Examples with UriResource qupath.lib.io.UriResource used on opensource projects

Example 1 with UriResource

use of qupath.lib.io.UriResource in project qupath by qupath.

the class QP method loadObjectClassifier.

/**
 * Load an object classifier for a project or file path.
 *
 * @param names the names of the classifier within the current project, or file paths to a classifier to load from disk.
 * 				If more than one name is provided, a composite classifier is created (applying each classifier in sequence).
 * @return the requested {@link ObjectClassifier}
 * @throws IllegalArgumentException if the classifier cannot be found
 */
public static ObjectClassifier<BufferedImage> loadObjectClassifier(String... names) throws IllegalArgumentException {
    var project = getProject();
    List<ObjectClassifier<BufferedImage>> classifiers = new ArrayList<>();
    for (String name : names) {
        ObjectClassifier<BufferedImage> classifier = null;
        Exception exception = null;
        if (project != null) {
            try {
                var objectClassifiers = project.getObjectClassifiers();
                if (objectClassifiers.contains(name))
                    classifier = objectClassifiers.get(name);
            } catch (Exception e) {
                exception = e;
                logger.debug("Object classifier '{}' not found in project", name);
            }
        }
        if (classifier == null) {
            try {
                var path = Paths.get(name);
                if (Files.exists(path))
                    classifier = ObjectClassifiers.readClassifier(path);
            } catch (Exception e) {
                exception = e;
                logger.debug("Object classifier '{}' cannot be read from file", name);
            }
        }
        if (classifier == null) {
            throw new IllegalArgumentException("Unable to find object classifier " + name, exception);
        }
        // Try to fix URIs, if we can
        if (classifier instanceof UriResource) {
            UriUpdater.fixUris((UriResource) classifier, project);
        }
        if (names.length == 1)
            return classifier;
        else
            classifiers.add(classifier);
    }
    return ObjectClassifiers.createCompositeClassifier(classifiers);
}

Example 2 with UriResource

use of qupath.lib.io.UriResource in project qupath by qupath.

the class QP method loadPixelClassifier.

/**
 * Load a pixel classifier for a project or file path.
 *
 * @param name the name of the classifier within the current project, or file path to a classifier to load from disk.
 * @return the requested {@link PixelClassifier}
 * @throws IllegalArgumentException if the classifier cannot be found
 */
public static PixelClassifier loadPixelClassifier(String name) throws IllegalArgumentException {
    var project = getProject();
    Exception exception = null;
    PixelClassifier pixelClassifier = null;
    if (project != null) {
        try {
            var pixelClassifiers = project.getPixelClassifiers();
            if (pixelClassifiers.contains(name))
                pixelClassifier = pixelClassifiers.get(name);
        } catch (Exception e) {
            exception = e;
            logger.debug("Pixel classifier '{}' not found in project", name);
        }
    }
    try {
        var path = Paths.get(name);
        if (Files.exists(path))
            pixelClassifier = PixelClassifiers.readClassifier(path);
    } catch (Exception e) {
        exception = e;
        logger.debug("Pixel classifier '{}' cannot be read from file", name);
    }
    if (pixelClassifier == null)
        throw new IllegalArgumentException("Unable to find pixel classifier " + name, exception);
    // Fix URIs if we need to
    if (pixelClassifier instanceof UriResource) {
        UriUpdater.fixUris((UriResource) pixelClassifier, project);
    }
    return pixelClassifier;
}

Example 3 with UriResource

use of qupath.lib.io.UriResource in project qupath by qupath.

the class LoadResourceCommand method run.

