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Add run API using a builder pattern. Part of this enables specification of the output classes, enabling users to output nested annotations, detections, or just cells (with or without nuclei). Enables the flexible selection of input channels with indices or names. Also mildly restructure code around the output converter/output handler.
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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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