Examples with PathObject qupath.lib.objects.PathObject used on opensource projects

Example 31 with PathObject

use of qupath.lib.objects.PathObject in project qupath by qupath.

the class PathObjectSelectionModel method setSelectedObjects.

/**
 * Specify a collection of objects to be selected, and which among them should be the primary.
 * <p>
 * Any previous selection is reset.
 *
 * @param pathObjects
 * @param primarySelectedObject
 */
public synchronized void setSelectedObjects(Collection<? extends PathObject> pathObjects, final PathObject primarySelectedObject) {
    if (pathObjects == null || pathObjects.isEmpty()) {
        clearSelection();
        return;
    }
    // Check if we have any changes to make
    if (pathObjectSelected == primarySelectedObject && selectedSet.size() == pathObjects.size() && selectedSet.containsAll(pathObjects))
        return;
    // Update selected objects
    PathObject previousSelected = pathObjectSelected;
    selectedSet.clear();
    selectedSet.addAll(pathObjects);
    // This shouldn't be needed... and yet it is?
    selectedSet.remove(null);
    // if (selectedObject == null) {
    // updateToLastSelectedObject();
    // } else
    pathObjectSelected = primarySelectedObject;
    firePathObjectSelectionChangedEvent(pathObjectSelected, previousSelected);
}

Example 32 with PathObject

use of qupath.lib.objects.PathObject in project qupath by qupath.

the class PathObjectSelectionModel method selectObjects.

/**
 * Ensure the specified objects are selected.
 * <p>
 * The selection state of other objects will not be modified.
 *
 * @param pathObjects
 */
public void selectObjects(Collection<? extends PathObject> pathObjects) {
    if (selectedSet.addAll(pathObjects)) {
        PathObject previousSelected = pathObjectSelected;
        if (previousSelected == null)
            updateToLastSelectedObject();
        firePathObjectSelectionChangedEvent(pathObjectSelected, previousSelected);
    }
}

Example 33 with PathObject

use of qupath.lib.objects.PathObject in project qupath by qupath.

the class PathObjectSelectionModel method setSelectedObject.

/**
 * Select the specified object to be the primary selected object, optionally retaining the
 * existing selected objects.
 *
 * @param pathObject
 * @param addToSelection add to the existing selection, rather than allowing only the specified object to be selected
 *
 * @see #setSelectedObject(PathObject)
 */
public void setSelectedObject(PathObject pathObject, boolean addToSelection) {
    if (!addToSelection) {
        setSelectedObject(pathObject);
        return;
    }
    if (pathObject == null)
        return;
    PathObject previousSelected = pathObjectSelected;
    selectedSet.add(pathObject);
    pathObjectSelected = pathObject;
    firePathObjectSelectionChangedEvent(pathObjectSelected, previousSelected);
}

Example 34 with PathObject

use of qupath.lib.objects.PathObject in project qupath by qupath.

the class AbstractPlugin method getTasks.

/**
 * Get a collection of tasks to perform.
 *
 * This will be called from {@link #runPlugin(PluginRunner, String)} <b>after</b> a call to {@link #parseArgument(ImageData, String)}.
 *
 * The default implementation simply calls {@link #getParentObjects(PluginRunner)}, then {@link #addRunnableTasks(ImageData, PathObject, List)}
 * for every parent object that was returned.
 *
 * @param runner
 * @return
 */
protected Collection<Runnable> getTasks(final PluginRunner<T> runner) {
    Collection<? extends PathObject> parentObjects = getParentObjects(runner);
    if (parentObjects == null || parentObjects.isEmpty())
        return Collections.emptyList();
    List<Runnable> tasks = new ArrayList<>(parentObjects.size());
    long startTime = System.currentTimeMillis();
    for (PathObject pathObject : parentObjects) {
        addRunnableTasks(runner.getImageData(), pathObject, tasks);
    }
    long endTime = System.currentTimeMillis();
    logger.debug("Time to add plugin tasks: {} ms", endTime - startTime);
    return tasks;
}

Example 35 with PathObject

use of qupath.lib.objects.PathObject in project qupath by qupath.

the class PathIO method exportObjectsAsGeoJSON.

/**
 * Export a collection of objects as a GeoJSON "FeatureCollection" to an output stream.
 * @param stream
 * @param pathObjects
 * @param options
 * @throws IOException
 */
public static void exportObjectsAsGeoJSON(OutputStream stream, Collection<? extends PathObject> pathObjects, GeoJsonExportOptions... options) throws IOException {
    Collection<GeoJsonExportOptions> optionList = Arrays.asList(options);
    // If exclude measurements, 'transform' each PathObject to get rid of measurements
    if (optionList.contains(GeoJsonExportOptions.EXCLUDE_MEASUREMENTS))
        pathObjects = pathObjects.stream().map(e -> PathObjectTools.transformObject(e, null, false)).collect(Collectors.toList());
    var writer = new OutputStreamWriter(new BufferedOutputStream(stream), StandardCharsets.UTF_8);
    var gson = GsonTools.getInstance(optionList.contains(GeoJsonExportOptions.PRETTY_JSON));
    if (optionList.contains(GeoJsonExportOptions.FEATURE_COLLECTION))
        gson.toJson(GsonTools.wrapFeatureCollection(pathObjects), writer);
    else if (pathObjects.size() == 1) {
        gson.toJson(pathObjects.iterator().next(), writer);
    } else {
        gson.toJson(pathObjects, new TypeToken<List<PathObject>>() {
        }.getType(), writer);
    }
    writer.flush();
}