Merge pull request #6 from qupath/0.5.0

Seemingly working 0.5.0

.github/workflows/gradle.yml

@@ -24,15 +24,15 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up JDK 11
+    - 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

@@ -11,15 +11,15 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up JDK 11
+    - 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

@@ -10,15 +10,15 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up JDK 11
+    - 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:

CHANGELOG.md

@@ -0,0 +1,7 @@
+## v0.2.0
+
+* Support for QuPath v0.5.0
+
+## v0.1.0
+
+* Initial release

build.gradle

@@ -1,16 +1,39 @@
 plugins {
-  id 'java-library'
-  id 'maven-publish'
-  // To manage included native libraries
-  alias(libs.plugins.javacpp)
+	id 'java-library'
+	id 'maven-publish'
+	// To manage included native libraries
+	id 'org.openjfx.javafxplugin' version '0.1.0'
 }
 
 ext.moduleName = 'qupath.extension.bioimageio'
 ext.qupathVersion = gradle.ext.qupathVersion
+ext.qupathJavaVersion = 17
 
-description = 'QuPath extension to use the Bioimage Model Zoo (bioimage.io)'
-version = "0.1.0"
+base {
+	description = 'QuPath extension to use the Bioimage Model Zoo (bioimage.io)'
+	version = "0.2.0-SNAPSHOT"
+	group = 'io.github.qupath'
+}
+
+// Looks redundant to include this here and in settings.gradle,
+// but helps overcome some gradle trouble when including this as a subproject
+// within QuPath itself (which is useful during development).
+repositories {
+	// Add this if you need access to dependencies only installed locally
+	//  mavenLocal()
 
+	mavenCentral()
+
+	// Add scijava - which is where QuPath's jars are hosted
+	maven {
+		url "https://maven.scijava.org/content/repositories/releases"
+	}
+
+	maven {
+		url "https://maven.scijava.org/content/repositories/snapshots"
+	}
+
+}
 
 dependencies {
     implementation "io.github.qupath:qupath-gui-fx:${qupathVersion}"
@@ -20,9 +43,10 @@ dependencies {
     // These are included in QuPath distributions
     implementation libs.bundles.logging
     implementation libs.snakeyaml
+	implementation libs.controlsfx
 
     testImplementation libs.junit
-    testRuntimeOnly libs.junit.engine
+    testRuntimeOnly libs.junit.platform
 
 }
 
@@ -41,11 +65,11 @@ tasks.register("copyDependencies", Copy) {
 }
 
 /*
- * Ensure Java 11 compatibility
+ * Ensure Java compatibility
  */
 java {
     toolchain {
-        languageVersion = JavaLanguageVersion.of(11)
+        languageVersion = JavaLanguageVersion.of(qupathJavaVersion)
     }
     if (project.properties['sources'])
 	    withSourcesJar()
@@ -114,7 +138,6 @@ publishing {
 
 	publications {
 		mavenJava(MavenPublication) {
-			groupId = 'io.github.qupath'
 			from components.java
 
 			pom {
@@ -128,3 +151,4 @@ publishing {
 		}
 	}
 }
+

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,7 @@
 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-8.5-bin.zip
+networkTimeout=10000
+validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

gradlew

@@ -55,7 +55,7 @@
 #       Darwin, MinGW, and NonStop.
 #
 #   (3) This script is generated from the Groovy template
-#       https://github.com/gradle/gradle/blob/master/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+#       https://github.com/gradle/gradle/blob/HEAD/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
 #       within the Gradle project.
 #
 #       You can find Gradle at https://github.com/gradle/gradle/.
@@ -80,13 +80,11 @@ do
     esac
 done
 
-APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
-
-APP_NAME="Gradle"
+# This is normally unused
+# shellcheck disable=SC2034
 APP_BASE_NAME=${0##*/}
-
-# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+# Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036)
+APP_HOME=$( cd "${APP_HOME:-./}" > /dev/null && pwd -P ) || exit
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD=maximum
@@ -133,22 +131,29 @@ location of your Java installation."
     fi
 else
     JAVACMD=java
-    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+    if ! command -v java >/dev/null 2>&1
+    then
+        die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
 
 Please set the JAVA_HOME variable in your environment to match the
 location of your Java installation."
+    fi
 fi
 
