel().getSelectedCells().stream().filter(p -> !IMAGE_NAME.equals(p.getTableColumn().getText())).collect(Collectors.toList());
            if (positions.isEmpty())
                return;
            if (positions.size() == 1) {
                setTextForSelectedCells(positions, null);
            } else {
                if (Dialogs.showConfirmDialog("Project metadata", "Clear metadata for " + positions.size() + " selected cells?")) {
                    setTextForSelectedCells(positions, null);
                }
            }
            table.refresh();
        }
    });
    BooleanBinding selectedCells = Bindings.createBooleanBinding(() -> table.getSelectionModel().selectedItemProperty() == null, table.getSelectionModel().selectedItemProperty());
    MenuBar menubar = new MenuBar();
    Menu menuEdit = new Menu("Edit");
    MenuItem miCopy = new MenuItem("Copy selected cells");
    miCopy.disableProperty().bind(selectedCells);
    miCopy.setAccelerator(new KeyCodeCombination(KeyCode.C, KeyCombination.SHORTCUT_DOWN));
    miCopy.setOnAction(e -> copySelectedCellsToClipboard(table, true));
    MenuItem miCopyFull = new MenuItem("Copy full table");
    miCopyFull.setOnAction(e -> copyEntireTableToClipboard(table));
    MenuItem miPaste = new MenuItem("Paste");
    miPaste.setAccelerator(new KeyCodeCombination(KeyCode.V, KeyCombination.SHORTCUT_DOWN));
    miPaste.disableProperty().bind(selectedCells);
    miPaste.setOnAction(e -> pasteClipboardContentsToTable(table));
    MenuItem miSet = new MenuItem("Set cell contents");
    miSet.disableProperty().bind(selectedCells);
    miSet.setOnAction(e -> {
        String input = Dialogs.showInputDialog("Set metadata cells", "Metadata text", "");
        if (input == null)
            return;
        setTextForSelectedCells(table.getSelectionModel().getSelectedCells(), input);
        table.refresh();
    });
    menuEdit.getItems().addAll(miCopy, miCopyFull, miPaste, miSet);
    menubar.getMenus().add(menuEdit);
    BorderPane pane = new BorderPane();
    pane.setTop(menubar);
    pane.setCenter(table);
    // menubar.setUseSystemMenuBar(true);
    menubar.useSystemMenuBarProperty().bindBidirectional(PathPrefs.useSystemMenubarProperty());
    Dialog<ButtonType> dialog = new Dialog<>();
    var qupath = QuPathGUI.getInstance();
    if (qupath != null)
        dialog.initOwner(qupath.getStage());
    dialog.setTitle("Project metadata");
    dialog.setHeaderText(null);
    dialog.setResizable(true);
    dialog.getDialogPane().setContent(pane);
    dialog.getDialogPane().getButtonTypes().setAll(ButtonType.OK, ButtonType.CANCEL);
    dialog.getDialogPane().setPrefWidth(500);
    Optional<ButtonType> result = dialog.showAndWait();
    if (result.isPresent() && result.get().getButtonData() == ButtonData.OK_DONE) {
        // Make the changes
        for (ImageEntryWrapper wrapper : entries) {
            wrapper.commitChanges();
        }
        // Write the project
        ProjectBrowser.syncProject(project);
    }
// Stage stage = new Stage();
// stage.initOwner(qupath.getStage());
// stage.setTitle("Project metadata");
// stage.setScene(new Scene(pane, 500, 400));
// stage.showAndWait();
}

Example 3 with ProjectImageEntry

use of qupath.lib.projects.ProjectImageEntry in project qupath by qupath.

the class QuPathGUI method openImage.

/**
 * Open a new whole slide image server, or ImageData.
 * If the path is the same as a currently-open server, do nothing.
