Merge pull request #8 from petebankhead/dev

Initial update for v0.5.0

.github/workflows/gradle.yml

@@ -23,16 +23,16 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up JDK 11
+    - uses: actions/checkout@v4
+    - name: Set up JDK 17
       uses: actions/setup-java@v3
       with:
-        java-version: '11'
+        java-version: '17'
         distribution: 'temurin'
     - name: Validate Gradle wrapper
-      uses: gradle/wrapper-validation-action@e6e38bacfdf1a337459f332974bb2327a31aaf4b
+      uses: gradle/wrapper-validation-action@v1
     - name: Build with Gradle
-      uses: gradle/gradle-build-action@67421db6bd0bf253fb4bd25b31ebb98943c375e1
+      uses: gradle/gradle-build-action@v2
       with:
         arguments: build
     - uses: actions/upload-artifact@v3

.github/workflows/publish-release.yml

@@ -10,16 +10,16 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up JDK 11
+    - uses: actions/checkout@v4
+    - name: Set up JDK 17
       uses: actions/setup-java@v3
       with:
-        java-version: '11'
+        java-version: '17'
         distribution: 'temurin'
     - name: Validate Gradle wrapper
-      uses: gradle/wrapper-validation-action@e6e38bacfdf1a337459f332974bb2327a31aaf4b
+      uses: gradle/wrapper-validation-action@v1
     - name: Publish snapshot
-      uses: gradle/gradle-build-action@67421db6bd0bf253fb4bd25b31ebb98943c375e1
+      uses: gradle/gradle-build-action@v2
       with:
         arguments: publish -P release=true
       env:

.github/workflows/publish-snapshot.yml

@@ -9,16 +9,16 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up JDK 11
+    - uses: actions/checkout@v4
+    - name: Set up JDK 17
       uses: actions/setup-java@v3
       with:
-        java-version: '11'
+        java-version: '17'
         distribution: 'temurin'
     - name: Validate Gradle wrapper
-      uses: gradle/wrapper-validation-action@e6e38bacfdf1a337459f332974bb2327a31aaf4b
+      uses: gradle/wrapper-validation-action@v1
     - name: Publish snapshot
-      uses: gradle/gradle-build-action@67421db6bd0bf253fb4bd25b31ebb98943c375e1
+      uses: gradle/gradle-build-action@v2
       with:
         arguments: publish
       env:

build.gradle

@@ -1,17 +1,18 @@
 plugins {
   id 'java-library'
   id 'maven-publish'
-  // To manage included native libraries
-  alias(libs.plugins.javacpp)
-  // Need to use this instead (without version) if running as a QuPath subproject
-//  id 'org.bytedeco.gradle-javacpp-platform'
+  id 'com.github.johnrengelman.shadow' version '8.1.1'
+  id 'org.openjfx.javafxplugin' version '0.1.0'
+  // Version in settings.gradle
+  id 'org.bytedeco.gradle-javacpp-platform'
 }
 
 ext.moduleName = 'qupath.extension.djl'
 ext.qupathVersion = gradle.ext.qupathVersion
 
 description = 'QuPath extension to use Deep Java Library'
-version = "0.2.0"
+version = "0.3.0-SNAPSHOT"
+group = 'io.github.qupath'
 
 def djlVersion = libs.versions.deepJavaLibrary.get()
 
@@ -33,11 +34,12 @@ repositories {
 
 
 dependencies {
-    implementation "io.github.qupath:qupath-gui-fx:${qupathVersion}"
-
+	shadow "io.github.qupath:qupath-gui-fx:${qupathVersion}"
+	shadow libs.qupath.fxtras
+
     // These are included in QuPath distributions
-    implementation libs.bundles.logging
-    implementation libs.snakeyaml
+	shadow libs.bundles.logging
+	shadow libs.snakeyaml
 
     implementation "ai.djl:api:$djlVersion"
 
@@ -61,11 +63,11 @@ tasks.register("copyDependencies", Copy) {
 }
 
 /*
- * Ensure Java 11 compatibility
+ * Ensure Java 17 compatibility
  */
 java {
     toolchain {
-        languageVersion = JavaLanguageVersion.of(11)
+        languageVersion = JavaLanguageVersion.of(17)
     }
     if (project.properties['sources'])
 	    withSourcesJar()
@@ -134,7 +136,6 @@ publishing {
 
 	publications {
 		mavenJava(MavenPublication) {
-			groupId = 'io.github.qupath'
 			from components.java
 
 			pom {

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.5.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.4-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

gradlew

@@ -205,6 +205,12 @@ set -- \
         org.gradle.wrapper.GradleWrapperMain \
         "$@"
 
