Pass optional arguments

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

@@ -36,7 +36,9 @@
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
+import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.Objects;
 import java.util.Optional;
 import java.util.concurrent.ArrayBlockingQueue;
@@ -57,11 +59,13 @@ public class InstanSeg {
     private final Device device;
     private final TaskRunner taskRunner;
     private final Class<? extends PathObject> preferredOutputClass;
+    private final Map<String, Object> optionalArgs = new LinkedHashMap<>();
 
     // 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.
+    // However, we might want to reinstate it, possibly as a proportion of the padding amount.
     private final int boundaryThreshold = 1;
 
+
     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
@@ -74,6 +78,7 @@ private InstanSeg(Builder builder) {
         this.preferredOutputClass = builder.preferredOutputClass;
         this.randomColors = builder.randomColors;
         this.makeMeasurements = builder.makeMeasurements;
+        this.optionalArgs.putAll(builder.optionalArgs);
     }
 
     /**
@@ -215,7 +220,7 @@ 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 +397,7 @@ public static final class Builder {
         private Collection<? extends ColorTransforms.ColorTransform> channels;
         private InstanSegModel model;
         private Class<? extends PathObject> preferredOutputClass;
+        private Map<String, Object> optionalArgs;
 
         Builder() {}
 
@@ -653,6 +659,17 @@ 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, ?> optionalArgs) {
+            this.optionalArgs.putAll(optionalArgs);
+            return this;
+        }
+
+
         /**
          * Request to make measurements from the objects created by InstanSeg.
          * @return this builder

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

@@ -1,20 +1,29 @@
 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.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 import org.bytedeco.opencv.opencv_core.Mat;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import qupath.ext.djl.DjlTools;
 
-import java.util.Arrays;
-
 
 class MatTranslator implements Translator<Mat, Mat> {
+    private static final Logger logger = LoggerFactory.getLogger(MatTranslator.class);
 
     private final String inputLayoutNd;
     private final String outputLayoutNd;
     private final int[] outputChannels;
+    private final Map<String, Object> optionalArgs = new HashMap<>();
 
     /**
      * Create a translator from InstanSeg input to output.
@@ -23,10 +32,11 @@ 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, ?> optionalArgs) {
         this.inputLayoutNd = inputLayoutNd;
         this.outputLayoutNd = outputLayoutNd;
         this.outputChannels = convertBooleanArray(outputChannels);
+        this.optionalArgs.putAll(optionalArgs);
     }
 
     private static int[] convertBooleanArray(boolean[] array) {
@@ -55,9 +65,44 @@ 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, ?> optionalArgs, NDManager manager) {
+        List<NDArray> arrays = new ArrayList<>();
+        for (var es : optionalArgs.entrySet()) {
+            var val = es.getValue();
+            NDArray array = null;
+            switch (val) {
+                case NDArray ndarray -> array = ndarray;
+                case String s -> array = manager.create(s);
+                case Boolean bool -> array = manager.create(bool);
+                case Byte b -> array = manager.create(b);
+                case Integer integer -> array = manager.create(integer);
+                case Long l -> array = manager.create(l);
+                case Number num ->
+                    // Default to float for all other numbers
+                    // (not double, which would fail with MPS)
+                        array = manager.create(num.floatValue());
+                case boolean[] arr -> array = manager.create(arr);
+                case byte[] arr -> array = manager.create(arr);
+                case int[] arr -> array = manager.create(arr);
+                case long[] arr -> array = manager.create(arr);
+                case float[] arr -> array = manager.create(arr);
+                case null, default ->
+                        logger.warn("Unsupported optional argument: name={}, type={}",
+                                es.getKey(), val == null ? "null" : val.getClass());
+            }
+            if (array != null) {
+                array.setName("args." + es.getKey());
+                arrays.add(array);
+            }
+        }
+        return arrays;
+    }
+
     @Override
     public Mat processOutput(TranslatorContext ctx, NDList list) {
         var array = list.getFirst();

src/main/java/qupath/ext/instanseg/ui/InstanSegController.java

@@ -481,19 +481,21 @@ private void configureRunning() {
      * This may be called when the selected model is changed, or an existing model is downloaded.
      */
     private void refreshModelChoice() {
+        var modelDir = InstanSegUtils.getModelDirectory().orElse(null);
+        if (modelDir == null)
+            return;
+
         var model = selectedModel.get();
         if (model == null)
             return;
 
-        var modelDir = InstanSegUtils.getModelDirectory().orElse(null);
         try {
             model.checkIfDownloaded(modelDir.resolve("downloaded"), false);
         } catch (IOException e) {
             logger.debug("Error checking zip or RDF file(s); this shouldn't happen", e);
             Dialogs.showErrorNotification(resources.getString("title"), resources.getString("error.checkingModel"));
         }
-        boolean isDownloaded = modelDir != null && model.isValid();
-        if (!isDownloaded || qupath.getImageData() == null) {
+        if (!model.isValid() || qupath.getImageData() == null) {
             return;
         }
         var numChannels = model.getNumChannels();

src/main/java/qupath/ext/instanseg/ui/Watcher.java

@@ -242,7 +242,7 @@ private void handleModelPathsChanged(ListChangeListener.Change<? extends Path> c
             try {
                 set.add(InstanSegModel.fromPath(modelPath));
             } catch (IOException e) {
-                logger.error("Unable to load model from path", e);
+                logger.error("Unable to load model from {}", modelPath, e);
             }
         }
         models.setAll(set);