Merge pull request #17 from petebankhead/cell-objects

Support cell object creation

build.gradle

@@ -20,7 +20,7 @@ base {
 
 ext.qupathVersion = gradle.ext.qupathVersion
 
-// Should be Java 17 for QuPath v0.5.0
+// Should be Java 21 for QuPath v0.6.0
 ext.qupathJavaVersion = 21
 
 /**

settings.gradle

@@ -4,12 +4,12 @@ pluginManagement {
         // Specifying it here, rather than build.gradle, makes it possible
         // to include the extension as a subproject of QuPath itself
         // (which is useful during development)
-        id 'org.bytedeco.gradle-javacpp-platform' version '1.5.9'
+        id 'org.bytedeco.gradle-javacpp-platform' version '1.5.10'
     }
 }
 
 rootProject.name = 'qupath-extension-instanseg'
-gradle.ext.qupathVersion = "0.6.0"
+gradle.ext.qupathVersion = "0.6.0-SNAPSHOT"
 
 dependencyResolutionManagement {
 

src/main/java/qupath/ext/instanseg/core/InstanSegTask.java

@@ -30,7 +30,9 @@
 import static qupath.lib.gui.scripting.QPEx.createTaskRunner;
 
 public class InstanSegTask extends Task<Void> {
+
     private static final Logger logger = LoggerFactory.getLogger(InstanSegTask.class);
+
     private final int tileSize, nThreads;
     private final List<ColorTransforms.ColorTransform> channels;
     private final double downsample;

src/main/java/qupath/ext/instanseg/core/InstanSegUtils.java

@@ -16,6 +16,7 @@
 import java.util.List;
 
 public class InstanSegUtils {
+
     private static final Logger logger = LoggerFactory.getLogger(InstanSegUtils.class);
 
     private InstanSegUtils() {

src/main/java/qupath/ext/instanseg/core/OutputToObjectConverter.java

@@ -2,43 +2,64 @@
 
 import org.bytedeco.opencv.opencv_core.Mat;
 import org.locationtech.jts.geom.Envelope;
-import qupath.lib.experimental.pixels.OpenCVProcessor;
+import qupath.lib.analysis.images.ContourTracing;
 import qupath.lib.experimental.pixels.OutputHandler;
 import qupath.lib.experimental.pixels.Parameters;
 import qupath.lib.experimental.pixels.PixelProcessorUtils;
 import qupath.lib.objects.PathObject;
-import qupath.lib.objects.classes.PathClass;
+import qupath.lib.objects.PathObjects;
 import qupath.lib.roi.GeometryTools;
-import qupath.lib.scripting.QP;
+import qupath.lib.roi.interfaces.ROI;
 import qupath.opencv.tools.OpenCVTools;
 
 import java.util.ArrayList;
 import java.util.List;
-import java.util.stream.IntStream;
+import java.util.Map;
+import java.util.Random;
+import java.util.stream.Collectors;
 
 class OutputToObjectConverter implements OutputHandler.OutputToObjectConverter<Mat, Mat, Mat> {
 
-    private final OutputHandler.OutputToObjectConverter<Mat, Mat, Mat> converter = OpenCVProcessor.createDetectionConverter();
+    private static long seed = 1243;
 
