Download models

build.gradle

@@ -49,6 +49,7 @@ dependencies {
     shadow libs.qupath.fxtras
     shadow libs.bioimageio.spec
     shadow libs.deepJavaLibrary
+    shadow libs.commonmark
 
     implementation 'io.github.qupath:qupath-extension-djl:0.3.0'
 

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

@@ -28,9 +28,9 @@ private DetectionMeasurer(Collection<ObjectMeasurements.Compartments> compartmen
                               Collection<ObjectMeasurements.ShapeFeatures> shapeFeatures,
                               double downsample) {
         this.shapeFeatures = shapeFeatures;
-        this.downsample = downsample;
         this.compartments = compartments;
         this.measurements = measurements;
+        this.downsample = downsample;
     }
 
     /**
@@ -93,15 +93,15 @@ public static class Builder {
                 .filter(m -> m != ObjectMeasurements.Measurements.VARIANCE) // Skip variance - we have standard deviation
                 .toList();
         private Collection<ObjectMeasurements.ShapeFeatures> shapeFeatures = Arrays.asList(ObjectMeasurements.ShapeFeatures.values());
-        private double pixelSize;
+        private double downsample;
 
         /**
-         * Set the pixel size that measurements should be made at.
-         * @param pixelSize The pixel size that detections/annotations/etc were made at.
-         * @return A modified builder.
+         * Set the desired downsample.
+         * @param downsample
+         * @return
          */
-        public Builder pixelSize(double pixelSize) {
-            this.pixelSize = pixelSize;
+        public Builder downsample(double downsample) {
+            this.downsample = downsample;
             return this;
         }
 
@@ -140,7 +140,7 @@ public Builder shapeFeatures(Collection<ObjectMeasurements.ShapeFeatures> shapeF
          * @return An immutable detection measurer.
          */
         public DetectionMeasurer build() {
-            return new DetectionMeasurer(compartments, measurements, shapeFeatures, pixelSize);
+            return new DetectionMeasurer(compartments, measurements, shapeFeatures, downsample);
         }
     }
 }

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

@@ -31,6 +31,7 @@
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.List;
+import java.util.Optional;
 import java.util.concurrent.ArrayBlockingQueue;
 import java.util.concurrent.BlockingQueue;
 import java.util.stream.IntStream;
@@ -126,7 +127,7 @@ public static Builder builder() {
     public void makeMeasurements(ImageData<BufferedImage> imageData, Collection<? extends PathObject> detections) {
         double downsample = model.getPreferredDownsample(imageData.getServer().getPixelCalibration());
         DetectionMeasurer.builder()
-                .pixelSize(downsample)
+                .downsample(downsample)
                 .build()
                 .makeMeasurements(imageData, detections);
     }
@@ -135,8 +136,11 @@ private InstanSegResults runInstanSeg(Collection<? extends PathObject> pathObjec
 
         long startTime = System.currentTimeMillis();
 
-        Path modelPath;
-        modelPath = model.getPath().resolve("instanseg.pt");
+        Optional<Path> oModelPath = model.getPath();
+        if (!oModelPath.isPresent()) {
+            return new InstanSegResults(0, 0, 0, 0, 0);
+        }
+        Path modelPath = oModelPath.get().resolve("instanseg.pt");
         int nPredictors = 1; // todo: change me?
 
         // Optionally pad images so that every tile has the required size.
@@ -506,15 +510,6 @@ public Builder modelPath(String path) throws IOException {
             return modelPath(Path.of(path));
         }
 
-        /**
-         * Set the specific model to be used
-         * @param name The name of a built-in model
-         * @return A modified builder
-         */
-        public Builder modelName(String name) {
-            return model(InstanSegModel.fromName(name));
-        }
-
         /**
          * Set the device to be used
          * @param deviceName The name of the device to be used (eg, "gpu", "mps").