 # Increase the maximum file descriptors if we can.
 if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
     case $MAX_FD in #(
       max*)
+        # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC2039,SC3045
         MAX_FD=$( ulimit -H -n ) ||
             warn "Could not query maximum file descriptor limit"
     esac
     case $MAX_FD in  #(
       '' | soft) :;; #(
       *)
+        # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC2039,SC3045
         ulimit -n "$MAX_FD" ||
             warn "Could not set maximum file descriptor limit to $MAX_FD"
     esac
@@ -193,18 +198,28 @@ if "$cygwin" || "$msys" ; then
     done
 fi
 
-# Collect all arguments for the java command;
-#   * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of
-#     shell script including quotes and variable substitutions, so put them in
-#     double quotes to make sure that they get re-expanded; and
-#   * put everything else in single quotes, so that it's not re-expanded.
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+
+# Collect all arguments for the java command:
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments,
+#     and any embedded shellness will be escaped.
+#   * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be
+#     treated as '${Hostname}' itself on the command line.
 
 set -- \
         "-Dorg.gradle.appname=$APP_BASE_NAME" \
         -classpath "$CLASSPATH" \
         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 +25,8 @@
 if "%OS%"=="Windows_NT" setlocal
 
 set DIRNAME=%~dp0
-if "%DIRNAME%" == "" set DIRNAME=.
+if "%DIRNAME%"=="" set DIRNAME=.
+@rem This is normally unused
 set APP_BASE_NAME=%~n0
 set APP_HOME=%DIRNAME%
 
@@ -40,7 +41,7 @@ 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 +76,15 @@ 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

@@ -1,29 +1,35 @@
+pluginManagement {
+	plugins {
+		id 'org.bytedeco.gradle-javacpp-platform' version '1.5.9'
+	}
+}
+
 rootProject.name = 'qupath-extension-bioimageio'
 
-gradle.ext.qupathVersion = "0.4.0-SNAPSHOT"
+
+gradle.ext.qupathVersion = "0.5.0"
 
 dependencyResolutionManagement {
 
-	repositories {
-
-//	  mavenLocal()
-
-	  mavenCentral()
-
-	  maven {
-	    url "https://maven.scijava.org/content/repositories/releases"
-	  }
-
-	  maven {
-	    url "https://maven.scijava.org/content/repositories/snapshots"
-	  }
-
+	// Access QuPath's version catalog for dependency versions
+	versionCatalogs {
+		libs {
+			from("io.github.qupath:qupath-catalog:${gradle.ext.qupathVersion}")
+		}
 	}
 
+	repositories {
 
-    versionCatalogs {
-        libs {
-            from("io.github.qupath:qupath-catalog:${gradle.ext.qupathVersion}")
-        }
-    }
-}
+		mavenCentral()
+
+		// Add scijava - which is where QuPath's jars are hosted
+		maven {
+			url "https://maven.scijava.org/content/repositories/releases"
+		}
+
+		maven {
+			url "https://maven.scijava.org/content/repositories/snapshots"
+		}
+
+	}
+}

src/main/java/qupath/ext/bioimageio/BioimageIoCommand.java

@@ -187,13 +187,6 @@ static void showDialog(ImageData<?> imageData, String path) throws IOException {
 
 
 
-//	static PixelClassifier buildPixelClassifier(DnnParameters params, DnnModel<?> model) {
-//		// TODO: Check how to handle padding
-//		var predictionOp = ImageOps.ML.dnn(model, params.getTileWidth(), params.getTileHeight(), Padding.empty());
-//		
-//		return buildPixelClassifier2(params, predictionOp);
-//	}
-
 	static class DnnBuilderPane {
 
 		private QuPathGUI qupath;
@@ -607,8 +600,9 @@ private static void tryToShowImages(Collection<? extends ImagePlus> imps) {
 					var cls = Class.forName("qupath.imagej.gui.IJExtension");
 					var method = cls.getDeclaredMethod("getImageJInstance");
 					ij = (ImageJ)method.invoke(null);
-				} catch (Exception e) {
-					logger.debug("Unable to create ImageJ instance: " + e.getLocalizedMessage(), e);
+				} catch (Throwable t) {
+					// We can get errors here, but should be able to recover
+					logger.warn("Unable to create ImageJ instance: " + t.getLocalizedMessage(), t);
 				}
 			}
 			if (ij != null)