@Override
public void run() {
    String title = resourceType.getDialogTitle();
    var cachedServers = new WeakHashMap<ImageData<BufferedImage>, ImageServer<BufferedImage>>();
    var overlay = PixelClassificationOverlay.create(qupath.getOverlayOptions(), cachedServers, new ColorModelRenderer(null));
    overlay.setMaxThreads(nThreads);
    for (var viewer : qupath.getViewers()) viewer.setCustomPixelLayerOverlay(overlay);
    var comboClassifiers = new ComboBox<String>();
    try {
        updateAvailableItems(comboClassifiers.getItems());
    } catch (IOException e) {
        logger.error(e.getLocalizedMessage(), e);
    }
    var selectedResource = Bindings.createObjectBinding(() -> {
        String name = comboClassifiers.getSelectionModel().getSelectedItem();
        cachedServers.clear();
        if (name != null) {
            try {
                var project = qupath.getProject();
                var manager = resourceType.getManager(project);
                S resource;
                if (manager != null && manager.contains(name))
                    resource = manager.get(name);
                else
                    resource = extras.get(name);
                if (resource instanceof UriResource) {
                    UriUpdater.fixUris((UriResource) resource, project);
                }
                return resource;
            } catch (Exception ex) {
                // TODO: Investigate why this is triggered twice
                Dialogs.showErrorNotification(resourceType.getDialogTitle(), ex);
            }
        }
        return null;
    }, comboClassifiers.getSelectionModel().selectedItemProperty());
    var label = new Label(resourceType.choosePrompt());
    label.setLabelFor(comboClassifiers);
    selectedResource.addListener((v, o, n) -> {
        cachedServers.clear();
        updateServers(n, cachedServers);
    });
    // Add file chooser
    var menu = new ContextMenu();
    var miLoadClassifier = new MenuItem("Import from files");
    miLoadClassifier.setOnAction(e -> {
        List<File> files = Dialogs.promptForMultipleFiles(title, null, resourceType.filePrompt(), "json");
        if (files == null || files.isEmpty())
            return;
        try {
            addExternalJson(files, resourceType.getManager(qupath.getProject()), extras);
            updateAvailableItems(comboClassifiers.getItems());
        } catch (IOException ex) {
            Dialogs.showErrorMessage(title, ex);
        }
    });
    var miOpenAsText = new MenuItem("Show as text");
    miOpenAsText.setOnAction(e -> {
        var name = comboClassifiers.getSelectionModel().getSelectedItem();
        var resource = selectedResource.get();
        if (resource == null)
            return;
        try {
            // Pass the resource class, since it can be required for including the appropriate JSON properties
            var json = GsonTools.getInstance(true).toJson(resource, resourceType.getResourceClass());
            if (!name.endsWith(".json"))
                name = name + ".json";
            // Show in script editor if possible; this may include better formatting and syntax highlighting
            var scriptEditor = qupath == null ? null : qupath.getScriptEditor();
            if (scriptEditor != null)
                scriptEditor.showScript(name, json);
            else
                Dialogs.showTextWindow(qupath.getStage(), name, json, Modality.NONE, false);
        } catch (Exception ex) {
            Dialogs.showErrorMessage("Show model as text", "Unable to create a text representation of '" + name + "', sorry!");
        }
    });
    miOpenAsText.disableProperty().bind(selectedResource.isNull());
    // Enable setting number of threads
    var miThreads = new MenuItem("Set parallel threads");
    miThreads.setOnAction(e -> {
        var params = new ParameterList().addIntParameter("nThreads", "Number of parallel threads", nThreads, null, "Number of threads to use for live prediction");
        if (!Dialogs.showParameterDialog("Set parallel threads", params))
            return;
        // var result = Dialogs.showInputDialog("Set parallel threads", "Number of threads to use for live prediction", (double)nThreads);
        var val = params.getIntParameterValue("nThreads");
        if (val == nThreads)
            return;
        if (val < 0)
            nThreads = PathPrefs.numCommandThreadsProperty().get();
        else
            nThreads = Math.max(1, val);
        if (overlay != null)
            overlay.setMaxThreads(nThreads);
    });
    menu.getItems().addAll(miLoadClassifier, miOpenAsText, new SeparatorMenuItem(), miThreads);
    var btnLoadExistingClassifier = GuiTools.createMoreButton(menu, Side.RIGHT);
    var classifierName = new SimpleStringProperty(null);
    classifierName.bind(comboClassifiers.getSelectionModel().selectedItemProperty());
    var pane = new GridPane();
    pane.setPadding(new Insets(10.0));
    pane.setHgap(5);
    pane.setVgap(10);
    pane.setPrefWidth(350.0);
    int row = 0;
    PaneTools.addGridRow(pane, row++, 0, "Choose model to apply to the current image", label, comboClassifiers, btnLoadExistingClassifier);
    PaneTools.setToExpandGridPaneWidth(comboClassifiers);
    if (resourceType.getResourceClass().equals(PixelClassifier.class)) {
        var labelRegion = new Label("Region");
        var comboRegionFilter = PixelClassifierUI.createRegionFilterCombo(qupath.getOverlayOptions());
        @SuppressWarnings("unchecked") var tilePane = PixelClassifierUI.createPixelClassifierButtons(qupath.imageDataProperty(), (ObjectExpression<PixelClassifier>) selectedResource, classifierName);
        PaneTools.addGridRow(pane, row++, 0, "Control where the pixel classification is applied during preview", labelRegion, comboRegionFilter, comboRegionFilter);
        PaneTools.addGridRow(pane, row++, 0, "Apply pixel classification", tilePane, tilePane, tilePane);
        PaneTools.setToExpandGridPaneWidth(tilePane);
    } else if (resourceType.getResourceClass().equals(DensityMapBuilder.class)) {
        @SuppressWarnings("unchecked") var buttonPane = DensityMapUI.createButtonPane(qupath, qupath.imageDataProperty(), (ObjectExpression<DensityMapBuilder>) selectedResource, classifierName, Bindings.createObjectBinding(() -> overlay), false);
        PaneTools.addGridRow(pane, row++, 0, null, buttonPane, buttonPane, buttonPane);
        PaneTools.setToExpandGridPaneWidth(buttonPane);
    }
    // Handle drag and drop
    pane.setOnDragOver(e -> {
        e.acceptTransferModes(TransferMode.COPY);
        e.consume();
    });
    pane.setOnDragDropped(e -> {
        logger.trace("File(s) dragged onto pane");
        Dragboard dragboard = e.getDragboard();
        if (dragboard.hasFiles()) {
            try {
                addExternalJson(dragboard.getFiles(), resourceType.getManager(qupath.getProject()), extras);
                updateAvailableItems(comboClassifiers.getItems());
            } catch (Exception ex) {
                Dialogs.showErrorMessage(title, ex);
            }
        }
    });
    var stage = new Stage();
    stage.setTitle(title);
    stage.setScene(new Scene(pane));
    stage.initOwner(qupath.getStage());
    stage.sizeToScene();
    stage.setResizable(false);
    stage.show();
    stage.setOnHiding(e -> {
        if (overlay != null)
            overlay.stop();
        logger.debug("Resetting overlay");
        for (var viewer : qupath.getViewers()) {
            if (viewer.getCustomPixelLayerOverlay() == overlay)
                viewer.resetCustomPixelLayerOverlay();
        }
    });
    stage.focusedProperty().addListener((v, o, n) -> {
        if (n && overlay != null) {
            for (var viewer : qupath.getViewers()) viewer.setCustomPixelLayerOverlay(overlay);
        }
        // Make sure we have all the servers we need - but don't reset existing ones
        updateServers(selectedResource.get(), cachedServers);
    });
    overlay.setLivePrediction(true);
}