 *
 * @param viewer the viewer into which the image should be opened
 * @param pathNew
 * @param prompt if true, give the user the opportunity to cancel opening if a whole slide server is already set
 * @param includeURLs if true, any prompt should support URL input and not only a file chooser
 * @return true if the server was set for this GUI, false otherwise
 * @throws IOException
 */
public boolean openImage(QuPathViewer viewer, String pathNew, boolean prompt, boolean includeURLs) throws IOException {
    if (viewer == null) {
        if (getViewers().size() == 1)
            viewer = getViewer();
        else {
            Dialogs.showErrorMessage("Open image", "Please specify the viewer where the image should be opened!");
            return false;
        }
    }
    ImageServer<BufferedImage> server = viewer.getServer();
    String pathOld = null;
    File fileBase = null;
    if (server != null) {
        var uris = server.getURIs();
        if (uris.size() == 1) {
            var uri = uris.iterator().next();
            pathOld = uri.toString();
            try {
                var path = GeneralTools.toPath(uri);
                if (path != null)
                    fileBase = path.toFile().getParentFile();
            } catch (Exception e) {
            }
            ;
        }
    // pathOld = server.getPath();
    // try {
    // fileBase = new File(pathOld).getParentFile();
    // } catch (Exception e) {};
    }
    // Prompt for a path, if required
    File fileNew = null;
    if (pathNew == null) {
        if (includeURLs) {
            pathNew = Dialogs.promptForFilePathOrURL("Choose path", pathOld, fileBase, null);
            if (pathNew == null)
                return false;
            fileNew = new File(pathNew);
        } else {
            fileNew = Dialogs.promptForFile(null, fileBase, null);
            if (fileNew == null)
                return false;
            pathNew = fileNew.getAbsolutePath();
        }
    } else
        fileNew = new File(pathNew);
    // If we have a file, check if it is a data file - if so, handle differently
    if (fileNew.isFile() && GeneralTools.checkExtensions(pathNew, PathPrefs.getSerializationExtension()))
        return openSavedData(viewer, fileNew, false, true);
    // Check for project file
    if (fileNew.isFile() && GeneralTools.checkExtensions(pathNew, ProjectIO.getProjectExtension())) {
        logger.info("Trying to load project {}", fileNew.getAbsolutePath());
        try {
            Project<BufferedImage> project = ProjectIO.loadProject(fileNew, BufferedImage.class);
            if (project != null) {
                setProject(project);
                return true;
            }
        } catch (Exception e) {
            Dialogs.showErrorMessage("Open project", e);
            logger.error("Error opening project " + fileNew.getAbsolutePath(), e);
            return false;
        }
    }
    // Try opening an image, unless it's the same as the image currently open
    if (!pathNew.equals(pathOld)) {
        // If we have a project, show the import dialog
        if (getProject() != null) {
            List<ProjectImageEntry<BufferedImage>> entries = ProjectCommands.promptToImportImages(this, pathNew);
            if (entries.isEmpty())
                return false;
            return openImageEntry(entries.get(0));
        }
        ImageServer<BufferedImage> serverNew = null;
        UriImageSupport<BufferedImage> support = ImageServerProvider.getPreferredUriImageSupport(BufferedImage.class, pathNew);
        List<ServerBuilder<BufferedImage>> builders = support == null ? Collections.emptyList() : support.getBuilders();
        if (builders.isEmpty()) {
            String message = "Unable to build ImageServer for " + pathNew + ".\nSee View > Show log for more details";
            Dialogs.showErrorMessage("Unable to build server", message);
            return false;
        } else if (builders.size() == 1) {
            try {
                serverNew = builders.get(0).build();
            } catch (Exception e) {
                logger.error("Error building server: " + e.getLocalizedMessage(), e);
            }
        } else {
            var selector = new ServerSelector(builders);
            serverNew = selector.promptToSelectServer();
            if (serverNew == null)
                return false;
        }
        if (serverNew != null) {
            if (pathOld != null && prompt && !viewer.getHierarchy().isEmpty()) {
                if (!Dialogs.showYesNoDialog("Replace open image", "Close " + ServerTools.getDisplayableImageName(server) + "?"))
