Add Apply SoftMax as Model Configuration option

Author: avyan-k

src/main/java/qupath/ext/wsinfer/WSInfer.java

@@ -194,7 +194,7 @@ public static void runInference(ImageData<BufferedImage> imageData, WSInferModel
         }
 
         boolean applySoftmax = true;
-        Translator translator = buildTranslator(wsiModel, pipeline, applySoftmax);
+        Translator translator = buildTranslator(wsiModel, pipeline);
         Criteria<Image, Classifications> criteria = buildCriteria(wsiModel, translator, device);
         List<String> classNames = wsiModel.getConfiguration().getClassNames();
         long startTime = System.currentTimeMillis();
@@ -308,13 +308,13 @@ private static boolean isMPS(Device device) {
     }
 
 
-    private static Translator<Image, Classifications> buildTranslator(WSInferModel wsiModel, Pipeline pipeline, boolean applySoftmax) {
+    private static Translator<Image, Classifications> buildTranslator(WSInferModel wsiModel, Pipeline pipeline) {
         // We should use ImageClassificationTranslator.builder() in the future if this is updated to work with MPS
         // (See javadocs for MpsSupport.WSInferClassificationTranslator for details)
         //        ImageClassificationTranslator.Builder builder = ImageClassificationTranslator.builder()
         return MpsSupport.WSInferClassificationTranslator.builder()
                 .optSynset(wsiModel.getConfiguration().getClassNames())
-                .optApplySoftmax(applySoftmax)
+                .optApplySoftmax(wsiModel.getConfiguration().isApplySoftmax())
                 .setPipeline(pipeline)
                 .build();
     }

src/main/java/qupath/ext/wsinfer/models/WSInferModelConfiguration.java

@@ -45,6 +45,9 @@ public class WSInferModelConfiguration {
     @SerializedName("spacing_um_px")
     private double spacingUmPx;
 
+    @SerializedName("apply_softmax")
+    private boolean applySoftmax = true;
+
     private List<WSInferTransform> transform;
 
     /**
@@ -78,4 +81,12 @@ public double getPatchSizePixels() {
     public double getSpacingMicronPerPixel() {
         return spacingUmPx;
     }
+
+    /**
+     * Whether to apply softmax to model output
+     * @return
+     */
+    public boolean isApplySoftmax() {
+        return applySoftmax;
+    }
 }