Add Python environment installation prompt and validation logic

Extend Appose integration with a user confirmation dialog for Python environment installation. Refactor environment setup to include validation via `ApposeUtils`.

Author: Stefan Hahmann

src/main/java/org/mastodon/mamut/detection/DeepLearningDetector.java

@@ -33,6 +33,8 @@
 import java.util.List;
 import java.util.Map;
 
+import javax.swing.JOptionPane;
+
 import net.imglib2.Interval;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.img.Img;
@@ -49,6 +51,7 @@
 import org.mastodon.mamut.util.ByteFormatter;
 import org.mastodon.mamut.util.ImgUtils;
 import org.mastodon.mamut.util.LabelImageUtils;
+import org.mastodon.mamut.util.appose.ApposeUtils;
 import org.mastodon.tracking.detection.AbstractDetectorOp;
 import org.mastodon.tracking.detection.DetectionCreatorFactory;
 import org.mastodon.tracking.detection.DetectionUtil;
@@ -110,15 +113,35 @@ public void compute( final List< SourceAndConverter< ? > > sources, final ModelG
 		statusService.showStatus( "Detecting spots..." );
 		try
 		{
-			log.info( "Initialize python environment." );
-			log.info( "On first time use this requires internet connection and may take a couple of minutes." );
-			log.info( "Progress can be observed using FIJI console: FIJI > Window > Console." );
+			log.info( "Initialize python environment.\n" );
+			boolean isEnvInstalled = ApposeUtils.checkEnvironmentInstalled( getPythonEnvName() );
+			if ( !isEnvInstalled )
+			{
+				log.info( "Python environment not yet installed, but can be installed now.\n" );
+				int result = JOptionPane.showConfirmDialog(
+						null,
+						"The required Python environment is not installed.\nWould you like to install it now?\n\nNote: This requires an internet connection and may take several minutes.",
+						"Python Environment Installation",
+						JOptionPane.YES_NO_OPTION,
+						JOptionPane.QUESTION_MESSAGE
+				);
+				if ( result != JOptionPane.YES_OPTION )
+				{
+					log.info( "Python environment installation declined by user." );
+					ok = false;
+					errorMessage = "Python environment installation was declined. Cannot proceed without the required environment.";
+					return;
+				}
+				log.info( "User confirmed installation. Installing Python environment.\n" );
+				log.info( "Installation progress can be observed using FIJI console: FIJI > Window > Console.\n" );
+			}
+			ApposeUtils.confirmEnvInstallation( getPythonEnvName(), log );
 			Environment environment = Appose.mamba().scheme( "environment.yml" ).content( getPythonEnvContent() ).logDebug()
 					.subscribeProgress( ( title, cur, max ) -> logger.info( "{}: {}/{}", title, cur, max ) )
 					.subscribeOutput( logger::info )
 					.subscribeError( logger::error ).build();
 			if ( logger.isInfoEnabled() )
-				logger.info( "Set up environment. Path: {}", environment.base() );
+				logger.info( "Set up environment finished. Path: {}", environment.base() );
 			try (Service python = environment.python())
 			{
 				if ( isWindows() )
@@ -335,6 +358,8 @@ public Map< String, Object > getDefaultSettings()
 
 	protected abstract String getPythonEnvContent();
 
+	protected abstract String getPythonEnvName();
+
 	protected String getPythonEnvInit()
 	{
 		return "import numpy\n";

src/main/java/org/mastodon/mamut/detection/cellpose/Cellpose3Detector.java

@@ -54,6 +54,7 @@
 
 import org.apposed.appose.Service;
 import org.mastodon.mamut.detection.DeepLearningDetector;
+import org.mastodon.mamut.detection.stardist.StarDist;
 import org.mastodon.tracking.mamut.detection.SpotDetectorOp;
 import org.scijava.Priority;
 import org.scijava.plugin.Plugin;
@@ -152,6 +153,12 @@ protected String getPythonEnvContent()
 		return Cellpose3.ENV_FILE_CONTENT;
 	}
 
