Examples with ServerBuilder qupath.lib.images.servers.ImageServerBuilder.ServerBuilder used on opensource projects

Example 1 with ServerBuilder

use of qupath.lib.images.servers.ImageServerBuilder.ServerBuilder 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 ServerBuilder

use of qupath.lib.images.servers.ImageServerBuilder.ServerBuilder 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 3 with ServerBuilder

use of qupath.lib.images.servers.ImageServerBuilder.ServerBuilder in project qupath by qupath.

the class PathIO method extractServerBuilder.

/**
 * Extract a {@link ServerBuilder} from a String.
 * This may represent an image path (for v0.2 and earlier) or JSON (from v0.3).
 *
 * @param <T>
 * @param serverString
 * @param warnIfInvalid log warnings if the server is a different version
 * @return
 * @throws IOException
 */
private static <T> ServerBuilder<T> extractServerBuilder(String serverString, boolean warnIfInvalid) throws IOException {
    if (serverString.startsWith("Image path: ")) {
        String serverPath = serverString.substring("Image path: ".length()).trim();
        URI uri = ImageServerProvider.legacyPathToURI(serverPath);
        if (warnIfInvalid)
            logger.warn("Attempting to extract server from legacy data file - this may result in errors");
        return DefaultImageServerBuilder.createInstance(null, uri);
    } else {
        String json = serverString;
        var wrapper = GsonTools.getInstance().fromJson(json, ServerBuilderWrapper.class);
        if (warnIfInvalid && !Objects.equals(wrapper.dataVersion, DATA_FILE_VERSION)) {
            logger.warn("Attempting to read data file version {} written by QuPath {} (expected data file version {})", wrapper.dataVersion, wrapper.qupathVersion, DATA_FILE_VERSION);
        }
        return (ServerBuilder<T>) wrapper.server;
    }
}