Improve directory size calculation with Unix support and symbolic link handling

Author: stefanhahmann

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

@@ -41,7 +41,7 @@
 import net.imglib2.view.IntervalView;
 import net.imglib2.view.Views;
 
-import org.mastodon.mamut.util.ApposeProcess;
+import org.mastodon.mamut.util.appose.ApposeProcess;
 import org.mastodon.mamut.util.ByteFormatter;
 import org.mastodon.mamut.detection.util.SpimImageProperties;
 import org.mastodon.mamut.model.ModelGraph;

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

@@ -41,7 +41,7 @@
 
 import org.apposed.appose.NDArray;
 import org.apposed.appose.Service;
-import org.mastodon.mamut.util.ApposeProcess;
+import org.mastodon.mamut.util.appose.ApposeProcess;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

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

@@ -37,6 +37,24 @@
  */
 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";
+
 	private final ModelType modelType;
 	private double anisotropy = 1;
 
@@ -87,21 +105,7 @@ protected String getEvaluateModelCommand()
 	@Override
 	protected String generateEnvFileContent()
 	{
-		return "name: cellpose3\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"
-				+ getApposePythonVersion()
-				+ "  - pytorch\n"
-				+ "  - pytorch-cuda\n"
-				+ "  - numpy\n";
+		return ENV_FILE_CONTENT;
 	}
 
 	public enum ModelType

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

@@ -36,6 +36,24 @@
  */
 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 Cellpose4() throws IOException
 	{
 		super();
@@ -66,21 +84,6 @@ protected String getEvaluateModelCommand()
 	@Override
 	protected String generateEnvFileContent()
 	{
-		return "name: cellpose4\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"
-				// + getApposeVersion().substring( 2 ) + "\n"
-				+ "  - pytorch\n"
-				+ "  - pytorch-cuda\n"
-				+ "  - numpy\n"
-				+ "  - pip\n"
-				+ "  - pip:\n"
-				+ "    " + getApposePythonVersion() + "\n";
+		return ENV_FILE_CONTENT;
 	}
 }

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

@@ -57,6 +57,23 @@
  */
 public class StarDist extends Segmentation
 {
+	public static final String ENV_NAME = "stardist";
+
+	public static final String ENV_FILE_CONTENT = "name: " + ENV_NAME + "\n"
+			+ "channels:\n"
+			+ "  - conda-forge\n"
+			+ "channel_priority: strict\n"
+			+ "dependencies:\n"
+			+ "  - python=3.10\n"
+			+ getCuda()
+			+ "  - numpy<1.24\n"
+			+ "  - pip\n"
+			+ "  - pip:\n"
+			+ "    - numpy<1.24\n"
+			+ getTensorflow()
+			+ "    - stardist==0.8.5\n"
+			+ "    - appose==" + APPOSE_PYTHON_VERSION + "\n";
+
 	private static final Logger logger = LoggerFactory.getLogger( MethodHandles.lookup().lookupClass() );
 
 	private final ModelType modelType;
@@ -146,31 +163,18 @@ private static void createConfigFromBioimageio( final ModelDescriptor descriptor
 	@Override
 	protected String generateEnvFileContent()
 	{
-		return "name: stardist\n"
-				+ "channels:\n"
-				+ "  - conda-forge\n"
-				+ "channel_priority: strict\n"
-				+ "dependencies:\n"
-				+ "  - python=3.10\n"
-				+ getCuda()
-				+ "  - numpy<1.24\n"
-				+ "  - pip\n"
-				+ "  - pip:\n"
-				+ "    - numpy<1.24\n"
-				+ getTensorflow()
-				+ "    - stardist==0.8.5\n"
-				+ getApposePythonVersion();
+		return ENV_FILE_CONTENT;
 	}
 
-	private String getCuda()
+	private static String getCuda()
 	{
 		if ( System.getProperty( "os.name" ).toLowerCase().contains( "mac" ) )
 			return "";
 		return "  - cudatoolkit=11.2\n"
 				+ "  - cudnn=8.1.0\n";
 	}
 
-	private String getTensorflow()
+	private static String getTensorflow()
 	{
 		if ( System.getProperty( "os.name" ).toLowerCase().contains( "mac" ) )
 			return "    - tensorflow-macos==2.10\n"

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

@@ -11,12 +11,27 @@
 import java.util.HashMap;
 import java.util.Map;
 
+import org.mastodon.mamut.util.appose.ApposeProcess;
 import org.mastodon.tracking.detection.DetectorKeys;
 
 public class TrackastraUtils
 {
+
 	public static final String TRACKASTRA_VERSION = "0.4.2";
 
+	public static final String ENV_NAME = "trackastra";
+
+	public static final String ENV_FILE_CONTENT = "name: " + ENV_NAME + "\n"
+			+ "channels:\n"
+			+ "  - conda-forge\n"
+			+ "channel_priority: strict\n"
+			+ "dependencies:\n"
+			+ "  - python=3.10\n"
+			+ "  - pip\n"
+			+ "  - pip:\n"
+			+ "    - appose==" + ApposeProcess.APPOSE_PYTHON_VERSION + "\n"
+			+ "    - trackastra==" + TRACKASTRA_VERSION + "\n";
+
 	public static final String KEY_EDGE_THRESHOLD = "trackastraEdgeThreshold";
 
 	public static final String KEY_TRACKASTRA_MODE = "trackastraMode";
@@ -46,18 +61,9 @@ private TrackastraUtils()
 		// prevent instantiation
 	}
 
