Leos comments (#44)

* Address comments in #42

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

@@ -22,7 +22,6 @@ public class DetectionMeasurer {
     private final Collection<ObjectMeasurements.ShapeFeatures> shapeFeatures;
     private final double pixelSize;
 
-
     private DetectionMeasurer(Collection<ObjectMeasurements.Compartments> compartments,
                               Collection<ObjectMeasurements.Measurements> measurements,
                               Collection<ObjectMeasurements.ShapeFeatures> shapeFeatures,

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

@@ -165,7 +165,6 @@ public Builder currentImageData() {
             return this;
         }
 
-
         /**
          * Set the channels to be used in inference
          * @param channels A collection of channels to be used in inference

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

@@ -49,7 +49,6 @@ private InstanSegModel(BioimageIoSpec.BioimageIoModel bioimageIoModel) {
         this.name = model.getName();
     }
 
-
     private InstanSegModel(URL modelURL, String name) {
         this.modelURL = modelURL;
         this.name = name;
@@ -75,26 +74,80 @@ public static InstanSegModel fromName(String name) {
         throw new UnsupportedOperationException("Fetching models by name is not yet implemented!");
     }
 
-    public BioimageIoSpec.BioimageIoModel getModel() {
-        if (model == null) {
-            try {
-                fetchModel();
-            } catch (IOException e) {
-                // todo: exception handling here, or...?
-                throw new RuntimeException(e);
-            }
-        }
-        return model;
-    }
-
+    /**
+     * Get the pixel size in the X dimension.
+     * @return the pixel size in the X dimension.
+     */
     public Double getPixelSizeX() {
         return getPixelSize().get("x");
     }
 
+    /**
+     * Get the pixel size in the Y dimension.
+     * @return the pixel size in the Y dimension.
+     */
     public Double getPixelSizeY() {
         return getPixelSize().get("y");
     }
 
+    /**
+     * Get the path where the model is stored on disk.
+     * @return A path on disk, or an exception if it can't be found.
+     */
+    public Path getPath() {
+        if (path == null) {
+            fetchModel();
+        }
+        return path;
+    }
+
+    @Override
+    public String toString() {
+        return getName();
+    }
+
+    /**
+     * Check if a path is (likely) a valid InstanSeg model.
+     * @param path The path to a folder.
+     * @return True if the folder contains an instanseg.pt file and an accompanying rdf.yaml.
+     * Does not currently validate the contents of either, but may in future check
+     * the yaml contents and the checksum of the pt file.
+     */
+    public static boolean isValidModel(Path path) {
+        // return path.toString().endsWith(".pt"); // if just looking at pt files
+        if (Files.isDirectory(path)) {
+            return Files.exists(path.resolve("instanseg.pt")) && Files.exists(path.resolve("rdf.yaml"));
+        }
+        return false;
+    }
+
+    /**
+     * The number of tiles that failed during processing.
+     * @return The count of the number of failed tiles.
+     */
+    public int nFailed() {
+        return nFailed;
+    }
+
+    /**
+     * Get the model name
+     * @return A string
+     */
+    String getName() {
+        return name;
+    }
+
+    /**
+     * Retrieve the BioImage model spec.
+     * @return The BioImageIO model spec for this InstanSeg model.
+     */
+    BioimageIoSpec.BioimageIoModel getModel() {
+        if (model == null) {
+            fetchModel();
+        }
+        return model;
+    }
+
     private Map<String, Double> getPixelSize() {
         // todo: this code is horrendous
         var map = new HashMap<String, Double>();
@@ -105,45 +158,23 @@ private Map<String, Double> getPixelSize() {
         return map;
     }
 
-    private void fetchModel() throws IOException {
+    private void fetchModel() {
         if (modelURL == null) {
             throw new NullPointerException("Model URL should not be null for a local model!");
         }
         downloadAndUnzip(modelURL, getUserDir().resolve("instanseg"));
     }
 
-    private static void downloadAndUnzip(URL url, Path localDirectory) throws IOException {
+    private static void downloadAndUnzip(URL url, Path localDirectory) {
         // todo: implement
     }
 
-
     private static Path getUserDir() {
         Path userPath = UserDirectoryManager.getInstance().getUserPath();
         Path cachePath = Paths.get(System.getProperty("user.dir"), ".cache", "QuPath");
         return userPath == null || userPath.toString().isEmpty() ?  cachePath : userPath;
     }
 
-    public String getName() {
-        return name;
-    }
-
-    public Path getPath() {
-        if (path == null) {
-            try {
-                fetchModel();
-            } catch (IOException e) {
-                // todo: handle here, or...?
-                throw new RuntimeException(e);
-            }
-        }
-        return path;
-    }
-
-    @Override
-    public String toString() {
-        return getName();
-    }
-
     void runInstanSeg(
             ImageData<BufferedImage> imageData,
             Collection<PathObject> pathObjects,
@@ -158,7 +189,8 @@ void runInstanSeg(
             TaskRunner taskRunner) {
 
         nFailed = 0;
-        Path modelPath = getPath().resolve("instanseg.pt");
+        Path modelPath;
+        modelPath = getPath().resolve("instanseg.pt");
         int nPredictors = 1; // todo: change me?
 