                    return false;
            }
            ImageData<BufferedImage> imageData = null;
            if (serverNew != null) {
                int minSize = PathPrefs.minPyramidDimensionProperty().get();
                if (serverNew.nResolutions() == 1 && Math.max(serverNew.getWidth(), serverNew.getHeight()) > minSize) {
                    // Check if we have any hope at all with the current settings
                    long estimatedBytes = (long) serverNew.getWidth() * (long) serverNew.getHeight() * (long) serverNew.nChannels() * (long) serverNew.getPixelType().getBytesPerPixel();
                    double requiredBytes = estimatedBytes * (4.0 / 3.0);
                    if (prompt && imageRegionStore != null && requiredBytes >= imageRegionStore.getTileCacheSize()) {
                        logger.warn("Selected image is {} x {} x {} pixels ({})", serverNew.getWidth(), serverNew.getHeight(), serverNew.nChannels(), serverNew.getPixelType());
                        Dialogs.showErrorMessage("Image too large", "Non-pyramidal image is too large for the available tile cache!\n" + "Try converting the image to a pyramidal file format, or increasing the memory available to QuPath.");
                        return false;
                    }
                    // Offer to pyramidalize
                    var serverWrapped = ImageServers.pyramidalize(serverNew);
                    if (serverWrapped.nResolutions() > 1) {
                        if (prompt) {
                            var response = Dialogs.showYesNoCancelDialog("Auto pyramidalize", "QuPath works best with large images saved in a pyramidal format.\n\n" + "Do you want to generate a pyramid dynamically from " + ServerTools.getDisplayableImageName(serverNew) + "?" + "\n(This requires more memory, but is usually worth it)");
                            if (response == DialogButton.CANCEL)
                                return false;
                            if (response == DialogButton.YES)
                                serverNew = serverWrapped;
                        }
                    }
                }
                imageData = createNewImageData(serverNew);
            }
            viewer.setImageData(imageData);
            if (imageData.getImageType() == ImageType.UNSET && PathPrefs.imageTypeSettingProperty().get() == ImageTypeSetting.PROMPT) {
                var type = GuiTools.estimateImageType(serverNew, imageRegionStore.getThumbnail(serverNew, 0, 0, true));
                ImageDetailsPane.promptToSetImageType(imageData, type);
            }
            return true;
        } else {
            // Show an error message if we can't open the file
            Dialogs.showErrorNotification("Open image", "Sorry, I can't open " + pathNew);
        // logger.error("Unable to build whole slide server for path '{}'", pathNew);
        }
    }
    return false;
}

Example 4 with ProjectImageEntry

use of qupath.lib.projects.ProjectImageEntry in project qupath by qupath.

the class MeasurementExporter method exportMeasurements.

/**
 * Exports the measurements of one or more entries in the project.
 * This function first opens all the images in the project to store
 * all the column names and values of the measurements.
 * Then, it loops through the maps containing the values to write
 * them to the given output stream.
 * @param stream
 */
public void exportMeasurements(OutputStream stream) {
    long startTime = System.currentTimeMillis();
    Map<ProjectImageEntry<?>, String[]> imageCols = new HashMap<>();
    Map<ProjectImageEntry<?>, Integer> nImageEntries = new HashMap<>();
    List<String> allColumns = new ArrayList<>();
    Multimap<String, String> valueMap = LinkedListMultimap.create();
    String pattern = "(?=(?:[^\"]*\"[^\"]*\")*[^\"]*$)";
    for (ProjectImageEntry<?> entry : imageList) {
        try {
            ImageData<?> imageData = entry.readImageData();
            ObservableMeasurementTableData model = new ObservableMeasurementTableData();
            Collection<PathObject> pathObjects = imageData == null ? Collections.emptyList() : imageData.getHierarchy().getObjects(null, type);
            if (filter != null)
                pathObjects = pathObjects.stream().filter(filter).collect(Collectors.toList());
            model.setImageData(imageData, pathObjects);
            List<String> data = SummaryMeasurementTableCommand.getTableModelStrings(model, separator, excludeColumns);
            // Get header
            String[] header;
            String headerString = data.get(0);