     @Override
-    public List<PathObject> convertToObjects(Parameters<Mat, Mat> params, Mat output) {
-        List<PathObject> detections = new ArrayList<>();
-        var channels = OpenCVTools.splitChannels(output);
-        IntStream.range(0, channels.size()).parallel().forEach(
-                i -> {
-                    List<PathObject> pathObjects = converter.convertToObjects(params, channels.get(i));
-                    PathClass pathClass = switch(i) {
-                        case 0 -> QP.getPathClass("Nucleus3", QP.makeRGB(200, 70, 70));
-                        case 1 -> QP.getPathClass("Cell5", QP.makeRGB(90, 220, 90));
-                        default -> throw new IllegalArgumentException("Dunno what to make of channel " + i);
-                    };
-                    for (var p: pathObjects) {
-                        p.setPathClass(pathClass);
-                    }
-                    detections.addAll(pathObjects);
-                }
-        );
-        return detections;
+    public List<PathObject> convertToObjects(Parameters params, Mat output) {
+        int nChannels = output.channels();
+        if (nChannels < 1 || nChannels > 2)
+            throw new IllegalArgumentException("Expected 1 or 2 channels, but found " + nChannels);
+
+        List<Map<Number, ROI>> roiMaps = new ArrayList<>();
+        for (var mat : OpenCVTools.splitChannels(output)) {
+            var image = OpenCVTools.matToSimpleImage(mat, 0);
+            roiMaps.add(
+                    ContourTracing.createROIs(image, params.getRegionRequest(), 1, -1)
+            );
+        }
+        if (roiMaps.size() == 1) {
+            // One-channel detected, represent using detection objects
+            return roiMaps.get(0).values().stream()
+                    .map(roi -> PathObjects.createDetectionObject(roi))
+                    .collect(Collectors.toList());
+        } else {
+            // Two channels detected, represent using cell objects
+            // We assume that the labels are matched - and we can't have a nucleus without a cell
+            Map<Number, ROI> nucleusROIs = roiMaps.get(0);
+            Map<Number, ROI> cellROIs = roiMaps.get(1);
+            List<PathObject> cells = new ArrayList<>();
+            var rng = new Random(seed);
+            for (var entry : cellROIs.entrySet()) {
+                var cell = entry.getValue();
+                var nucleus = nucleusROIs.getOrDefault(entry.getKey(), null);
+                var cellObject = PathObjects.createCellObject(cell, nucleus);
+                cellObject.setColor(
+                        rng.nextInt(255),
+                        rng.nextInt(255),
+                        rng.nextInt(255)
+                );
+                cells.add(cellObject);
+            }
+            return cells;
+        }
     }
 
     static class PruneObjectOutputHandler<S, T, U> implements OutputHandler<S, T, U> {
@@ -66,7 +87,7 @@ public boolean handleOutput(Parameters<S, T> params, U output) {
                 parentOrProxy.clearChildObjects();
 
                 // remove features within N pixels of the region request boundaries
-                var regionRequest = GeometryTools.createRectangle(
+                var bounds = GeometryTools.createRectangle(
                         params.getRegionRequest().getX(), params.getRegionRequest().getY(),
                         params.getRegionRequest().getWidth(), params.getRegionRequest().getHeight());
 
@@ -76,7 +97,7 @@ public boolean handleOutput(Parameters<S, T> params, U output) {
                 // QP.addObject(PathObjects.createAnnotationObject(GeometryTools.geometryToROI(regionRequest, ImagePlane.getPlane(0,0))));
 
                 newObjects = newObjects.parallelStream()
-                        .filter(p -> doesntTouchBoundaries(p.getROI().getGeometry().getEnvelopeInternal(), regionRequest.getEnvelopeInternal(), boundaryThreshold, maxX, maxY))
+                        .filter(p -> doesntTouchBoundaries(p.getROI().getGeometry().getEnvelopeInternal(), bounds.getEnvelopeInternal(), boundaryThreshold, maxX, maxY))
                         .toList();
 
                 if (!newObjects.isEmpty()) {

src/main/java/qupath/ext/instanseg/ui/MessageTextHelper.java

@@ -20,7 +20,6 @@
 
 import java.awt.image.BufferedImage;
 import java.util.Collection;
-import java.util.List;
 import java.util.ResourceBundle;
 
 /**

src/main/java/qupath/ext/instanseg/ui/PytorchManager.java

@@ -1,19 +1,3 @@
-/**
- * Copyright 2023 University of Edinburgh
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
 package qupath.ext.instanseg.ui;
 
 import ai.djl.engine.Engine;