Implement model versioning

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

@@ -247,6 +247,7 @@ private InstanSegResults runInstanSeg(ImageData<BufferedImage> imageData, Collec
                         .postProcess(postProcessor)
                         .downsample(downsample)
                         .build();
+
                 processor.processObjects(taskRunner, imageData, pathObjects);
                 int nObjects = pathObjects.stream().mapToInt(PathObject::nChildObjects).sum();
                 if (predictionProcessor instanceof TilePredictionProcessor tileProcessor) {

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

@@ -30,6 +30,7 @@
 public class InstanSegModel {
 
     private static final Logger logger = LoggerFactory.getLogger(InstanSegModel.class);
+    private String version;
     private URL modelURL = null;
 
     /**
@@ -44,11 +45,13 @@ public class InstanSegModel {
     private InstanSegModel(BioimageIoSpec.BioimageIoModel bioimageIoModel) {
         this.model = bioimageIoModel;
         this.path = Paths.get(model.getBaseURI());
+        this.version = model.getVersion();
         this.name = model.getName();
     }
 
-    private InstanSegModel(String name, URL modelURL) {
+    private InstanSegModel(String name, String version, URL modelURL) {
         this.name = name;
+        this.version = version;
         this.modelURL = modelURL;
     }
 
@@ -68,30 +71,29 @@ public static InstanSegModel fromPath(Path path) throws IOException {
      * @param browserDownloadUrl The download URL from eg GitHub
      * @return A handle on the created model
      */
-    public static InstanSegModel fromURL(String name, URL browserDownloadUrl) {
-        return new InstanSegModel(name, browserDownloadUrl);
+    public static InstanSegModel fromURL(String name, String version, URL browserDownloadUrl) {
+        return new InstanSegModel(name, version, browserDownloadUrl);
     }
 
     /**
      * Check if the model has been downloaded already.
-     * @return True if a flag has been set.
+     * @return True if the model has a known path that exists and is valid, or if a suitable directory can be found in the localModelPath
      */
     public boolean isDownloaded(Path localModelPath) {
         // Check path first - *sometimes* the model might be downloaded, but have a name
         // that doesn't match with the filename (although we'd prefer this didn't happen...)
-        if (path != null && model != null && Files.exists(path))
+        if (path != null && model != null && isValidModel(path))
             return true;
-        // todo: this should also check if the contents are what we expect
-        if (Files.exists(localModelPath.resolve(name))) {
-            try {
-                download(localModelPath);
-            } catch (IOException e) {
-                logger.error("Model directory exists but is not valid", e);
-            }
-        } else {
+        if (!Files.exists(localModelPath.resolve(name).resolve(version))) {
             // The model may have been deleted or renamed - we won't be able to load it
             return false;
         }
+
+        try {
+            download(localModelPath);
+        } catch (IOException e) {
+            logger.error("Model directory exists but is not valid", e);
+        }
         return path != null && model != null;
     }
 
@@ -100,14 +102,16 @@ public boolean isDownloaded(Path localModelPath) {
      * @throws IOException If an error occurs when downloading, unzipping, etc.
      */
     public void download(Path localModelPath) throws IOException {
-        if (path != null && Files.exists(path) && model != null)
+        if (path != null && isValidModel(path) && model != null) {
             return;
+        }
         var zipFile = downloadZipIfNeeded(
                 this.modelURL,
                 localModelPath,
-                name);
+                name + "-" + version);
         this.path = unzipIfNeeded(zipFile);
         this.model = BioimageIoSpec.parseModel(path.toFile());
+        this.version = model.getVersion();
     }
 
     /**
@@ -213,8 +217,8 @@ public Optional<Path> getPath() {
     @Override
     public String toString() {
         String name = getName();
-        String parent = getPath().map(Path::getFileName).map(Path::toString).orElse(null);
-        String version = getModel().map(BioimageIoSpec.BioimageIoModel::getVersion).orElse(null);
+        String parent = getPath().map(Path::getParent).map(Path::getFileName).map(Path::toString).orElse(null);
+        String version = getModel().map(BioimageIoSpec.BioimageIoModel::getVersion).orElse(this.version);
         if (parent != null && !parent.equals(name)) {
             name = parent + "/" + name;
         }
@@ -290,16 +294,20 @@ private static boolean isDownloadedAlready(Path zipFile) {
         return Files.exists(zipFile);
     }
 