            if (headerString.chars().filter(e -> e == '"').count() > 1)
                header = headerString.split(separator.equals("\t") ? "\\" + separator : separator + pattern, -1);
            else
                header = headerString.split(separator);
            imageCols.put(entry, header);
            nImageEntries.put(entry, data.size() - 1);
            for (String col : header) {
                if (!allColumns.contains(col) && !excludeColumns.contains(col))
                    allColumns.add(col);
            }
            // To keep the same column order, just delete non-relevant columns
            if (!includeOnlyColumns.isEmpty())
                allColumns.removeIf(n -> !includeOnlyColumns.contains(n));
            for (int i = 1; i < data.size(); i++) {
                String[] row;
                String rowString = data.get(i);
                // Check if some values in the row are escaped
                if (rowString.chars().filter(e -> e == '"').count() > 1)
                    row = rowString.split(separator.equals("\t") ? "\\" + separator : separator + pattern, -1);
                else
                    row = rowString.split(separator);
                // Put value in map
                for (int elem = 0; elem < row.length; elem++) {
                    if (allColumns.contains(header[elem]))
                        valueMap.put(header[elem], row[elem]);
                }
            }
        } catch (Exception e) {
            logger.error(e.getLocalizedMessage(), e);
        }
    }
    try (PrintWriter writer = new PrintWriter(new OutputStreamWriter(stream, StandardCharsets.UTF_8))) {
        writer.write(String.join(separator, allColumns));
        writer.write(System.lineSeparator());
        Iterator[] its = new Iterator[allColumns.size()];
        for (int col = 0; col < allColumns.size(); col++) {
            its[col] = valueMap.get(allColumns.get(col)).iterator();
        }
        for (ProjectImageEntry<?> entry : imageList) {
            for (int nObject = 0; nObject < nImageEntries.get(entry); nObject++) {
                for (int nCol = 0; nCol < allColumns.size(); nCol++) {
                    if (Arrays.stream(imageCols.get(entry)).anyMatch(allColumns.get(nCol)::equals)) {
                        String val = (String) its[nCol].next();
                        // NaN values -> blank
                        if (val.equals("NaN"))
                            val = "";
                        writer.write(val);
                    }
                    if (nCol < allColumns.size() - 1)
                        writer.write(separator);
                }
                writer.write(System.lineSeparator());
            }
        }
    } catch (Exception e) {
        logger.error("Error writing to file: " + e.getLocalizedMessage(), e);
    }
    long endTime = System.currentTimeMillis();
    long timeMillis = endTime - startTime;
    String time = null;
    if (timeMillis > 1000 * 60)
        time = String.format("Total processing time: %.2f minutes", timeMillis / (1000.0 * 60.0));
    else if (timeMillis > 1000)
        time = String.format("Total processing time: %.2f seconds", timeMillis / (1000.0));
    else
        time = String.format("Total processing time: %d milliseconds", timeMillis);
    logger.info("Processed {} images", imageList.size());
    logger.info(time);
}

Example 5 with ProjectImageEntry

use of qupath.lib.projects.ProjectImageEntry in project qupath by qupath.

the class ProjectBrowser method getPopup.

ContextMenu getPopup() {
    Action actionOpenImage = new Action("Open image", e -> qupath.openImageEntry(getSelectedEntry()));
    Action actionRemoveImage = new Action("Remove image(s)", e -> {
        Collection<ImageRow> imageRows = getSelectedImageRowsRecursive();
        Collection<ProjectImageEntry<BufferedImage>> entries = ProjectTreeRow.getEntries(imageRows);
        if (entries.isEmpty())
            return;
        // Don't allow us to remove any entries that are currently open (in any viewer)
        for (var viewer : qupath.getViewers()) {
            var imageData = viewer.getImageData();
            var entry = imageData == null ? null : getProject().getEntry(imageData);
            if (entry != null && entries.contains(entry)) {
                Dialogs.showErrorMessage("Remove project entries", "Please close all images you want to remove!");
                return;
            }
        }
        if (entries.size() == 1) {
            if (!Dialogs.showConfirmDialog("Remove project entry", "Remove " + entries.iterator().next().getImageName() + " from project?"))
