Enable confirmEnvInstallation flag and inject logger in detector/linker tests for enhanced flexibility and debugging.

Author: Stefan Hahmann

src/test/java/org/mastodon/mamut/detection/cellpose/Cellpose3DetectorTest.java

@@ -54,6 +54,7 @@
 import org.mastodon.mamut.io.importer.labelimage.util.DemoUtils;
 import org.mastodon.mamut.model.Model;
 import org.mastodon.tracking.detection.DetectorKeys;
+import org.mastodon.tracking.mamut.detection.AbstractSpotDetectorOp;
 import org.scijava.Context;
 
 import io.scif.img.ImgOpener;
@@ -63,12 +64,18 @@ class Cellpose3DetectorTest
 
 	@Disabled( "This test is disabled, because it has very long runtime (> 2 minutes)" )
 	@Test
-	void testCompute3D() throws IllegalAccessException, URISyntaxException
+	void testCompute3D() throws IllegalAccessException, URISyntaxException, NoSuchFieldException
 	{
 		Cellpose3Detector detector = new Cellpose3Detector();
+		detector.setConfirmEnvInstallation( false );
 
 		try (Context context = new Context())
 		{
+			org.scijava.log.Logger log = context.getService( org.scijava.log.LogService.class ).subLogger( "Cellpose3DetectorTest" );
+			Field logger = AbstractSpotDetectorOp.class.getDeclaredField( "log" );
+			logger.setAccessible( true );
+			logger.set( detector, log );
+
 			ImgOpener imgOpener = new ImgOpener();
 			URL url3d = getClass().getClassLoader().getResource( "org/mastodon/mamut/appose/nuclei_3d.tif" );
 			URL url2d = getClass().getClassLoader().getResource( "org/mastodon/mamut/appose/blobs.tif" );

src/test/java/org/mastodon/mamut/detection/cellpose/Cellpose4DetectorTest.java

@@ -51,6 +51,7 @@
 import org.mastodon.mamut.io.importer.labelimage.util.SphereRenderer;
 import org.mastodon.mamut.model.Model;
 import org.mastodon.tracking.detection.DetectorKeys;
+import org.mastodon.tracking.mamut.detection.AbstractSpotDetectorOp;
 import org.scijava.Context;
 
 
@@ -59,13 +60,19 @@ class Cellpose4DetectorTest
 
 	@Disabled( "This test is disabled, because it has very long runtime (> 5 minutes)" )
 	@Test
-	void testCompute3D() throws IllegalAccessException
+	void testCompute3D() throws IllegalAccessException, NoSuchFieldException
 	{
 		Cellpose4Detector detector = new Cellpose4Detector();
+		detector.setConfirmEnvInstallation( false );
 		Model model = new Model();
 
 		try (Context context = new Context())
 		{
+			org.scijava.log.Logger log = context.getService( org.scijava.log.LogService.class ).subLogger( "Cellpose4DetectorTest" );
+			Field logger = AbstractSpotDetectorOp.class.getDeclaredField( "log" );
+			logger.setAccessible( true );
+			logger.set( detector, log );
+
 			Img< FloatType > img = ArrayImgs.floats( 12, 12, 12 );
 			SphereRenderer.renderSphere( new int[] { 5, 5, 5 }, 5, 100, img );
 			context.inject( detector ); // make sure the detector is initialized with the context

src/test/java/org/mastodon/mamut/detection/stardist/StarDistDetectorTest.java

@@ -48,6 +48,7 @@
 import org.mastodon.mamut.io.importer.labelimage.util.DemoUtils;
 import org.mastodon.mamut.model.Model;
 import org.mastodon.tracking.detection.DetectorKeys;
+import org.mastodon.tracking.mamut.detection.AbstractSpotDetectorOp;
 import org.mastodon.tracking.mamut.trackmate.wizard.descriptors.StarDistDetectorDescriptor;
 import org.scijava.Context;
 
@@ -57,12 +58,18 @@ class StarDistDetectorTest
 {
 	@Disabled( "This test is disabled, because it has very long runtime (> 2 minutes)" )
 	@Test
-	void testCompute3D() throws IllegalAccessException, URISyntaxException
+	void testCompute3D() throws IllegalAccessException, URISyntaxException, NoSuchFieldException
 	{
 		StarDistDetector detector = new StarDistDetector();
+		detector.setConfirmEnvInstallation( false );
 
 		try (Context context = new Context())
 		{
+			org.scijava.log.Logger log = context.getService( org.scijava.log.LogService.class ).subLogger( "StarDistDetectorTest" );
+			Field logger = AbstractSpotDetectorOp.class.getDeclaredField( "log" );
+			logger.setAccessible( true );
+			logger.set( detector, log );
+
 			ImgOpener imgOpener = new ImgOpener();
 			URL url3d = getClass().getClassLoader().getResource( "org/mastodon/mamut/appose/nuclei_3d.tif" );
 			URL url2d = getClass().getClassLoader().getResource( "org/mastodon/mamut/appose/blobs.tif" );

src/test/java/org/mastodon/mamut/linking/trackastra/TrackastraLinkerTest.java

@@ -50,6 +50,7 @@ void testLinking3D() throws IOException, SpimDataException, NoSuchFieldException
 		assertEquals( 10, graph.vertices().size() );
 		assertEquals( 0, graph.edges().size() );
 		TrackastraLinker< Spot, Link > linker = new TrackastraLinker<>();
+		linker.setConfirmEnvInstallation( false );
 		Map< String, Object > settingsMap = TrackastraUtils.getDefaultTrackAstraSettingsMap();
 		settingsMap.put( KEY_MAX_TIMEPOINT, 4 );
 		settingsMap.put( KEY_SOURCE, appModel.getSharedBdvData().getSources().get( 0 ).getSpimSource() );
@@ -91,6 +92,7 @@ void testLinking2D() throws IOException, SpimDataException, NoSuchFieldException
 		assertEquals( 13, graph.vertices().size() );
 		assertEquals( 0, graph.edges().size() );
 		TrackastraLinker< Spot, Link > linker = new TrackastraLinker<>();
+		linker.setConfirmEnvInstallation( false );
 		Map< String, Object > settingsMap = TrackastraUtils.getDefaultTrackAstraSettingsMap();
 		settingsMap.put( KEY_MAX_TIMEPOINT, 4 );
 		settingsMap.put( KEY_SOURCE, appModel.getSharedBdvData().getSources().get( 0 ).getSpimSource() );