Fix (Windows) Cellpose 3/4 issues by migrating environments to TOML

src/main/java/org/mastodon/mamut/detection/cellpose/Cellpose3.java

@@ -33,6 +33,7 @@
 import javax.annotation.Nullable;
 
 import org.apposed.appose.Service;
+import org.mastodon.mamut.util.ResourceUtils;
 
 /**
  * Cellpose3 is a specialized implementation of the {@link Cellpose} class, specifically
@@ -43,21 +44,11 @@ public class Cellpose3 extends Cellpose
 {
 	public static final String ENV_NAME = "cellpose3";
 
-	public static final String ENV_FILE_CONTENT = "name: " + ENV_NAME + "\n"
-			+ "channels:\n"
-			+ "  - nvidia\n"
-			+ "  - pytorch\n"
-			+ "  - conda-forge\n"
-			+ "channel_priority: strict\n"
-			+ "dependencies:\n"
-			+ "  - python=3.10\n"
-			+ "  - pip\n"
-			+ "  - pip:\n"
-			+ "    - cellpose==3.1.1.2\n"
-			+ "    - appose==" + APPOSE_PYTHON_VERSION + "\n"
-			+ "  - pytorch\n"
-			+ "  - pytorch-cuda\n"
-			+ "  - numpy\n";
+	public static final String ENV_FILE_CONTENT =
+			ResourceUtils.readResourceAsString( "org/mastodon/mamut/detection/cellpose/cellpose3.toml", Cellpose3.class )
+					.replace( "{ENV_NAME}", ENV_NAME )
+					.replace( "{APPOSE_VERSION}", APPOSE_PYTHON_VERSION );
+
 
 	private final ModelType modelType;
 

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

@@ -179,7 +179,7 @@ protected String getPythonEnvName()
 	@Override
 	protected Builder< ? > getBuilder()
 	{
-		return Appose.mamba().scheme( "environment.yml" );
+		return Appose.pixi();
 	}
 
 	@Override

src/main/java/org/mastodon/mamut/detection/cellpose/Cellpose4.java

@@ -33,6 +33,7 @@
 import javax.annotation.Nullable;
 
 import org.apposed.appose.Service;
+import org.mastodon.mamut.util.ResourceUtils;
 
 /**
  * Cellpose3 is a specialized implementation of the {@link Cellpose} class, specifically
@@ -42,21 +43,10 @@ public class Cellpose4 extends Cellpose
 {
 	public static final String ENV_NAME = "cellpose4";
 
-	public static final String ENV_FILE_CONTENT = "name: " + ENV_NAME + "\n"
-			+ "channels:\n"
-			+ "  - nvidia\n"
-			+ "  - pytorch\n"
-			+ "  - conda-forge\n"
-			+ "channel_priority: strict\n"
-			+ "dependencies:\n"
-			+ "  - python=3.10\n"
-			+ "  - cellpose==4.0.6\n"
-			+ "  - pytorch\n"
-			+ "  - pytorch-cuda\n"
-			+ "  - numpy\n"
-			+ "  - pip\n"
-			+ "  - pip:\n"
-			+ "    - appose==" + APPOSE_PYTHON_VERSION + "\n";
+	public static final String ENV_FILE_CONTENT =
+			ResourceUtils.readResourceAsString( "org/mastodon/mamut/detection/cellpose/cellpose4.toml", Cellpose4.class )
+					.replace( "{ENV_NAME}", ENV_NAME )
+					.replace( "{APPOSE_VERSION}", APPOSE_PYTHON_VERSION );
 
 	public Cellpose4( final Service python, final @Nullable org.scijava.log.Logger scijavaLogger ) throws IOException
 	{

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

@@ -163,7 +163,7 @@ protected String getPythonEnvName()
 	@Override
 	protected Builder< ? > getBuilder()
 	{
-		return Appose.mamba().scheme( "environment.yml" );
+		return Appose.pixi();
 	}
 
 	@Override

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

@@ -178,13 +178,13 @@ private Path getStarDistModelRoot()
 	{
 		if ( modelType.getModelPath() == null )
 			return null;
-		return Paths.get( System.getProperty( "user.home" ), ".local", "share", "appose", "stardist", "models", modelType.getModelPath() );
+		return Paths.get( System.getProperty( "user.home" ), ".local", "share", "appose", ENV_NAME, "models", modelType.getModelPath() );
 	}
 
 	private static void createConfigFromBioimageio( final ModelDescriptor descriptor, final String modelDir )
 			throws IOException
 	{
-		Map< String, Object > stardistMap = Cast.unchecked( descriptor.getConfig().getSpecMap().get( "stardist" ) );
+		Map< String, Object > stardistMap = Cast.unchecked( descriptor.getConfig().getSpecMap().get( ENV_NAME ) );
 		Map< String, Object > stardistConfig = Cast.unchecked( stardistMap.get( "config" ) );
 		File jsonFile = new File( modelDir, "config.json" );
 		logger.info( "Creating config.json file: {}", jsonFile.getAbsolutePath() );

