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Fix ROI conversion from instance segmentation mask #42

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Merged
petebankhead merged 2 commits into from
Nov 11, 2025
Merged

Fix ROI conversion from instance segmentation mask #42

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329f6ca
Fix ROI conversion from instance segmentation mask
ajay1685 Nov 6, 2025
9af2196
Update version, minor format change
petebankhead Nov 11, 2025
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2 changes: 1 addition & 1 deletion build.gradle.kts
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ plugins {

qupathExtension {
name = "qupath-extension-djl"
version = "0.4.0"
version = "0.4.1-SNAPSHOT"
group = "io.github.qupath"
description = "QuPath extension to use Deep Java Library"
automaticModule = "qupath.extension.djl"
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102 changes: 53 additions & 49 deletions src/main/java/qupath/ext/djl/DjlZoo.java
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Original file line number Diff line number Diff line change
Expand Up @@ -16,32 +16,6 @@

package qupath.ext.djl;

import java.awt.image.BandedSampleModel;
import java.awt.image.BufferedImage;
import java.awt.image.DataBufferFloat;
import java.awt.image.WritableRaster;
import java.io.IOException;
import java.lang.reflect.Type;
import java.net.URI;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import java.util.UUID;
import java.util.concurrent.ConcurrentHashMap;
import java.util.function.Function;
import java.util.stream.Collectors;

import ai.djl.repository.MRL;
import org.locationtech.jts.geom.util.AffineTransformation;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import ai.djl.Application;
import ai.djl.MalformedModelException;
import ai.djl.Model;
Expand All @@ -55,13 +29,14 @@
import ai.djl.modality.cv.output.DetectedObjects;
import ai.djl.modality.cv.output.DetectedObjects.DetectedObject;
import ai.djl.modality.cv.output.Joints;
import ai.djl.ndarray.NDList;
import ai.djl.ndarray.types.LayoutType;
import ai.djl.ndarray.types.Shape;
import ai.djl.modality.cv.output.Landmark;
import ai.djl.modality.cv.output.Mask;
import ai.djl.modality.cv.translator.BigGANTranslator;
import ai.djl.ndarray.NDList;
import ai.djl.ndarray.types.LayoutType;
import ai.djl.ndarray.types.Shape;
import ai.djl.repository.Artifact;
import ai.djl.repository.MRL;
import ai.djl.repository.zoo.Criteria;
import ai.djl.repository.zoo.ModelNotFoundException;
import ai.djl.repository.zoo.ModelZoo;
Expand All @@ -72,6 +47,9 @@
import ai.djl.util.ClassLoaderUtils;
import ai.djl.util.Pair;
import ai.djl.util.PairList;
import org.locationtech.jts.geom.util.AffineTransformation;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import qupath.lib.analysis.images.ContourTracing;
import qupath.lib.analysis.images.SimpleImage;
import qupath.lib.geom.Point2;
Expand All @@ -95,6 +73,27 @@
import qupath.lib.roi.RoiTools;
import qupath.lib.roi.interfaces.ROI;

import java.awt.image.BandedSampleModel;
import java.awt.image.BufferedImage;
import java.awt.image.DataBufferFloat;
import java.awt.image.WritableRaster;
import java.io.IOException;
import java.lang.reflect.Type;
import java.net.URI;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import java.util.UUID;
import java.util.concurrent.ConcurrentHashMap;
import java.util.function.Function;
import java.util.stream.Collectors;

/**
* Helper class for working with DeepJavaLibrary model zoos.
*
Expand Down Expand Up @@ -316,13 +315,13 @@ private static TranslatorFactory getTranslatorFactory(String factoryClass) {
* @return
*/
public static ROI createROI(DetectedObject obj, ImageRegion region) {
var box = obj.getBoundingBox();
if (box instanceof Mask) {
return createROI((Mask)box, region, 0.5);
} else if (box instanceof Landmark) {
return createROI((Landmark)box, region);
BoundingBox box = obj.getBoundingBox();
if (box instanceof Mask mask) {
return createROI(mask, region, 0.5);
} else if (box instanceof Landmark landmark) {
return createROI(landmark, region);
} else
return createROI((BoundingBox)box, region);
return createROI(box, region);
}

/**
Expand All @@ -335,17 +334,21 @@ public static ROI createROI(BoundingBox box, ImageRegion region) {
var bounds = box.getBounds();
double xo = 0.0;
double yo = 0.0;
double xScale = 1.0;
double yScale = 1.0;
var plane = ImagePlane.getDefaultPlane();
if (region != null) {
plane = region.getImagePlane();
xo = region.getMinX();
yo = region.getMinY();
xScale = region.getWidth();
yScale = region.getHeight();
}
return ROIs.createRectangleROI(
xo + bounds.getX() * region.getWidth(),
yo + bounds.getY() * region.getHeight(),
bounds.getWidth() * region.getWidth(),
bounds.getHeight() * region.getHeight(),
xo + bounds.getX() * xScale,
yo + bounds.getY() * yScale,
bounds.getWidth() * xScale,
bounds.getHeight() * yScale,
plane);
}

Expand All @@ -358,17 +361,16 @@ public static ROI createROI(BoundingBox box, ImageRegion region) {
*/
public static ROI createROI(Mask mask, ImageRegion region, double threshold) {
float[][] probs = mask.getProbDist();
int w = probs.length;
int h = probs[0].length;
int h = probs.length;
int w = probs[0].length;
var buffer = new DataBufferFloat(w * h, 1);
var sampleModel = new BandedSampleModel(buffer.getDataType(), w, h, 1);
var raster = WritableRaster.createWritableRaster(sampleModel, buffer, null);
for (int x = 0; x < w; x++) {
float[] col = probs[x];
for (int y = 0; y < h; y++) {
raster.setSample(x, y, 0, col[y]);
}
}
for (int y = 0; y < h; y++) {
for (int x = 0; x < w; x++) {
raster.setSample(x, y, 0, probs[y][x]);
}
}
if (region == null)
region = ImageRegion.createInstance(0, 0, w, h, 0, 0);
var geometry = ContourTracing.createTracedGeometry(raster, threshold, Double.POSITIVE_INFINITY, 0, null);
Expand All @@ -377,8 +379,10 @@ public static ROI createROI(Mask mask, ImageRegion region, double threshold) {

var transform = new AffineTransformation();
transform.scale(1.0/raster.getWidth(), 1.0/raster.getHeight());
transform.scale(bounds.getWidth(), bounds.getHeight());
transform.translate(bounds.getX(), bounds.getY());
if(!mask.isFullImageMask()) {
transform.scale(bounds.getWidth(), bounds.getHeight());
transform.translate(bounds.getX(), bounds.getY());
}
transform.scale(region.getWidth(), region.getHeight());
transform.translate(region.getX(), region.getY());

Expand Down