Merge pull request #36 from alanocallaghan/java-17

Support for QuPath 0.5 and local models

CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog
 
+## v0.3.0
+
+* Add support for QuPath v0.5
+* Enable auto-updating (see https://github.com/qupath/qupath-extension-wsinfer/issues/40)
+* Add support for local models (see https://github.com/qupath/qupath-extension-wsinfer/issues/32)
+
 ## v0.2.1
 
 * Fix CPU/GPU support (https://github.com/qupath/qupath-extension-wsinfer/issues/41)
@@ -14,4 +20,4 @@
 
 ## v0.1.0
 
-* First release!
+* First release!

build.gradle

@@ -1,22 +1,23 @@
 plugins {
-  // Main gradle plugin for building a Java library
-  id 'java-library'
-  // To create a shadow/fat jar that bundle up all dependencies
-  id 'com.github.johnrengelman.shadow' version '7.1.2'
-  // Include this plugin to avoid downloading JavaCPP dependencies for all platforms
-  id 'org.bytedeco.gradle-javacpp-platform'
+    // Main gradle plugin for building a Java library
+    id 'java-library'
+    // To create a shadow/fat jar that bundle up all dependencies
+    id 'com.github.johnrengelman.shadow' version '7.1.2'
+    // Include this plugin to avoid downloading JavaCPP dependencies for all platforms
+    id 'org.bytedeco.gradle-javacpp-platform'
+    id 'org.openjfx.javafxplugin' version '0.1.0'
 }
 
 ext.moduleName = 'io.github.qupath.extension.wsinfer'
 
-version = "0.2.1"
+version = "0.3.0"
 description = 'An extension to run WSInfer in QuPath'
 
 // The default 'gradle.ext.qupathVersion' reads this from settings.gradle.
 ext.qupathVersion = gradle.ext.qupathVersion
 
 // Generally 11 for QuPath v0.4.3, but will be 17 for QuPath v0.5.0
-ext.qupathJavaVersion = 11
+ext.qupathJavaVersion = 17
 
 def djlVersion = libs.versions.deepJavaLibrary.get()
 
@@ -36,6 +37,8 @@ dependencies {
     // Main QuPath user interface jar.
     // Automatically includes other QuPath jars as subdependencies.
     implementation "io.github.qupath:qupath-gui-fx:${qupathVersion}"
+    implementation 'io.github.qupath:qupath-fxtras:0.1.0'
+    implementation 'org.commonmark:commonmark:0.21.0'
 
     // For logging - the version comes from QuPath's version catalog at
     // https://github.com/qupath/qupath/blob/main/gradle/libs.versions.toml

settings.gradle

@@ -6,7 +6,7 @@ pluginManagement {
 
 rootProject.name = 'qupath-extension-wsinfer'
 
-gradle.ext.qupathVersion = "0.4.4"
+gradle.ext.qupathVersion = "0.5.0-SNAPSHOT"
 
 dependencyResolutionManagement {
 
@@ -31,4 +31,4 @@ dependencyResolutionManagement {
         }
 
     }
-}
+}

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

@@ -38,7 +38,7 @@
 import qupath.ext.wsinfer.models.WSInferTransform;
 import qupath.ext.wsinfer.models.WSInferUtils;
 import qupath.ext.wsinfer.ui.WSInferPrefs;
-import qupath.lib.gui.dialogs.Dialogs;
+import qupath.lib.gui.tools.GuiTools;
 import qupath.lib.images.ImageData;
 import qupath.lib.images.servers.ImageServer;
 import qupath.lib.images.servers.PixelCalibration;
@@ -151,7 +151,7 @@ public static void runInference(ImageData<BufferedImage> imageData, WSInferModel
     public static void runInference(ImageData<BufferedImage> imageData, WSInferModel wsiModel, ProgressListener progressListener) throws InterruptedException, ModelNotFoundException, MalformedModelException, IOException, TranslateException {
         Objects.requireNonNull(wsiModel, "Model cannot be null");
         if (imageData == null) {
-            Dialogs.showNoImageError(resources.getString("title"));
+            GuiTools.showNoImageError(resources.getString("title"));
         }
 
         // Try to get some tiles we can use

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

@@ -23,6 +23,7 @@
 import qupath.ext.wsinfer.ui.WSInferCommand;
 import qupath.lib.common.Version;
 import qupath.lib.gui.QuPathGUI;
+import qupath.lib.gui.extensions.GitHubProject;
 import qupath.lib.gui.extensions.QuPathExtension;
 import qupath.lib.gui.prefs.PathPrefs;
 