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

@@ -46,7 +46,7 @@
 import javax.swing.SwingUtilities;
 
 import org.apache.commons.lang3.tuple.Pair;
-import org.apposed.appose.Appose;
+import org.apposed.appose.Builder;
 import org.apposed.appose.builder.Builders;
 import org.apposed.appose.util.Environments;
 import org.mastodon.mamut.util.ByteFormatter;
@@ -71,9 +71,9 @@ private ApposeUtils()
 	 *                   to set up the environment.
 	 * @throws IOException If an I/O error occurs during the installation process.
 	 */
-	public static void installEnvironment( final String envContent ) throws IOException
+	public static void installEnvironment(final String envContent, final Builder<?> envBuilder) throws IOException
 	{
-		Appose.mamba().content( envContent ).scheme( "environment.yml" ).logDebug().rebuild();
+		envBuilder.content( envContent ).logDebug().rebuild();
 	}
 
 	/**

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

@@ -60,6 +60,8 @@
 
 import net.miginfocom.swing.MigLayout;
 
+import org.apposed.appose.Appose;
+import org.apposed.appose.Builder;
 import org.apposed.appose.util.Environments;
 import org.mastodon.app.MastodonIcons;
 import org.mastodon.mamut.detection.cellpose.Cellpose3;
@@ -104,10 +106,10 @@ public PythonEnvironmentManagerUI( JFrame owner )
 	private void initEnvironmentPanels()
 	{
 		environmentPanels = new ArrayList<>();
-		environmentPanels.add( new EnvironmentPanel( Cellpose3.ENV_NAME, Cellpose3.ENV_FILE_CONTENT ) );
-		environmentPanels.add( new EnvironmentPanel( Cellpose4.ENV_NAME, Cellpose4.ENV_FILE_CONTENT ) );
-		environmentPanels.add( new EnvironmentPanel( StarDist.ENV_NAME, StarDist.ENV_FILE_CONTENT ) );
-		environmentPanels.add( new EnvironmentPanel( TrackastraUtils.ENV_NAME, TrackastraUtils.ENV_FILE_CONTENT ) );
+		environmentPanels.add( new EnvironmentPanel( Cellpose3.ENV_NAME, Cellpose3.ENV_FILE_CONTENT, Appose.pixi() ) );
+		environmentPanels.add( new EnvironmentPanel( Cellpose4.ENV_NAME, Cellpose4.ENV_FILE_CONTENT, Appose.pixi() ) );
+		environmentPanels.add( new EnvironmentPanel( StarDist.ENV_NAME, StarDist.ENV_FILE_CONTENT, Appose.pixi() ) );
+		environmentPanels.add( new EnvironmentPanel( TrackastraUtils.ENV_NAME, TrackastraUtils.ENV_FILE_CONTENT, Appose.mamba().scheme( "environment.yml" ) ) );
 	}
 
 	private void initLayout()
@@ -163,6 +165,8 @@ private class EnvironmentPanel extends JPanel
 
 		private final String envContent;
 
+		private final Builder< ? > envBuilder;
+
 		private final JLabel statusIcon;
 
 		private final JLabel statusLabel;
@@ -173,11 +177,12 @@ private class EnvironmentPanel extends JPanel
 
 		private final JLabel sizeValueLabel;
 
-		private EnvironmentPanel( String envName, String envContent )
+		private EnvironmentPanel( final String envName, final String envContent, final Builder< ? > envBuilder )
 		{
 			super( new MigLayout( "fill, insets 8", "[][80!][grow][]", "[]5[]5[]" ) );
 			this.envName = envName;
 			this.envContent = envContent;
+			this.envBuilder = envBuilder;
 
 			statusIcon = new JLabel();
 			statusLabel = new JLabel();
@@ -358,7 +363,7 @@ private void installEnvironmentUI()
 					() -> {
 						try
 						{
-							ApposeUtils.installEnvironment( envContent );
+							ApposeUtils.installEnvironment( envContent, envBuilder );
 						}
 						catch ( IOException e )
 						{