+	@Override
+	protected String getPythonEnvName()
+	{
+		return Cellpose3.ENV_NAME;
+	}
+
 	@Override
 	protected String getImportScript( final boolean dataIs2D )
 	{

src/main/java/org/mastodon/mamut/detection/cellpose/Cellpose4Detector.java

@@ -50,6 +50,7 @@
 
 import org.apposed.appose.Service;
 import org.mastodon.mamut.detection.DeepLearningDetector;
+import org.mastodon.mamut.detection.stardist.StarDist;
 import org.mastodon.tracking.mamut.detection.SpotDetectorOp;
 import org.mastodon.tracking.mamut.trackmate.wizard.descriptors.cellpose.Cellpose4DetectorDescriptor;
 import org.scijava.Priority;
@@ -137,6 +138,12 @@ protected String getPythonEnvContent()
 		return Cellpose4.ENV_FILE_CONTENT;
 	}
 
+	@Override
+	protected String getPythonEnvName()
+	{
+		return Cellpose4.ENV_NAME;
+	}
+
 	@Override
 	protected String getImportScript( final boolean dataIs2D )
 	{

src/main/java/org/mastodon/mamut/detection/stardist/StarDistDetector.java

@@ -151,6 +151,12 @@ protected String getPythonEnvContent()
 		return StarDist.ENV_FILE_CONTENT;
 	}
 
+	@Override
+	protected String getPythonEnvName()
+	{
+		return StarDist.ENV_NAME;
+	}
+
 	@Override
 	protected String getImportScript( final boolean dataIs2D )
 	{

src/main/java/org/mastodon/mamut/linking/trackastra/TrackastraLinker.java

@@ -15,6 +15,7 @@
 import net.imglib2.util.Cast;
 
 import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.tuple.Pair;
 import org.apposed.appose.Appose;
 import org.apposed.appose.Environment;
 import org.apposed.appose.Service;
@@ -28,6 +29,7 @@
 import org.mastodon.mamut.linking.trackastra.appose.types.RegionProps;
 import org.mastodon.mamut.linking.trackastra.appose.types.SingleTimepointRegionProps;
 import org.mastodon.mamut.util.ResourceUtils;
+import org.mastodon.mamut.util.appose.ApposeUtils;
 import org.mastodon.spatial.HasTimepoint;
 import org.mastodon.spatial.SpatioTemporalIndex;
 import org.mastodon.tracking.linking.graph.AbstractGraphParticleLinkerOp;
@@ -57,10 +59,20 @@ public void mutate1( final ReadOnlyGraph< V, E > graph, final SpatioTemporalInde
 		Environment environment;
 		try
 		{
-			environment = Appose.mamba().scheme( "environment.yml" ).content( TrackastraUtils.ENV_FILE_CONTENT ).logDebug()
-					.subscribeProgress( ( title, cur, max ) -> log.info( "{}: {}/{}", title, cur, max ) )
-					.subscribeOutput( log::info )
-					.subscribeError( log::error ).build();
+			Pair< Boolean, String > checkResult = ApposeUtils.confirmEnvInstallation( TrackastraUtils.ENV_NAME, logger );
+			if ( Boolean.TRUE.equals( checkResult.getKey() ) )
+			{
+				environment = Appose.mamba().scheme( "environment.yml" ).content( TrackastraUtils.ENV_FILE_CONTENT ).logDebug()
+						.subscribeProgress( ( title, cur, max ) -> log.info( "{}: {}/{}", title, cur, max ) )
+						.subscribeOutput( log::info )
+						.subscribeError( log::error ).build();
+			}
+			else
+			{
+				ok = false;
+				errorMessage = checkResult.getValue();
+				return;
+			}
 		}
 		catch ( IOException e )
 		{

src/main/java/org/mastodon/mamut/util/appose/ApposeUtils.java

@@ -17,6 +17,7 @@
 import javax.swing.JOptionPane;
 import javax.swing.SwingUtilities;
 