@@ -32,7 +33,7 @@
  * QuPath extension to run patch-based deep learning inference with WSInfer.
  * See https://wsinfer.readthedocs.io for more info.
  */
-public class WSInferExtension implements QuPathExtension {
+public class WSInferExtension implements QuPathExtension, GitHubProject {
 	private final static ResourceBundle resources = ResourceBundle.getBundle("qupath.ext.wsinfer.ui.strings");
 
 	private final static Logger logger = LoggerFactory.getLogger(WSInferExtension.class);
@@ -48,8 +49,6 @@ public class WSInferExtension implements QuPathExtension {
 	private final BooleanProperty enableExtensionProperty = PathPrefs.createPersistentPreference(
 			"enableExtension", true);
 
-
-
 	@Override
 	public void installExtension(QuPathGUI qupath) {
 		if (isInstalled) {
@@ -84,4 +83,8 @@ public Version getQuPathVersion() {
 		return EXTENSION_QUPATH_VERSION;
 	}
 
+	@Override
+	public GitHubRepo getRepository() {
+		return GitHubRepo.create(getName(), "qupath", "qupath-extension-wsinfer");
+	}
 }

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

@@ -1,4 +1,4 @@
-/**
+ /**
  * Copyright 2023 University of Edinburgh
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
@@ -16,22 +16,21 @@
 
 package qupath.ext.wsinfer.models;
 
-import com.google.gson.annotations.SerializedName;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import qupath.ext.wsinfer.ui.WSInferPrefs;
-import qupath.lib.io.GsonTools;
-
-import java.io.File;
-import java.io.IOException;
-import java.math.BigInteger;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.nio.charset.StandardCharsets;
-import java.nio.file.Files;
-import java.nio.file.Paths;
-import java.security.MessageDigest;
-import java.security.NoSuchAlgorithmException;
+ import com.google.gson.annotations.SerializedName;
+ import org.slf4j.Logger;
+ import org.slf4j.LoggerFactory;
+ import qupath.ext.wsinfer.ui.WSInferPrefs;
+ import qupath.lib.io.GsonTools;
+
+ import java.io.File;
+ import java.io.IOException;
+ import java.math.BigInteger;
+ import java.net.URL;
+ import java.nio.charset.StandardCharsets;
+ import java.nio.file.Files;
+ import java.nio.file.Paths;
+ import java.security.MessageDigest;
+ import java.security.NoSuchAlgorithmException;
 
 // Equivalent to config.json files from hugging face
 public class WSInferModel {
@@ -42,10 +41,10 @@ public class WSInferModel {
     private WSInferModelConfiguration configuration;
 
     @SerializedName("hf_repo_id")
-    private String hfRepoId;
+    String hfRepoId;
 
     @SerializedName("hf_revision")
-    private String hfRevision;
+    String hfRevision;
 
     public String getName() {
         return hfRepoId;
@@ -86,6 +85,15 @@ public File getCFFile() {
         return getFile("config.json");
     }
 
+
+    /**
+     * Get the configuration file. Note that it is not guaranteed that the model has been downloaded.
+     * @return path to model config file in cache dir
+     */
+    public File getREADMEFile() {
+        return getFile("README.md");
+    }
+
     /**
      * Check if the model files exist and are valid.
      * @return true if the files exist and the SHA matches, and the config is valid.
@@ -118,7 +126,7 @@ private File getFile(String f) {
         return Paths.get(getModelDirectory().toString(), f).toFile();
     }
 
-    private File getModelDirectory() {
+    File getModelDirectory() {
         return Paths.get(WSInferPrefs.modelDirectoryProperty().get(), hfRepoId, hfRevision).toFile();
     }
 
@@ -177,11 +185,16 @@ public synchronized void downloadModel() throws IOException {
         }
         downloadFileToCacheDir("torchscript_model.pt");
         downloadFileToCacheDir("config.json");
+        downloadFileToCacheDir("README.md");
+
+        // this downloads the LFS pointer, not the actual .pt file
+        // the LFS pointer contains a SHA256 checksum
         URL url = new URL(String.format("https://huggingface.co/%s/raw/%s/torchscript_model.pt", hfRepoId, hfRevision));
         WSInferUtils.downloadURLToFile(url, getPointerFile());
         if (!isValid() || !checkSHAMatches()) {
             throw new IOException("Error downloading model files");
         }
+
     }
 
     private void downloadFileToCacheDir(String file) throws IOException {

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

@@ -33,6 +33,6 @@ public class WSInferModelCollection {
      * @return
      */
     public Map<String, WSInferModel> getModels() {
-        return Collections.unmodifiableMap(models);
+        return Collections.synchronizedMap(models);
     }
 }