+# Stop when "xargs" is not available.
+if ! command -v xargs >/dev/null 2>&1
+then
+    die "xargs is not available"
+fi
+
 # Use "xargs" to parse quoted args.
 #
 # With -n1 it outputs one arg per line, with the quotes and backslashes removed.

gradlew.bat

@@ -14,7 +14,7 @@
 @rem limitations under the License.
 @rem
 
-@if "%DEBUG%" == "" @echo off
+@if "%DEBUG%"=="" @echo off
 @rem ##########################################################################
 @rem
 @rem  Gradle startup script for Windows
@@ -25,7 +25,7 @@
 if "%OS%"=="Windows_NT" setlocal
 
 set DIRNAME=%~dp0
-if "%DIRNAME%" == "" set DIRNAME=.
+if "%DIRNAME%"=="" set DIRNAME=.
 set APP_BASE_NAME=%~n0
 set APP_HOME=%DIRNAME%
 
@@ -40,7 +40,7 @@ if defined JAVA_HOME goto findJavaFromJavaHome
 
 set JAVA_EXE=java.exe
 %JAVA_EXE% -version >NUL 2>&1
-if "%ERRORLEVEL%" == "0" goto execute
+if %ERRORLEVEL% equ 0 goto execute
 
 echo.
 echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
@@ -75,13 +75,15 @@ set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
 
 :end
 @rem End local scope for the variables with windows NT shell
-if "%ERRORLEVEL%"=="0" goto mainEnd
+if %ERRORLEVEL% equ 0 goto mainEnd
 
 :fail
 rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
 rem the _cmd.exe /c_ return code!
-if  not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
-exit /b 1
+set EXIT_CODE=%ERRORLEVEL%
+if %EXIT_CODE% equ 0 set EXIT_CODE=1
+if not ""=="%GRADLE_EXIT_CONSOLE%" exit %EXIT_CODE%
+exit /b %EXIT_CODE%
 
 :mainEnd
 if "%OS%"=="Windows_NT" endlocal

settings.gradle

@@ -1,6 +1,12 @@
+pluginManagement {
+	plugins {
+		id 'org.bytedeco.gradle-javacpp-platform' version '1.5.9'
+	}
+}
+
 rootProject.name = 'qupath-extension-djl'
 
-gradle.ext.qupathVersion = "0.4.0"
+gradle.ext.qupathVersion = "0.5.0-SNAPSHOT"
 
 dependencyResolutionManagement {
 

src/main/java/qupath/ext/djl/DjlDnnModel.java

@@ -101,10 +101,14 @@ private void ensureInitialized() {
 						}
 
 						if (this.outputs == null || this.outputs.isEmpty()) {
-							var description = model.describeOutput();
-							if (description != null && !description.isEmpty())
-								outputs = description.stream().collect(Collectors.toMap(p -> p.getKey(), p -> DjlTools.convertShape(p.getValue())));
-							else
+							try {
+								var description = model.describeOutput();
+								if (description != null && !description.isEmpty())
+									outputs = description.stream().collect(Collectors.toMap(p -> p.getKey(), p -> DjlTools.convertShape(p.getValue())));
+							} catch (Exception e) {
+								logger.debug(e.getMessage(), e);
+							}
+							if (this.outputs == null || this.outputs.isEmpty())
 								outputs = Map.of(DnnModel.DEFAULT_OUTPUT_NAME, DnnShape.UNKNOWN_SHAPE);
 						}
 

src/main/java/qupath/ext/djl/DjlDnnModelBuilder.java

@@ -64,6 +64,11 @@ private static String estimateEngine(URI uri) {
 			if (Engine.hasEngine(DjlTools.ENGINE_PYTORCH))
 				return DjlTools.ENGINE_PYTORCH;
 		}
+
+		if (urlString.endsWith(".tflite")) {
+			if (Engine.hasEngine(DjlTools.ENGINE_TFLITE))
+				return DjlTools.ENGINE_TFLITE;
+		}
 
 		var path = GeneralTools.toPath(uri);
 		if (path != null) {

src/main/java/qupath/ext/djl/DjlEngineCommand.java

@@ -20,6 +20,7 @@
 import java.util.Set;
 import java.util.concurrent.Callable;
 import java.util.concurrent.ExecutionException;
+import java.util.concurrent.Executors;
 import java.util.concurrent.TimeUnit;
 import java.util.concurrent.TimeoutException;
 