                return;
        } else if (!Dialogs.showYesNoDialog("Remove project entries", String.format("Remove %d entries?", entries.size())))
            return;
        var result = Dialogs.showYesNoCancelDialog("Remove project entries", "Delete all associated data?");
        if (result == DialogButton.CANCEL)
            return;
        project.removeAllImages(entries, result == DialogButton.YES);
        refreshTree(null);
        syncProject(project);
        if (tree != null) {
            boolean isExpanded = tree.getRoot() != null && tree.getRoot().isExpanded();
            tree.setRoot(model.getRoot());
            tree.getRoot().setExpanded(isExpanded);
        }
    });
    Action actionDuplicateImages = new Action("Duplicate image(s)", e -> {
        Collection<ImageRow> imageRows = getSelectedImageRowsRecursive();
        if (imageRows.isEmpty()) {
            logger.debug("Nothing to duplicate - no entries selected");
            return;
        }
        boolean singleImage = false;
        String name = "";
        String title = "Duplicate images";
        String namePrompt = "Append to image name";
        String nameHelp = "Specify text to append to the image name to distinguish duplicated images";
        if (imageRows.size() == 1) {
            title = "Duplicate image";
            namePrompt = "Duplicate image name";
            nameHelp = "Specify name for the duplicated image";
            singleImage = true;
            name = imageRows.iterator().next().getDisplayableString();
            name = GeneralTools.generateDistinctName(name, project.getImageList().stream().map(p -> p.getImageName()).collect(Collectors.toSet()));
        }
        var params = new ParameterList().addStringParameter("name", namePrompt, name, nameHelp).addBooleanParameter("copyData", "Also duplicate data files", true, "Duplicate any associated data files along with the image");
        if (!Dialogs.showParameterDialog(title, params))
            return;
        boolean copyData = params.getBooleanParameterValue("copyData");
        name = params.getStringParameterValue("name");
        // Ensure we have a single space and then the text to append, with extra whitespace removed
        if (!singleImage && !name.isBlank())
            name = " " + name.strip();
        for (var imageRow : imageRows) {
            try {
                var newEntry = project.addDuplicate(ProjectTreeRow.getEntry(imageRow), copyData);
                if (newEntry != null && !name.isBlank()) {
                    if (singleImage)
                        newEntry.setImageName(name);
                    else
                        newEntry.setImageName(newEntry.getImageName() + name);
                }
            } catch (Exception ex) {
                Dialogs.showErrorNotification("Duplicating image", "Error duplicating " + ProjectTreeRow.getEntry(imageRow).getImageName());
                logger.error(ex.getLocalizedMessage(), ex);
            }
        }
        try {
            project.syncChanges();
        } catch (Exception ex) {
            logger.error("Error synchronizing project changes: " + ex.getLocalizedMessage(), ex);
        }
        refreshProject();
        if (imageRows.size() == 1)
            logger.debug("Duplicated 1 image entry");
        else
            logger.debug("Duplicated {} image entries");
    });
    Action actionSetImageName = new Action("Rename image", e -> {
        TreeItem<ProjectTreeRow> path = tree.getSelectionModel().getSelectedItem();
        if (path == null)
            return;
        if (path.getValue().getType() == ProjectTreeRow.Type.IMAGE) {
            if (setProjectEntryImageName(ProjectTreeRow.getEntry(path.getValue())) && project != null)
                syncProject(project);
        }
    });
    // Add a metadata value
    Action actionAddMetadataValue = new Action("Add metadata", e -> {
        Project<BufferedImage> project = getProject();
        Collection<ImageRow> imageRows = getSelectedImageRowsRecursive();
        if (project != null && !imageRows.isEmpty()) {
            TextField tfMetadataKey = new TextField();
            var suggestions = project.getImageList().stream().map(p -> p.getMetadataKeys()).flatMap(Collection::stream).distinct().sorted().collect(Collectors.toList());
            TextFields.bindAutoCompletion(tfMetadataKey, suggestions);
            TextField tfMetadataValue = new TextField();
            Label labKey = new Label("New key");
            Label labValue = new Label("New value");