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

@@ -0,0 +1,69 @@
+/**
+ * Copyright 2023 University of Edinburgh
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package qupath.ext.wsinfer.models;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Objects;
+import java.util.ResourceBundle;
+
+public class WSInferModelLocal extends WSInferModel {
+
+    private final File modelDirectory;
+    private static final ResourceBundle resources = ResourceBundle.getBundle("qupath.ext.wsinfer.ui.strings");
+
+    /**
+     * Try to create a WSInfer model from a user directory.
+     * @param modelDirectory A user directory containing a
+     *                       torchscript.pt file and a config.json file
+     * @return A {@link WSInferModel} if the directory supplied is valid,
+     * otherwise nothing.
+     */
+    public static WSInferModelLocal createInstance(File modelDirectory) throws IOException {
+        return new WSInferModelLocal(modelDirectory);
+    }
+
+    private WSInferModelLocal(File modelDirectory) throws IOException {
+        this.modelDirectory = modelDirectory;
+        this.hfRepoId = modelDirectory.getName();
+        List<File> files = Arrays.asList(Objects.requireNonNull(modelDirectory.listFiles()));
+        if (!files.contains(getCFFile())) {
+            throw new IOException(resources.getString("error.localModel") + ": " + getCFFile().toString());
+        }
+        if (!files.contains(getTSFile())) {
+            throw new IOException(resources.getString("error.localModel") + ": " + getTSFile().toString());
+        }
+    }
+
+    @Override
+    File getModelDirectory() {
+        return this.modelDirectory;
+    }
+
+    @Override
+    public boolean isValid() {
+        return getTSFile().exists() && getConfiguration() != null;
+    }
+
+    @Override
+    public synchronized void downloadModel() {}
+
+    @Override
+    public synchronized void removeCache() {}
+}

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

@@ -16,10 +16,10 @@
 
 package qupath.ext.wsinfer.models;
 
-import org.apache.commons.compress.utils.IOUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import qupath.ext.wsinfer.ui.WSInferPrefs;
+import qupath.fx.dialogs.Dialogs;
 import qupath.lib.io.GsonTools;
 
 import java.io.File;
@@ -33,13 +33,16 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
+import java.util.Objects;
+import java.util.ResourceBundle;
 
 /**
  * Utility class to help with working with WSInfer models.
  */
 public class WSInferUtils {
 
     private static final Logger logger = LoggerFactory.getLogger(WSInferUtils.class);
+    private static final ResourceBundle resources = ResourceBundle.getBundle("qupath.ext.wsinfer.ui.strings");
 
     private static WSInferModelCollection cachedModelCollection;
 
@@ -64,9 +67,30 @@ public static WSInferModelCollection getModelCollection() {
                     cachedModelCollection = downloadModelCollection();
             }
         }
+        String localModelDirectory = WSInferPrefs.localDirectoryProperty().get();
+        if (localModelDirectory != null) {
+            addLocalModels(cachedModelCollection, localModelDirectory);
+        }
         return cachedModelCollection;
     }
 
+    private static void addLocalModels(WSInferModelCollection cachedModelCollection, String localModelDirectory) {
+        File modelDir = new File(localModelDirectory);
+        if (!modelDir.exists() || !modelDir.isDirectory()) {
+            return;
+        }
+        for (var model: Objects.requireNonNull(modelDir.listFiles())) {
+            if (model.isDirectory()) {
+                try {
+                    var localModel = WSInferModelLocal.createInstance(model);
+                    cachedModelCollection.getModels().put(localModel.getName(), localModel);
+                } catch (IOException e) {
+                    Dialogs.showErrorNotification(resources.getString("title"), e);
+                }
+            }
+        }
+    }
+
     /**
      * Download the model collection from the hugging face repo.
      * This replaces any previously cached version.

src/main/java/qupath/ext/wsinfer/ui/WSInferCommand.java

@@ -25,7 +25,8 @@
 import org.slf4j.LoggerFactory;
 import qupath.lib.gui.ExtensionClassLoader;
 import qupath.lib.gui.QuPathGUI;
-import qupath.lib.gui.dialogs.Dialogs;
+import qupath.fx.dialogs.Dialogs;
+
 
 import java.io.IOException;
 import java.net.URL;
@@ -72,7 +73,7 @@ private Stage createStage() throws IOException {
 
         // We need to use the ExtensionClassLoader to load the FXML, since it's in a different module
         var loader = new FXMLLoader(url, resources);
-        loader.setClassLoader(QuPathGUI.getExtensionClassLoader());
+        loader.setClassLoader(this.getClass().getClassLoader());
         VBox root = loader.load();
 
         // There's probably a better approach... but wrapping in a border pane