@@ -51,11 +52,12 @@
 import javafx.scene.shape.Circle;
 import javafx.stage.Modality;
 import javafx.stage.Stage;
+import qupath.fx.dialogs.Dialogs;
+import qupath.fx.utils.GridPaneUtils;
 import qupath.lib.common.GeneralTools;
+import qupath.lib.common.ThreadTools;
 import qupath.lib.gui.QuPathGUI;
-import qupath.lib.gui.dialogs.Dialogs;
 import qupath.lib.gui.tools.GuiTools;
-import qupath.lib.gui.tools.PaneTools;
 
 /**
  * Command to display Deep Java Library engines.
@@ -70,7 +72,7 @@ public class DjlEngineCommand {
 
 	private QuPathGUI qupath;
 
-	private static enum EngineStatus {
+	private enum EngineStatus {
 		UNAVAILABLE, UNKNOWN, PENDING, AVAILABLE, FAILED
 	}
 
@@ -115,23 +117,23 @@ private void init() {
 				"Download Deep Java Library engines for inference."
 				);
 		label.setWrapText(true);
-		PaneTools.addGridRow(pane, row++, 0, null, label, label);
+		GridPaneUtils.addGridRow(pane, row++, 0, null, label, label);
 		var label2 = new Label(
 				"These will be stored in the local directories shown."
 				);
 		label2.setWrapText(true);
-		PaneTools.addGridRow(pane, row++, 0, null, label2, label2);
+		GridPaneUtils.addGridRow(pane, row++, 0, null, label2, label2);
 
 		var label3 = new Label(
 				"Please check the original engine's website for any licensing information.\n"
 				);
 		label3.setWrapText(true);
-		PaneTools.addGridRow(pane, row++, 0, null, label3, label3);
+		GridPaneUtils.addGridRow(pane, row++, 0, null, label3, label3);
 
 		for (var name : Engine.getAllEngines()) {
 			var separator = new Separator(Orientation.HORIZONTAL);
-			PaneTools.addGridRow(pane, row++, 0, null, separator, separator);
-			PaneTools.setToExpandGridPaneWidth(separator);
+			GridPaneUtils.addGridRow(pane, row++, 0, null, separator, separator);
+			GridPaneUtils.setToExpandGridPaneWidth(separator);
 
 			var status = available.computeIfAbsent(name, n -> new SimpleObjectProperty<>(EngineStatus.UNKNOWN));
 
@@ -140,7 +142,7 @@ private void init() {
 			String tooltip = "Engine: " + name;
 			var labelName = new Label(name);
 			labelName.setStyle("-fx-font-weight: bold;");
-			PaneTools.addGridRow(pane, row++, 0, tooltip, labelName, labelName);
+			GridPaneUtils.addGridRow(pane, row++, 0, tooltip, labelName, labelName);
 
 			var labelPath = new Label(path.toString());
 			var btnDownload = new Button("Download");
@@ -223,10 +225,10 @@ private void init() {
 				else
 					logger.debug("Cannot open {} - directory does not exist", path);
 			});
-			PaneTools.addGridRow(pane, row++, 0, null, labelPathLabel, labelPath);
-			PaneTools.addGridRow(pane, row++, 0, null, btnDownload, btnDownload);
+			GridPaneUtils.addGridRow(pane, row++, 0, null, labelPathLabel, labelPath);
+			GridPaneUtils.addGridRow(pane, row++, 0, null, btnDownload, btnDownload);
 
-			PaneTools.setToExpandGridPaneWidth(labelName, labelPath, btnDownload);
+			GridPaneUtils.setToExpandGridPaneWidth(labelName, labelPath, btnDownload);
 
 			// Update the engine status quietly
 			checkEngineStatus(name, status, -1, true);
@@ -248,12 +250,12 @@ private void showDialog() {
 
 	private void checkEngineStatus(String name, ObjectProperty<EngineStatus> status, long timeoutMillis, boolean doQuietly) {
 		// Request the engine in a background thread, triggering download if necessary
-		var pool = qupath.createSingleThreadExecutor(this);
+		var pool = Executors.newSingleThreadExecutor(ThreadTools.createThreadFactory("djl-engine-request", true));
 		updateStatus(status, EngineStatus.PENDING);
 		var future = pool.submit((Callable<Boolean>)() -> checkEngineAvailability(name, status, doQuietly));
 		if (timeoutMillis <= 0)
 			return;
-
+		pool.shutdown();
 		try {
 			// Wait until the timeout - engine might already be available & return quickly
 			var result = future.get(timeoutMillis, TimeUnit.MILLISECONDS);

src/main/java/qupath/ext/djl/DjlExtension.java

@@ -77,7 +77,7 @@ public GitHubRepo getRepository() {
 
 	@Override
 	public Version getQuPathVersion() {
-		return Version.parse("0.4.0-SNAPSHOT");
+		return Version.parse("0.5.0-SNAPSHOT");
 	}