-	public static String getEnv( final String apposeVersion )
+	public static String getEnv()
 	{
-		return "name: trackastra\n"
-				+ "channels:\n"
-				+ "  - conda-forge\n"
-				+ "channel_priority: strict\n"
-				+ "dependencies:\n"
-				+ "  - python=3.10\n"
-				+ "  - pip\n"
-				+ "  - pip:\n"
-				+ apposeVersion + "\n"
-				+ "    - trackastra==" + TRACKASTRA_VERSION + "\n";
+		return ENV_FILE_CONTENT;
 	}
 
 	public static Map< String, Object > getDefaultTrackAstraSettingsMap()

src/main/java/org/mastodon/mamut/linking/trackastra/appose/computation/LinkPrediction.java

@@ -29,7 +29,7 @@
 import org.mastodon.mamut.linking.trackastra.TrackastraUtils;
 import org.mastodon.mamut.linking.trackastra.appose.types.RegionProps;
 import org.mastodon.mamut.model.Spot;
-import org.mastodon.mamut.util.ApposeProcess;
+import org.mastodon.mamut.util.appose.ApposeProcess;
 import org.mastodon.mamut.util.ResourceUtils;
 import org.mastodon.spatial.SpatioTemporalIndex;
 import org.mastodon.tracking.linking.EdgeCreator;
@@ -179,7 +179,7 @@ private float getFloat( RandomAccess< ? > ra, int col, int row )
 	@Override
 	protected String generateEnvFileContent()
 	{
-		return TrackastraUtils.getEnv( getApposePythonVersion() );
+		return TrackastraUtils.getEnv();
 	}
 
 	@Override

src/main/java/org/mastodon/mamut/linking/trackastra/appose/computation/RegionPropsComputation.java

@@ -33,7 +33,7 @@
 import org.mastodon.mamut.linking.trackastra.TrackastraUtils;
 import org.mastodon.mamut.linking.trackastra.appose.types.SingleTimepointRegionProps;
 import org.mastodon.mamut.model.Spot;
-import org.mastodon.mamut.util.ApposeProcess;
+import org.mastodon.mamut.util.appose.ApposeProcess;
 import org.mastodon.mamut.util.ImgUtils;
 import org.mastodon.mamut.util.ResourceUtils;
 import org.mastodon.spatial.SpatioTemporalIndex;
@@ -164,7 +164,7 @@ private void formatProgress( final int done, final int todo )
 	@Override
 	protected String generateEnvFileContent()
 	{
-		return TrackastraUtils.getEnv( getApposePythonVersion() );
+		return TrackastraUtils.getEnv();
 	}
 
 	@Override

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

@@ -0,0 +1,120 @@
+/*-
+ * #%L
+ * mastodon-deep-lineage
+ * %%
+ * Copyright (C) 2022 - 2025 Stefan Hahmann
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+package org.mastodon.mamut.util.appose;
+
+import static org.mastodon.app.ui.ViewMenuBuilder.item;
+import static org.mastodon.app.ui.ViewMenuBuilder.menu;
+
+import java.util.Collections;
+import java.util.List;
+
+import javax.swing.SwingUtilities;
+
+import org.mastodon.app.ui.ViewMenuBuilder;
+import org.mastodon.mamut.KeyConfigScopes;
+import org.mastodon.mamut.ProjectModel;
+import org.mastodon.mamut.plugin.MamutPlugin;
+import org.mastodon.ui.keymap.KeyConfigContexts;
+import org.scijava.AbstractContextual;
+import org.scijava.command.CommandService;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+import org.scijava.ui.behaviour.io.gui.CommandDescriptionProvider;
+import org.scijava.ui.behaviour.io.gui.CommandDescriptions;
+import org.scijava.ui.behaviour.util.AbstractNamedAction;
+import org.scijava.ui.behaviour.util.Actions;
+import org.scijava.ui.behaviour.util.RunnableAction;
+
+@SuppressWarnings( "unused" )
+@Plugin( type = MamutPlugin.class )
+public class ApposeEnvsPlugin extends AbstractContextual implements MamutPlugin
+{
+	private static final String COMMAND_NAME = "Python environments for detectors/linkers";
+
+	private static final String[] SHORT_CUT = { "ctrl shift P" };
+
+	private final AbstractNamedAction action;
+
+	@SuppressWarnings( "unused" )
+	@Parameter
+	private CommandService commandService;
+
+	@SuppressWarnings( "unused" )
+	public ApposeEnvsPlugin()
+	{
+		action = new RunnableAction( COMMAND_NAME, this::open );
+	}
+
+	@Override
+	public void setAppPluginModel( final ProjectModel projectModel )
+	{
+		// Nothing to do
+	}
+
+	@Override
+	public List< ViewMenuBuilder.MenuItem > getMenuItems()
+	{
+		return Collections.singletonList(
+				menu( "Plugins", menu( "Tracking", item( COMMAND_NAME ) ) ) );
+	}
+
+	@Override
+	public void installGlobalActions( Actions actions )
+	{
+		actions.namedAction( action, SHORT_CUT );
+	}
+
+	private void open()
+	{
+		SwingUtilities.invokeLater( () -> {
+			PythonEnvironmentManagerUI dialog = new PythonEnvironmentManagerUI( null );
+			dialog.setVisible( true );
+		} );
+	}
+
+	/*
+	 * Command descriptions for all provided commands
+	 */
+	@Plugin( type = CommandDescriptionProvider.class )
+	public static class Descriptions extends CommandDescriptionProvider
+	{
+		public Descriptions()
+		{
+			super( KeyConfigScopes.MAMUT, KeyConfigContexts.MASTODON );
+		}
+
+		@Override
+		public void getCommandDescriptions( final CommandDescriptions descriptions )
+		{
+			descriptions.add(
+					COMMAND_NAME, SHORT_CUT,
+					"Open the Python environment manager." );
+		}
+	}
+}