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NicoKiaruNicoKiaru
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first working version
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‎src/main/java/qupath/ext/biop/abba/ABBAExtension.java‎

Lines changed: 14 additions & 4 deletions
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@@ -3,29 +3,39 @@
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import qupath.lib.common.Version;
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import qupath.lib.gui.ActionTools;
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import qupath.lib.gui.QuPathGUI;
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import qupath.lib.gui.extensions.GitHubProject;
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import qupath.lib.gui.extensions.QuPathExtension;
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import qupath.lib.gui.tools.MenuTools;
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/**
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* Install Warpy as an extension.
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* Install ABBA extension as an extension.
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* <p>
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* Installs Warpy into QuPath, adding some metadata and adds the necessary global variables to QuPath's Preferences
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* Installs ABBA extension into QuPath, adding some metadata and adds the necessary global variables to QuPath's Preferences
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*
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* @author Nicolas Chiaruttini
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*/
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public class ABBAExtension implements QuPathExtension, GitHubProject {
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private final static Logger logger = LoggerFactory.getLogger(ABBAExtension.class);
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@Override
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public GitHubRepo getRepository() {
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return GitHubRepo.create("QuPath ABBA Extension", "biop", "qupath-extension-abba");
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}
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private static boolean alreadyInstalled = false;
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@Override
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public void installExtension(QuPathGUI qupath) {
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if (alreadyInstalled)
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return;
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alreadyInstalled = true;
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var actionLoadAtlasRois = ActionTools.createAction(new LoadAtlasRoisToQuPathCommand(qupath), "Load Atlas Annotations into Open Image");
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MenuTools.addMenuItems(qupath.getMenu("Extensions", false),
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MenuTools.createMenu("ABBA",actionLoadAtlasRois)
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);
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}
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@Override