 
@@ -227,27 +259,4 @@ private static void printResourceCount(String title, BaseNDManager manager) {
         manager.debugDump(2);
     }
 
-    /**
-     * Check if a path is (likely) a valid InstanSeg model.
-     * @param path The path to a folder.
-     * @return True if the folder contains an instanseg.pt file and an accompanying rdf.yaml.
-     * Does not currently validate the contents of either, but may in future check
-     * the yaml contents and the checksum of the pt file.
-     */
-    public static boolean isValidModel(Path path) {
-        // return path.toString().endsWith(".pt"); // if just looking at pt files
-        if (Files.isDirectory(path)) {
-            return Files.exists(path.resolve("instanseg.pt")) && Files.exists(path.resolve("rdf.yaml"));
-        }
-        return false;
-    }
-
-    /**
-     * The number of tiles that failed during processing.
-     * @return The count of the number of failed tiles.
-     */
-    public int nFailed() {
-        return nFailed;
-    }
-
 }

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

@@ -13,12 +13,18 @@ class MatTranslator implements Translator<Mat, Mat> {
 
     private final String inputLayoutNd;
     private final String outputLayoutNd;
-    private final boolean nucleiOnly;
+    private final boolean firstChannelOnly;
 
-    public MatTranslator(String inputLayoutNd, String outputLayoutNd, boolean nucleiOnly) {
+    /**
+     * Create a translator from InstanSeg input to output.
+     * @param inputLayoutNd N-dimensional output specification
+     * @param outputLayoutNd N-dimensional output specification
+     * @param firstChannelOnly Should the model only be concerned with the first output channel?
+     */
+    MatTranslator(String inputLayoutNd, String outputLayoutNd, boolean firstChannelOnly) {
         this.inputLayoutNd = inputLayoutNd;
         this.outputLayoutNd = outputLayoutNd;
-        this.nucleiOnly = nucleiOnly;
+        this.firstChannelOnly = firstChannelOnly;
     }
 
     /**
@@ -31,9 +37,8 @@ public NDList processInput(TranslatorContext ctx, Mat input) {
         var manager = ctx.getNDManager();
         var ndarray = DjlTools.matToNDArray(manager, input, inputLayoutNd);
         var out = new NDList(ndarray);
-        if (nucleiOnly) {
-            var inds = new int[]{1, 1};
-            inds[1] = 0;
+        if (firstChannelOnly) {
+            var inds = new int[]{1, 0};
             var array = manager.create(inds, new Shape(2));
             var arrayCPU = array.toDevice(Device.cpu(), false);
             out.add(arrayCPU);

src/main/java/qupath/ext/instanseg/ui/PytorchManager.java → src/main/java/qupath/ext/instanseg/core/PytorchManager.java

@@ -1,4 +1,4 @@
-package qupath.ext.instanseg.ui;
+package qupath.ext.instanseg.core;
 
 import ai.djl.engine.Engine;
 import ai.djl.engine.EngineException;
@@ -15,15 +15,28 @@
 /**
  * Helper class to manage access to PyTorch via Deep Java Library.
  */
-class PytorchManager {
+public class PytorchManager {
 
     private static final Logger logger = LoggerFactory.getLogger(PytorchManager.class);
 
+    /**
+     * Get the PyTorch engine, downloading if necessary.
+     * @return the engine if available, or null if this failed
+     */
+    public static Engine getEngineOnline() {
+        try {
+            return callOnline(() -> Engine.getEngine("PyTorch"));
+        } catch (Exception e) {
+            logger.error(e.getMessage(), e);
+            return null;
+        }
+    }
+
     /**
      * Get the available devices for PyTorch, including MPS if Apple Silicon.
      * @return Only "cpu" if no local engine is found.
      */
-    static Collection<String> getAvailableDevices() {
+    public static Collection<String> getAvailableDevices() {
         try {
             Set<String> availableDevices = new LinkedHashSet<>();
 
@@ -54,7 +67,7 @@ static Collection<String> getAvailableDevices() {
      * Query if the PyTorch engine is already available, without a need to download.
      * @return
      */
-    static boolean hasPyTorchEngine() {
+    public static boolean hasPyTorchEngine() {
         return getEngineOffline() != null;
     }
 
@@ -71,19 +84,6 @@ static Engine getEngineOffline() {
         }
     }
 
-    /**
-     * Get the PyTorch engine, downloading if necessary.
-     * @return the engine if available, or null if this failed
-     */
-    static Engine getEngineOnline() {
-        try {
-            return callOnline(() -> Engine.getEngine("PyTorch"));
-        } catch (Exception e) {
-            logger.error(e.getMessage(), e);
-            return null;
-        }
-    }
-
     /**
      * Call a function with the "offline" property set to true (to block automatic downloads).
      * @param callable

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

@@ -53,6 +53,14 @@ class TilePredictionProcessor implements Processor<Mat, Mat, Mat> {
         this.doPadding = doPadding;
     }
 
+    /**
+     * The number of tiles that failed during processing.
+     * @return The count of the number of failed tiles.
+     */
+    public int nFailed() {
+        return nFailed;
+    }
+
     @Override
     public Mat process(Parameters<Mat, Mat> params) throws IOException {
 
@@ -169,11 +177,5 @@ private static ImageOp getNormalization(ImageData<BufferedImage> imageData, Path
         return defaults;
     }
 
-    /**
-     * The number of tiles that failed during processing.
-     * @return The count of the number of failed tiles.
-     */
-    public int nFailed() {
-        return nFailed;
-    }
+
 }