            labKey.setLabelFor(tfMetadataKey);
            labValue.setLabelFor(tfMetadataValue);
            tfMetadataKey.setTooltip(new Tooltip("Enter the name for the metadata entry"));
            tfMetadataValue.setTooltip(new Tooltip("Enter the value for the metadata entry"));
            ProjectImageEntry<BufferedImage> entry = imageRows.size() == 1 ? ProjectTreeRow.getEntry(imageRows.iterator().next()) : null;
            int nMetadataValues = entry == null ? 0 : entry.getMetadataKeys().size();
            GridPane pane = new GridPane();
            pane.setVgap(5);
            pane.setHgap(5);
            pane.add(labKey, 0, 0);
            pane.add(tfMetadataKey, 1, 0);
            pane.add(labValue, 0, 1);
            pane.add(tfMetadataValue, 1, 1);
            String name = imageRows.size() + " images";
            if (entry != null) {
                name = entry.getImageName();
                if (nMetadataValues > 0) {
                    Label labelCurrent = new Label("Current metadata");
                    TextArea textAreaCurrent = new TextArea();
                    textAreaCurrent.setEditable(false);
                    String keyString = entry.getMetadataSummaryString();
                    if (keyString.isEmpty())
                        textAreaCurrent.setText("No metadata entries yet");
                    else
                        textAreaCurrent.setText(keyString);
                    textAreaCurrent.setPrefRowCount(3);
                    labelCurrent.setLabelFor(textAreaCurrent);
                    pane.add(labelCurrent, 0, 2);
                    pane.add(textAreaCurrent, 1, 2);
                }
            }
            Dialog<ButtonType> dialog = new Dialog<>();
            dialog.setTitle("Metadata");
            dialog.getDialogPane().getButtonTypes().setAll(ButtonType.OK, ButtonType.CANCEL);
            dialog.getDialogPane().setHeaderText("Set metadata for " + name);
            dialog.getDialogPane().setContent(pane);
            Optional<ButtonType> result = dialog.showAndWait();
            if (result.isPresent() && result.get() == ButtonType.OK) {
                String key = tfMetadataKey.getText().trim();
                String value = tfMetadataValue.getText();
                if (key.isEmpty()) {
                    logger.warn("Attempted to set metadata value for {}, but key was empty!", name);
                } else {
                    // Set metadata for all entries
                    for (var temp : imageRows) ProjectTreeRow.getEntry(temp).putMetadataValue(key, value);
                    syncProject(project);
                    tree.refresh();
                }
            }
        } else {
            Dialogs.showErrorMessage("Edit image description", "No entry is selected!");
        }
    });
    // Edit the description for the image
    Action actionEditDescription = new Action("Edit description", e -> {
        Project<?> project = getProject();
        ProjectImageEntry<?> entry = getSelectedEntry();
        if (project != null && entry != null) {
            if (showDescriptionEditor(entry)) {
                descriptionText.set(entry.getDescription());
                syncProject(project);
            }
        } else {
            Dialogs.showErrorMessage("Edit image description", "No entry is selected!");
        }
    });
    // Mask the name of the images and shuffle the entry
    Action actionMaskImageNames = ActionTools.createSelectableAction(PathPrefs.maskImageNamesProperty(), "Mask image names");
    // Refresh thumbnail according to current display settings
    Action actionRefreshThumbnail = new Action("Refresh thumbnail", e -> {
        TreeItem<ProjectTreeRow> path = tree.getSelectionModel().getSelectedItem();
        if (path == null)
            return;
        if (path.getValue().getType() == ProjectTreeRow.Type.IMAGE) {
            ProjectImageEntry<BufferedImage> entry = ProjectTreeRow.getEntry(path.getValue());
            if (!isCurrentImage(entry)) {
                logger.warn("Cannot refresh entry for image that is not open!");
                return;
            }
            BufferedImage imgThumbnail = qupath.getViewer().getRGBThumbnail();
            imgThumbnail = resizeForThumbnail(imgThumbnail);
            try {
                entry.setThumbnail(imgThumbnail);
            } catch (IOException e1) {
                logger.error("Error writing thumbnail", e1);
            }
            tree.refresh();
        }
    });
    // Open the project directory using Explorer/Finder etc.