‎src/main/java/qupath/ext/biop/abba/AtlasTools.java‎

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package qupath.ext.biop.abba;
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import ij.gui.Roi;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import qupath.ext.biop.abba.struct.AtlasHelper;
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import qupath.ext.biop.abba.struct.AtlasNode;
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import qupath.ext.biop.abba.struct.AtlasOntology;
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import qupath.imagej.tools.IJTools;
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import qupath.lib.common.ColorTools;
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import qupath.lib.gui.QuPathGUI;
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import qupath.lib.images.ImageData;
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import qupath.lib.images.servers.ImageServer;
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import qupath.lib.images.servers.RotatedImageServer;
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import qupath.lib.measurements.MeasurementList;
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import qupath.lib.measurements.MeasurementListFactory;
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import qupath.lib.objects.PathObject;
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import qupath.lib.objects.PathObjectTools;
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import qupath.lib.objects.PathObjects;
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import qupath.lib.projects.Project;
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import qupath.lib.projects.ProjectImageEntry;
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import qupath.lib.projects.Projects;
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import qupath.lib.roi.RoiTools;
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import qupath.lib.roi.interfaces.ROI;
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import qupath.lib.scripting.QP;
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import java.awt.*;
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import java.awt.geom.AffineTransform;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.nio.file.Paths;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Map;
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import java.util.concurrent.atomic.AtomicReference;
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import java.util.stream.Collectors;
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public class AtlasTools {
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final static Logger logger = LoggerFactory.getLogger(AtlasTools.class);
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private static QuPathGUI qupath = QuPathGUI.getInstance();
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private static String title = "Load ABBA RoiSets from current QuPath project";
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static private PathObject createAnnotationHierarchy(List<PathObject> annotations) {
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// Map the ID of the annotation to ease finding parents
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Map<Integer, PathObject> mappedAnnotations =
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annotations
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.stream()
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.collect(
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Collectors.toMap(e -> (int) (e.getMeasurementList().getMeasurementValue("ID")), e -> e)
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);
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AtomicReference<PathObject> rootReference = new AtomicReference<>();
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mappedAnnotations.forEach((id, annotation) -> {
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PathObject parent = mappedAnnotations.get((int) annotation.getMeasurementList().getMeasurementValue("Parent ID"));
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if (parent != null) {
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parent.addPathObject(annotation);
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} else {
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// Found the root Path Object
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rootReference.set(annotation);
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}
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});
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// Return just the root annotation from the atlas
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return rootReference.get();
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}
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static PathObject getWarpedAtlasRegions(ImageData imageData, String atlasName, boolean splitLeftRight) {
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List<PathObject> annotations = getFlattenedWarpedAtlasRegions(imageData, atlasName, splitLeftRight); // TODO
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if (splitLeftRight) {
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List<PathObject> annotationsLeft = annotations
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.stream()
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.filter(po -> po.getPathClass().isDerivedFrom(QP.getPathClass("Left")))
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.collect(Collectors.toList());
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List<PathObject> annotationsRight = annotations
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.stream()
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.filter(po -> po.getPathClass().isDerivedFrom(QP.getPathClass("Right")))
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.collect(Collectors.toList());
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PathObject rootLeft = createAnnotationHierarchy(annotationsLeft);
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PathObject rootRight = createAnnotationHierarchy(annotationsRight);
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ROI rootFused = RoiTools.combineROIs(rootLeft.getROI(), rootRight.getROI(), RoiTools.CombineOp.ADD);
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PathObject rootObject = PathObjects.createAnnotationObject(rootFused);
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rootObject.setName("Root");
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rootObject.addPathObject(rootLeft);
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rootObject.addPathObject(rootRight);
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return rootObject; // TODO
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} else {
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return createAnnotationHierarchy(annotations);
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}
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}
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public static List<PathObject> getFlattenedWarpedAtlasRegions(ImageData imageData, String atlasName, boolean splitLeftRight) {
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Project project = qupath.getProject();
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// Get the project folder and get the ontology
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Path ontologyPath = Paths.get(Projects.getBaseDirectory(project).getAbsolutePath(), atlasName+"-Ontology.json");
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AtlasOntology ontology = AtlasHelper.openOntologyFromJsonFile(ontologyPath.toString());
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// Loop through each ImageEntry
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ProjectImageEntry entry = project.getEntry(imageData);
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Path roisetPath = Paths.get(entry.getEntryPath().toString(), "ABBA-Roiset-"+atlasName+".zip");
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if (!Files.exists(roisetPath)) {
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logger.info("No RoiSets found in {}", roisetPath);
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return null;
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}
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// Get all the ROIs and add them as PathAnnotations
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List<Roi> rois = RoiSetLoader.openRoiSet(roisetPath.toAbsolutePath().toFile());
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logger.info("Loading {} Atlas Regions for {}", rois.size(), entry.getImageName());
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Roi left = rois.get(rois.size() - 2);
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Roi right = rois.get(rois.size() - 1);
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rois.remove(left);
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rois.remove(right);
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// Rotation for rotated servers
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ImageServer<?> server = imageData.getServer();
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AffineTransform transform = null;
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if (server instanceof RotatedImageServer) {
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// The roi will need to be transformed before being imported
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// First : get the rotation
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RotatedImageServer ris = (RotatedImageServer) server;
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switch (ris.getRotation()) {
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case ROTATE_NONE: // No rotation.
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break;
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case ROTATE_90: // Rotate 90 degrees clockwise.
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transform = AffineTransform.getRotateInstance(Math.PI/2.0);
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transform.translate(0, -server.getWidth());
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break;
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case ROTATE_180: // Rotate 180 degrees.
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transform = AffineTransform.getRotateInstance(Math.PI);
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transform.translate(-server.getWidth(), -server.getHeight());
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break;
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case ROTATE_270: // Rotate 270 degrees
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transform = AffineTransform.getRotateInstance(Math.PI*3.0/2.0);
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transform.translate(-server.getHeight(), 0);
149+
break;
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default:
151+
System.err.println("Unknow rotation for rotated image server: "+ris.getRotation());
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}
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}
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AffineTransform finalTransform = transform;
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List<PathObject> annotations = rois.stream().map(roi -> {
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// Create the PathObject
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//PathObject object = IJTools.convertToAnnotation( imp, imageData.getServer(), roi, 1, null );
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PathObject object = PathObjects.createAnnotationObject(IJTools.convertToROI(roi, 0, 0, 1, null));
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// Handles rotated image server
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if (finalTransform !=null) {
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object = PathObjectTools.transformObject(object, finalTransform, true);
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}
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// Add metadata to object as acquired from the Ontology
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int object_id = Integer.parseInt(roi.getName());
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// Get associated information
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AtlasNode node = ontology.getNodeFromId(object_id);
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String name = node.data().get(ontology.getNamingProperty());
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System.out.println("node:"+node.getId()+":"+name);
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object.setName(name);
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object.getMeasurementList().putMeasurement("ID", node.getId());
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if (node.parent()!=null) {
177+
object.getMeasurementList().putMeasurement("Parent ID", node.parent().getId());
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}
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object.getMeasurementList().putMeasurement("Side", 0);
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object.setPathClass(QP.getPathClass(name));
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object.setLocked(true);
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int[] rgba = node.getColor();
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int color = ColorTools.packRGB(rgba[0], rgba[1], rgba[2]);
184+
object.setColorRGB(color);
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return object;
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}).collect(Collectors.toList());
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if (splitLeftRight) {
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ROI leftROI = IJTools.convertToROI(left, 0, 0, 1, null);
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ROI rightROI = IJTools.convertToROI(right, 0, 0, 1, null);
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List<PathObject> splitObjects = new ArrayList<>();
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for (PathObject annotation : annotations) {
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ROI shapeLeft = RoiTools.combineROIs(leftROI, annotation.getROI(), RoiTools.CombineOp.INTERSECT);
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if (!shapeLeft.isEmpty()) {
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PathObject objectLeft = PathObjects.createAnnotationObject(shapeLeft, annotation.getPathClass(), duplicateMeasurements(annotation.getMeasurementList()));
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objectLeft.setName(annotation.getName());
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objectLeft.setPathClass(QP.getDerivedPathClass(QP.getPathClass("Left"), annotation.getPathClass().getName()));
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objectLeft.setColorRGB(annotation.getColorRGB());
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objectLeft.setLocked(true);
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splitObjects.add(objectLeft);
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}
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ROI shapeRight = RoiTools.combineROIs(rightROI, annotation.getROI(), RoiTools.CombineOp.INTERSECT);
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if (!shapeRight.isEmpty()) {
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PathObject objectRight = PathObjects.createAnnotationObject(shapeRight, annotation.getPathClass(), duplicateMeasurements(annotation.getMeasurementList()));
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objectRight.setName(annotation.getName());
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objectRight.setPathClass(QP.getDerivedPathClass(QP.getPathClass("Right"), annotation.getPathClass().getName()));
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objectRight.setColorRGB(annotation.getColorRGB());
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objectRight.setLocked(true);
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splitObjects.add(objectRight);
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}
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}
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return splitObjects;
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} else {
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return annotations;
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}
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}
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public static void loadWarpedAtlasAnnotations(ImageData imageData, String atlasName, boolean splitLeftRight) {
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imageData.getHierarchy().addPathObject(getWarpedAtlasRegions(imageData, atlasName, splitLeftRight));
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imageData.getHierarchy().fireHierarchyChangedEvent(AtlasTools.class);
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}
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private static MeasurementList duplicateMeasurements(MeasurementList measurements) {
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MeasurementList list = MeasurementListFactory.createMeasurementList(measurements.size(), MeasurementList.MeasurementListType.GENERAL);
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228+
for (int i = 0; i < measurements.size(); i++) {
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String name = measurements.getMeasurementName(i);
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double value = measurements.getMeasurementValue(i);
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list.addMeasurement(name, value);
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}
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return list;
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}
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}