+import org.apache.commons.lang3.tuple.Pair;
 import org.apposed.appose.Appose;
 import org.apposed.appose.builder.Builders;
 import org.apposed.appose.util.Environments;
@@ -137,7 +138,7 @@ public static void deleteDirectory( final File dir ) throws IOException
 	 * @param directory The directory whose size is to be calculated. Must not be null and must represent a valid directory.
 	 * @return The total size of the directory in bytes. If the directory does not exist or is null, the method will return 0.
 	 */
-	public static long calculateDirectorySize( File directory )
+	public static long calculateDirectorySize( final File directory )
 	{
 		if ( directory == null || !directory.exists() )
 		{
@@ -166,7 +167,7 @@ public static long calculateDirectorySize( File directory )
 	}
 
 	// --- Linux/macOS: actual disk usage, like du -sb ---
-	private static long calculateDiskUsageUnix( Path directory ) throws IOException
+	private static long calculateDiskUsageUnix( final Path directory ) throws IOException
 	{
 		final long[] total = { 0 };
 		boolean hasUnixView = supportsUnixAttributes();
@@ -205,7 +206,7 @@ private static boolean supportsUnixAttributes()
 	 * Returns the disk usage (in bytes) for a single file.
 	 * Uses actual allocated blocks if the unix view is supported.
 	 */
-	private static long getFileDiskUsage( Path file, boolean hasUnixView ) throws IOException
+	private static long getFileDiskUsage( final Path file, final boolean hasUnixView ) throws IOException
 	{
 		if ( !hasUnixView )
 			return Files.size( file );
@@ -224,7 +225,7 @@ private static long getFileDiskUsage( Path file, boolean hasUnixView ) throws IO
 	}
 
 	// --- Windows / fallback: logical file sizes only ---
-	private static long calculateFileLengthRecursive( File directory )
+	private static long calculateFileLengthRecursive( final File directory )
 	{
 		long size = 0;
 		File[] files = directory.listFiles();
@@ -242,4 +243,41 @@ else if ( file.isDirectory() )
 		}
 		return size;
 	}
+
+	/**
+	 * Checks whether a specific Python environment is installed and prompts the user to install it
+	 * if it is not already installed. The user is presented with a dialog box to confirm the installation.
+	 * If the user declines, the method a pair consisting of {@code false} and an appropriate message.
+	 *
+	 * @param envName The name of the environment to check. This should match the directory
+	 *                name inside the appose environments directory.
+	 * @param log     The logger instance used for logging messages during the environment check
+	 *                and installation process.
+	 * @return A pair where the first element is a boolean indicating if the environment is installed
+	 *         or was successfully triggered for installation, and the second element is a message
+	 *         providing additional information about the process or failure reason.
+	 */
+	public static Pair< Boolean, String > confirmEnvInstallation( final String envName, final org.scijava.log.Logger log )
+	{
+		boolean isEnvInstalled = checkEnvironmentInstalled( envName );
+		if ( !isEnvInstalled )
+		{
+			log.info( "Python environment not yet installed, but can be installed now.\n" );
+			int result = JOptionPane.showConfirmDialog(
+					null,
+					"The required Python environment is not installed.\nWould you like to install it now?\n\nNote: This requires an internet connection and may take several minutes.",
+					"Python Environment Installation",
+					JOptionPane.YES_NO_OPTION,
+					JOptionPane.QUESTION_MESSAGE
+			);
+			if ( result != JOptionPane.YES_OPTION )
+			{
+				log.info( "Python environment installation declined by user." );
+				return Pair.of( false, "Python environment installation was declined. Cannot proceed without the required environment." );
+			}
+			log.info( "User confirmed installation. Installing Python environment.\n" );
+			log.info( "Installation progress can be observed using FIJI console: FIJI > Window > Console.\n" );
+		}
+		return Pair.of( true, "" );
+	}
 }