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src/main/java/qupath/ext/instanseg/core/InstansegOutputToObjectConverter.java
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| package qupath.ext.instanseg.core; | ||
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| import org.bytedeco.opencv.opencv_core.Mat; | ||
| import org.slf4j.Logger; | ||
| import org.slf4j.LoggerFactory; | ||
| import qupath.lib.analysis.images.ContourTracing; | ||
| import qupath.lib.common.ColorTools; | ||
| import qupath.lib.experimental.pixels.OutputHandler; | ||
| import qupath.lib.experimental.pixels.Parameters; | ||
| import qupath.lib.objects.PathAnnotationObject; | ||
| import qupath.lib.objects.PathCellObject; | ||
| import qupath.lib.objects.PathDetectionObject; | ||
| import qupath.lib.objects.PathObject; | ||
| import qupath.lib.objects.PathObjects; | ||
| import qupath.lib.roi.interfaces.ROI; | ||
| import qupath.opencv.tools.OpenCVTools; | ||
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| import java.util.ArrayList; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
| import java.util.Random; | ||
| import java.util.function.BiFunction; | ||
| import java.util.function.Function; | ||
| import java.util.stream.Collectors; | ||
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| class InstansegOutputToObjectConverter implements OutputHandler.OutputToObjectConverter<Mat, Mat, Mat> { | ||
| private static final Logger logger = LoggerFactory.getLogger(InstansegOutputToObjectConverter.class); | ||
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| private static final long seed = 1243; | ||
| private final List<Class<? extends PathObject>> classes; | ||
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| InstansegOutputToObjectConverter(List<Class<? extends PathObject>> outputClasses) { | ||
| this.classes = outputClasses; | ||
| } | ||
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| @Override | ||
| public List<PathObject> convertToObjects(Parameters<Mat, Mat> params, Mat output) { | ||
| if (output == null) { | ||
| return List.of(); | ||
| } | ||
| int nChannels = output.channels(); | ||
| if (nChannels < 1 || nChannels > 2) | ||
| throw new IllegalArgumentException("Expected 1 or 2 channels, but found " + nChannels); | ||
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| 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) | ||
| ); | ||
| } | ||
| var rng = new Random(seed); | ||
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| BiFunction<ROI, ROI, PathObject> function; | ||
| if (classes.size() == 1) { | ||
| function = getOneClassBiFunction(classes, rng); | ||
| } else { | ||
| // if of length 2, then can be: | ||
| // detection <- annotation, annotation <- annotation, detection <- detection | ||
| assert classes.size() == 2; | ||
| function = getTwoClassBiFunction(classes, rng); | ||
| } | ||
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| if (roiMaps.size() == 1) { | ||
| // One-channel detected, represent using detection objects | ||
| return roiMaps.get(0).values().stream() | ||
| .map(roi -> function.apply(roi, null)) | ||
| .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> childROIs = roiMaps.get(0); | ||
| Map<Number, ROI> parentROIs = roiMaps.get(1); | ||
| List<PathObject> cells = new ArrayList<>(); | ||
| for (var entry : parentROIs.entrySet()) { | ||
| var parent = entry.getValue(); | ||
| var child = childROIs.getOrDefault(entry.getKey(), null); | ||
| var outputObject = function.apply(parent, child); | ||
| cells.add(outputObject); | ||
| } | ||
| return cells; | ||
| } | ||
| } | ||
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| private static BiFunction<ROI, ROI, PathObject> getOneClassBiFunction(List<Class<? extends PathObject>> classes, Random rng) { | ||
| // if of length 1, can be | ||
| // cellObject (with or without nucleus), annotations, detections | ||
| if (classes.get(0) == PathAnnotationObject.class) { | ||
| return createObjectsFun(PathObjects::createAnnotationObject, PathObjects::createAnnotationObject, rng); | ||
| } else if (classes.get(0) == PathDetectionObject.class) { | ||
| return createObjectsFun(PathObjects::createDetectionObject, PathObjects::createDetectionObject, rng); | ||
| } else if (classes.get(0) == PathCellObject.class) { | ||
| return createCellFun(rng); | ||
| } else { | ||
| logger.warn("Unknown output {}, defaulting to cells", classes.get(0)); | ||
| return createCellFun(rng); | ||
| } | ||
| } | ||
|
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| private static BiFunction<ROI, ROI, PathObject> getTwoClassBiFunction(List<Class<? extends PathObject>> classes, Random rng) { | ||
| Function<ROI, PathObject> fun0, fun1; | ||
| var knownClasses = List.of(PathDetectionObject.class, PathAnnotationObject.class); | ||
| if (!knownClasses.contains(classes.get(0)) || !knownClasses.contains(classes.get(1))) { | ||
| logger.warn("Unknown combination of outputs {} <- {}, defaulting to cells", classes.get(0), classes.get(1)); | ||
| return createCellFun(rng); | ||
| } | ||
| if (classes.get(0) == PathDetectionObject.class) { | ||
| fun0 = PathObjects::createDetectionObject; | ||
| } else { | ||
| fun0 = PathObjects::createAnnotationObject; | ||
| } | ||
| if (classes.get(1) == PathDetectionObject.class) { | ||
| fun1 = PathObjects::createDetectionObject; | ||
| } else { | ||
| fun1 = PathObjects::createAnnotationObject; | ||
| } | ||
| return createObjectsFun(fun0, fun1, rng); | ||
| } | ||
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| private static BiFunction<ROI, ROI, PathObject> createCellFun(Random rng) { | ||
| return (parent, child) -> { | ||
| var cell = PathObjects.createCellObject(parent, child); | ||
| var color = ColorTools.packRGB(rng.nextInt(255), rng.nextInt(255), rng.nextInt(255)); | ||
| cell.setColor(color); | ||
| return cell; | ||
| }; | ||
| } | ||
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| private static BiFunction<ROI, ROI, PathObject> createObjectsFun(Function<ROI, PathObject> createParentFun, Function<ROI, PathObject> createChildFun, Random rng) { | ||
| return (parent, child) -> { | ||
| var parentObj = createParentFun.apply(parent); | ||
| var color = ColorTools.packRGB(rng.nextInt(255), rng.nextInt(255), rng.nextInt(255)); | ||
| parentObj.setColor(color); | ||
| if (child != null) { | ||
| var childObj = createChildFun.apply(child); | ||
| childObj.setColor(color); | ||
| parentObj.addChildObject(childObj); | ||
| } | ||
| return parentObj; | ||
| }; | ||
| } | ||
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| } |
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