src/main/resources/org/mastodon/mamut/detection/cellpose/cellpose3.toml

@@ -0,0 +1,58 @@
+[workspace]
+name = "{ENV_NAME}"
+version = "0.0.1"
+description = "Cellpose3 segmentation environment."
+authors = ["Stefan Hahmann"]
+channels = ["conda-forge", "pytorch", "nvidia"]
+platforms = ["osx-arm64", "osx-64", "linux-64", "win-64"]
+
+[dependencies]
+numpy = ">=1.20,<2.1"
+pip = "*"
+
+[pypi-dependencies]
+appose = "=={APPOSE_VERSION}"
+
+# ---------------------------------------------------------------------------
+# macOS Apple Silicon
+# ---------------------------------------------------------------------------
+[target.osx-arm64.dependencies]
+python = "3.10.*"
+
+[target.osx-arm64.pypi-dependencies]
+cellpose = "==3.1.1.2"
+torch = "==2.10.0"
+torchvision = "==0.25.0"
+
+# ---------------------------------------------------------------------------
+# macOS Intel
+# ---------------------------------------------------------------------------
+[target.osx-64.dependencies]
+python = "3.10.*"
+
+[target.osx-64.pypi-dependencies]
+cellpose = "==3.1.1.2"
+torch = "==2.1.2"
+torchvision = "==0.16.2"
+
+# ---------------------------------------------------------------------------
+# Linux
+# ---------------------------------------------------------------------------
+[target.linux-64.dependencies]
+python = "3.10.*"
+pytorch = "*"
+pytorch-gpu = "*"
+
+[target.linux-64.pypi-dependencies]
+cellpose = "==3.1.1.2"
+
+# ---------------------------------------------------------------------------
+# Windows
+# ---------------------------------------------------------------------------
+[target.win-64.dependencies]
+python = "3.10.*"
+pytorch = "*"
+pytorch-gpu = "*"
+
+[target.win-64.pypi-dependencies]
+cellpose = "==3.1.1.2"

src/main/resources/org/mastodon/mamut/detection/cellpose/cellpose4.toml

@@ -0,0 +1,58 @@
+[workspace]
+name = "{ENV_NAME}"
+version = "0.0.1"
+description = "Cellpose4 segmentation environment."
+authors = ["Stefan Hahmann"]
+channels = ["conda-forge", "pytorch", "nvidia"]
+platforms = ["osx-arm64", "osx-64", "linux-64", "win-64"]
+
+[dependencies]
+numpy = "*"
+pip = "*"
+
+[pypi-dependencies]
+appose = "=={APPOSE_VERSION}"
+
+# ---------------------------------------------------------------------------
+# macOS Apple Silicon
+# ---------------------------------------------------------------------------
+[target.osx-arm64.dependencies]
+python = "3.11.*"
+
+[target.osx-arm64.pypi-dependencies]
+cellpose = "==4.0.8"
+torch = "==2.10.0"
+torchvision = "==0.25.0"
+
+# ---------------------------------------------------------------------------
+# macOS Intel
+# ---------------------------------------------------------------------------
+[target.osx-64.dependencies]
+python = "3.10.*"
+
+[target.osx-64.pypi-dependencies]
+cellpose = "==4.0.8"
+torch = "==2.1.2"
+torchvision = "==0.16.2"
+
+# ---------------------------------------------------------------------------
+# Linux
+# ---------------------------------------------------------------------------
+[target.linux-64.dependencies]
+python = "3.10.*"
+pytorch = "*"
+pytorch-gpu = "*"
+
+[target.linux-64.pypi-dependencies]
+cellpose = "==4.0.8"
+
+# ---------------------------------------------------------------------------
+# Windows
+# ---------------------------------------------------------------------------
+[target.win-64.dependencies]
+python = "3.10.*"
+pytorch = "*"
+pytorch-gpu = "*"
+
+[target.win-64.pypi-dependencies]
+cellpose = "==4.0.8"

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

@@ -58,7 +58,7 @@
 class Cellpose4DetectorTest
 {
 
-	@Disabled( "This test is disabled, because it has very long runtime (> 5 minutes)" )
+	// @Disabled( "This test is disabled, because it has very long runtime (> 5 minutes)" )
 	@Test
 	void testCompute3D() throws IllegalAccessException, NoSuchFieldException
 	{

src/test/java/org/mastodon/mamut/util/appose/ApposeUtilsTest.java

@@ -38,6 +38,8 @@
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 
+import org.apposed.appose.Appose;
+import org.apposed.appose.Builder;
 import org.junit.jupiter.api.Test;
 
 class ApposeUtilsTest
@@ -51,8 +53,9 @@ void testInstallDeleteExistsSize() throws IOException
 				+ "  - conda-forge\n"
 				+ "dependencies:\n"
 				+ "  - python=3.10\n";
+		Builder<?> envBuilder = Appose.mamba().scheme( "environment.yml" );
 
-		ApposeUtils.installEnvironment( testEnvContent );
+		ApposeUtils.installEnvironment( testEnvContent, envBuilder );
 		assertTrue( ApposeUtils.checkEnvironmentInstalled( testEnvName ) );
 		String size = ApposeUtils.calculateEnvironmentSize( testEnvName );
 		String numberPart = size.split( " " )[ 0 ]; // "123,4"