‎src/main/java/qupath/ext/biop/abba/Dummy.java‎

Lines changed: 0 additions & 8 deletions
This file was deleted.

‎src/main/java/qupath/ext/biop/abba/LoadAtlasRoisToQuPathCommand.java‎

Lines changed: 49 additions & 0 deletions
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package qupath.ext.biop.abba;
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3+
import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import qupath.lib.display.ImageDisplay;
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import qupath.lib.gui.QuPathGUI;
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import qupath.lib.gui.dialogs.Dialogs;
8+
import qupath.lib.images.ImageData;
9+
10+
public class LoadAtlasRoisToQuPathCommand implements Runnable {
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private static QuPathGUI qupath;
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private boolean splitLeftRight;
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private boolean doRun;
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public LoadAtlasRoisToQuPathCommand( final QuPathGUI qupath) {
18+
this.qupath = qupath;
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}
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public void run() {
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String splitMode =
24+
Dialogs.showChoiceDialog("Load Brain RoiSets into Image",
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"This will load any RoiSets Exported using the ABBA tool onto the current image.\nContinue?", new String[]{"Split Left and Right Regions", "Do not split"}, "Do not split");
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switch (splitMode) {
28+
case "Do not split" :
29+
splitLeftRight = false;
30+
doRun = true;
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break;
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case "Split Left and Right Regions" :
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splitLeftRight = true;
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doRun = true;
35+
break;
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default:
37+
// null returned -> cancelled
38+
doRun = false;
39+
return;
40+
}
41+
if (doRun) {
42+
ImageData imageData = qupath.getImageData();
43+
// TODO : Find atlas name
44+
AtlasTools.loadWarpedAtlasAnnotations(imageData, "Adult Mouse Brain - Allen Brain Atlas V3", splitLeftRight);
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System.out.println("Import DONE");
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}
47+
}
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}

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