    Action actionOpenProjectDirectory = createBrowsePathAction("Project...", () -> getProjectPath());
    Action actionOpenProjectEntryDirectory = createBrowsePathAction("Project entry...", () -> getProjectEntryPath());
    Action actionOpenImageServerDirectory = createBrowsePathAction("Image server...", () -> getImageServerPath());
    Menu menuSort = new Menu("Sort by...");
    ContextMenu menu = new ContextMenu();
    var hasProjectBinding = qupath.projectProperty().isNotNull();
    var menuOpenDirectories = MenuTools.createMenu("Open directory...", actionOpenProjectDirectory, actionOpenProjectEntryDirectory, actionOpenImageServerDirectory);
    menuOpenDirectories.visibleProperty().bind(hasProjectBinding);
    // MenuItem miOpenProjectDirectory = ActionUtils.createMenuItem(actionOpenProjectDirectory);
    MenuItem miOpenImage = ActionUtils.createMenuItem(actionOpenImage);
    MenuItem miRemoveImage = ActionUtils.createMenuItem(actionRemoveImage);
    MenuItem miDuplicateImage = ActionUtils.createMenuItem(actionDuplicateImages);
    MenuItem miSetImageName = ActionUtils.createMenuItem(actionSetImageName);
    MenuItem miRefreshThumbnail = ActionUtils.createMenuItem(actionRefreshThumbnail);
    MenuItem miEditDescription = ActionUtils.createMenuItem(actionEditDescription);
    MenuItem miAddMetadata = ActionUtils.createMenuItem(actionAddMetadataValue);
    MenuItem miMaskImages = ActionUtils.createCheckMenuItem(actionMaskImageNames);
    // Set visibility as menu being displayed
    menu.setOnShowing(e -> {
        TreeItem<ProjectTreeRow> selected = tree.getSelectionModel().getSelectedItem();
        ProjectImageEntry<BufferedImage> selectedEntry = selected == null ? null : ProjectTreeRow.getEntry(selected.getValue());
        var entries = getSelectedImageRowsRecursive();
        boolean isImageEntry = selectedEntry != null;
        // miOpenProjectDirectory.setVisible(project != null && project.getBaseDirectory().exists());
        miOpenImage.setVisible(isImageEntry);
        miDuplicateImage.setVisible(isImageEntry);
        miSetImageName.setVisible(isImageEntry);
        miAddMetadata.setVisible(!entries.isEmpty());
        miEditDescription.setVisible(isImageEntry);
        miRefreshThumbnail.setVisible(isImageEntry && isCurrentImage(selectedEntry));
        miRemoveImage.setVisible(selected != null && project != null && !project.getImageList().isEmpty());
        if (project == null) {
            menuSort.setVisible(false);
            return;
        }
        Map<String, MenuItem> newItems = new TreeMap<>();
        for (ProjectImageEntry<?> entry : project.getImageList()) {
            // Add all entry metadata keys
            for (String key : entry.getMetadataKeys()) {
                if (!newItems.containsKey(key))
                    newItems.put(key, ActionUtils.createMenuItem(createSortByKeyAction(key, key)));
            }
            // Add all additional keys
            for (String key : baseMetadataKeys) {
                if (!newItems.containsKey(key))
                    newItems.put(key, ActionUtils.createMenuItem(createSortByKeyAction(key, key)));
            }
        }
        menuSort.getItems().setAll(newItems.values());
        menuSort.getItems().add(0, ActionUtils.createMenuItem(createSortByKeyAction("None", null)));
        menuSort.getItems().add(1, new SeparatorMenuItem());
        menuSort.setVisible(true);
        if (menu.getItems().isEmpty())
            e.consume();
    });
    SeparatorMenuItem separator = new SeparatorMenuItem();
    separator.visibleProperty().bind(menuSort.visibleProperty());
    menu.getItems().addAll(miOpenImage, miRemoveImage, miDuplicateImage, new SeparatorMenuItem(), miSetImageName, miAddMetadata, miEditDescription, miMaskImages, miRefreshThumbnail, separator, menuSort);
    separator = new SeparatorMenuItem();
    separator.visibleProperty().bind(menuOpenDirectories.visibleProperty());
    if (Desktop.isDesktopSupported()) {
        menu.getItems().addAll(separator, menuOpenDirectories);
    }
    return menu;
}