Pass optional arguments

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

@@ -5,6 +5,7 @@
 import ai.djl.ndarray.BaseNDManager;
 import ai.djl.repository.zoo.Criteria;
 import ai.djl.training.util.ProgressBar;
+import java.util.HashMap;
 import org.bytedeco.opencv.global.opencv_core;
 import org.bytedeco.opencv.opencv_core.Mat;
 import org.slf4j.Logger;
@@ -37,6 +38,7 @@
 import java.util.Collection;
 import java.util.Collections;
 import java.util.List;
+import java.util.Map;
 import java.util.Objects;
 import java.util.Optional;
 import java.util.concurrent.ArrayBlockingQueue;
@@ -57,11 +59,19 @@ public class InstanSeg {
     private final Device device;
     private final TaskRunner taskRunner;
     private final Class<? extends PathObject> preferredOutputClass;
+    private final Map<String, Object> optionalArgs;
 
     // This was previously an adjustable parameter, but it's now fixed at 1 because we handle overlaps differently.
     // However we might want to reinstate it, possibly as a proportion of the padding amount.
     private final int boundaryThreshold = 1;
 
+    /**
+     * Run inference for the currently selected PathObjects in the current image.
+     */
+    public InstanSegResults detectObjects() {
+        return detectObjects(QP.getCurrentImageData());
+    }
+
     private InstanSeg(Builder builder) {
         this.tileDims = builder.tileDims;
         this.downsample = builder.downsample; // Optional... and not advised (use the model spec instead); set <= 0 to ignore
@@ -74,13 +84,7 @@ private InstanSeg(Builder builder) {
         this.preferredOutputClass = builder.preferredOutputClass;
         this.randomColors = builder.randomColors;
         this.makeMeasurements = builder.makeMeasurements;
-    }
-
-    /**
-     * Run inference for the currently selected PathObjects in the current image.
-     */
-    public InstanSegResults detectObjects() {
-        return detectObjects(QP.getCurrentImageData());
+        this.optionalArgs = builder.optionalArgs;
     }
 
     /**
@@ -215,7 +219,7 @@ private InstanSegResults runInstanSeg(ImageData<BufferedImage> imageData, Collec
                 .optModelUrls(String.valueOf(modelPath.toUri()))
                 .optProgress(new ProgressBar())
                 .optDevice(device) // Remove this line if devices are problematic!
-                .optTranslator(new MatTranslator(layout, layoutOutput, outputChannelArray))
+                .optTranslator(new MatTranslator(layout, layoutOutput, outputChannelArray, optionalArgs))
                 .build()
                 .loadModel()) {
 
@@ -392,6 +396,7 @@ public static final class Builder {
         private Collection<? extends ColorTransforms.ColorTransform> channels;
         private InstanSegModel model;
         private Class<? extends PathObject> preferredOutputClass;
+        private final Map<String, Object> optionalArgs = new HashMap<>();
 
         Builder() {}
 
@@ -653,6 +658,27 @@ public Builder outputAnnotations() {
             return this;
         }
 
+        /**
+         * Set a number of optional arguments
+         * @param optionalArgs The argument names and values.
+         * @return A modified builder.
+         */
+        public Builder args(Map<String, Object> optionalArgs) {
+            this.optionalArgs.putAll(optionalArgs);
+            return this;
+        }
+
+        /**
+         * Set a number of optional arguments
+         * @param name The argument name.
+         * @param value The argument value.
+         * @return A modified builder.
+         */
+        public Builder arg(String name, Object value) {
+            optionalArgs.put(name, value);
+            return this;
+        }
+
         /**
          * Request to make measurements from the objects created by InstanSeg.
          * @return this builder

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

@@ -1,9 +1,15 @@
 package qupath.ext.instanseg.core;
 
 import ai.djl.Device;
+import ai.djl.ndarray.NDArray;
 import ai.djl.ndarray.NDList;
+import ai.djl.ndarray.NDManager;
 import ai.djl.translate.Translator;
 import ai.djl.translate.TranslatorContext;
+import java.math.BigDecimal;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
 import org.bytedeco.opencv.opencv_core.Mat;
 import qupath.ext.djl.DjlTools;
 
@@ -15,6 +21,7 @@ class MatTranslator implements Translator<Mat, Mat> {
     private final String inputLayoutNd;
     private final String outputLayoutNd;
     private final int[] outputChannels;
+    private final Map<String, Object> optionalArgs;
 
     /**
      * Create a translator from InstanSeg input to output.
@@ -23,10 +30,11 @@ class MatTranslator implements Translator<Mat, Mat> {
      * @param outputChannels Array of channels to output; if null or empty, output all channels.
      *                       Values should be true for channels to output, false for channels to ignore.
      */
-    MatTranslator(String inputLayoutNd, String outputLayoutNd, boolean[] outputChannels) {
+    MatTranslator(String inputLayoutNd, String outputLayoutNd, boolean[] outputChannels, Map<String, Object> optionalArgs) {
         this.inputLayoutNd = inputLayoutNd;
         this.outputLayoutNd = outputLayoutNd;
         this.outputChannels = convertBooleanArray(outputChannels);
+        this.optionalArgs = optionalArgs;
     }
 
     private static int[] convertBooleanArray(boolean[] array) {
@@ -55,9 +63,24 @@ public NDList processInput(TranslatorContext ctx, Mat input) {
             var arrayCPU = array.toDevice(Device.cpu(), false);
             out.add(arrayCPU);
         }
+        List<NDArray> args = sanitizeOptionalArgs(optionalArgs, manager);
+        out.addAll(args);
         return out;
     }
 
+    private static List<NDArray> sanitizeOptionalArgs(Map<String, Object> optionalArgs, NDManager manager) {
+        List<NDArray> arrays = new ArrayList<>();
+        for (var es : optionalArgs.entrySet()) {
+            var val = es.getValue();
+            if (val instanceof Double || val instanceof BigDecimal) {
+                NDArray array = manager.create(((Number) val).floatValue());
+                array.setName("args." + es.getKey());
+                arrays.add(array);
+            }
+        }
+        return arrays;
+    }
+
     @Override
     public Mat processOutput(TranslatorContext ctx, NDList list) {
         var array = list.getFirst();