-    private static Path unzipIfNeeded(Path zipFile) throws IOException {
-        var outdir = zipFile.resolveSibling(zipFile.getFileName().toString().replace(".zip", ""));
+    private Path unzipIfNeeded(Path zipFile) throws IOException {
+        var zipSpec = BioimageIoSpec.parseModel(zipFile);
+        String version = zipSpec.getVersion();
+        var outdir = zipFile.resolveSibling(zipSpec.getName()).resolve(version);
         if (!isUnpackedAlready(outdir)) {
             try {
-                unzip(zipFile, zipFile.getParent());
+                unzip(zipFile, outdir);
                 // Files.delete(zipFile);
             } catch (IOException e) {
+                logger.error("Error unzipping model", e);
                 // clean up files just in case!
-                Files.deleteIfExists(zipFile);
                 Files.deleteIfExists(outdir);
+            } finally {
+                Files.deleteIfExists(zipFile);
             }
         }
         return outdir;
@@ -311,7 +319,7 @@ private static boolean isUnpackedAlready(Path outdir) {
 
     private static void unzip(Path zipFile, Path destination) throws IOException {
         if (!Files.exists(destination)) {
-            Files.createDirectory(destination);
+            Files.createDirectories(destination);
         }
         ZipInputStream zipIn = new ZipInputStream(new BufferedInputStream(new FileInputStream(zipFile.toFile())));
         ZipEntry entry = zipIn.getNextEntry();
@@ -358,8 +366,8 @@ private Optional<Map<String, Double>> getPixelSize() {
             var config = model.getConfig().getOrDefault("qupath", null);
             if (config instanceof Map configMap) {
                 var axes = (List) configMap.get("axes");
-                String x = (String) ((Map) (axes.get(0))).get("step");
-                String y = (String) ((Map) (axes.get(1))).get("step");
+                String x = String.valueOf(((Map) (axes.get(0))).get("step"));
+                String y = String.valueOf(((Map) (axes.get(1))).get("step"));
                 return Optional.of(Map.of(
                         "x", Double.valueOf(x),
                         "y", Double.valueOf(y)

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

@@ -83,7 +83,7 @@ public String toString() {
     static List<GitHubRelease> getReleases(Path modelDir) {
         Path cachedReleases = modelDir == null ? null : modelDir.resolve("releases.json");
 
-        String uString = "https://api.github.com/repos/instanseg/InstanSeg/releases";
+        String uString = "https://api.github.com/repos/alanocallaghan/InstanSeg/releases";
         HttpRequest request = HttpRequest.newBuilder()
                 .uri(URI.create(uString))
                 .GET()

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

@@ -55,6 +55,7 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.Comparator;
 import java.util.List;
 import java.util.Map;
@@ -549,6 +550,7 @@ private InstanSegModel downloadModel(InstanSegModel model, Path modelDir) {
             });
         } catch (IOException ex) {
             Dialogs.showErrorNotification(resources.getString("title"), resources.getString("error.downloading"));
+            logger.error("Error download model", ex);
         }
         return model;
     }
@@ -618,15 +620,18 @@ private static List<InstanSegModel> getRemoteModels() {
             logger.info("No releases found.");
             return List.of();
         }
-        var release = releases.getFirst();
-        var assets = GitHubUtils.getAssets(release);
         List<InstanSegModel> models = new ArrayList<>();
-        for (var asset : assets) {
-            models.add(
-                    InstanSegModel.fromURL(
-                            asset.getName().replace(".zip", ""),
-                            asset.getUrl())
-            );
+        for (var release: releases) {
+            var assets = GitHubUtils.getAssets(release);
+            for (var asset: assets) {
+                models.add(
+                        InstanSegModel.fromURL(
+                                asset.getName().replace(".zip", ""),
+                                release.getName(),
+                                asset.getUrl()
+                        )
+                );
+            }
         }
         return List.copyOf(models);
     }

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

@@ -74,11 +74,11 @@ private void handleModelDirectoryChange(ObservableValue<? extends Path> observab
         // Currently, we look *only* in the model directory for models
         // But we could register subdirectories here if we wanted (e.g. 'local', 'downloaded')
         if (oldPath != null) {
-            unregister(oldPath);
+            unregister(oldPath.resolve("local"));
         }
-        if (newPath != null && Files.isDirectory(newPath)) {
+        if (newPath != null && Files.isDirectory(newPath.resolve("local"))) {
             try {
-                register(newPath);
+                register(newPath.resolve("local"));
             } catch (IOException e) {
                 logger.error("Unable to register new model directory", e);
             }