Refactor AutoMicTools specific code into general table opening code

src/main/java/org/embl/mobie/MoBIE.java

@@ -187,20 +187,6 @@ public MoBIE( String tablePath, List< String > imageColumns, List< String > labe
 		openImagesAndLabels( imageSources, labelSources );
 	}
 
-	// opens an AutoMicTools table
-	// FIXME: Can we generalise this?
-	public MoBIE( String autoMicTablePath, GridType gridType, MoBIESettings settings )
-	{
-		this.settings = settings;
-
-		// FIXME: Can we generalise this and use the normal sources creator?
-		SourcesFromAutoMicTableCreator sourcesCreator = new SourcesFromAutoMicTableCreator( autoMicTablePath, gridType );
-		final List< ImageFileSources > imageSources = sourcesCreator.getImageSources();
-		final List< LabelFileSources > labelSources = sourcesCreator.getLabelSources();
-
-		openImagesAndLabels( imageSources, labelSources );
-	}
-
 	private void initTableSaw()
 	{
 		// force TableSaw class loading

src/main/java/org/embl/mobie/command/open/OpenTableCommand.java

@@ -28,6 +28,7 @@
  */
 package org.embl.mobie.command.open;
 
+import loci.common.DebugTools;
 import org.embl.mobie.MoBIE;
 import org.embl.mobie.MoBIESettings;
 import org.embl.mobie.command.CommandConstants;
@@ -66,6 +67,8 @@ public class OpenTableCommand implements Command {
 	@Override
 	public void run()
 	{
+		DebugTools.setRootLevel( "OFF" );
+
 		final GridType gridType = GridType.Stitched; // TODO: fetch from UI
 
 		final MoBIESettings settings = new MoBIESettings();

src/main/java/org/embl/mobie/command/open/omezarr/OpenOMEZARRCommand.java

@@ -44,8 +44,8 @@ public class OpenOMEZARRCommand implements Command {
 
     static { net.imagej.patcher.LegacyInjector.preinit(); }
 
-    @Parameter(label = "File path", style = "directory")
-    public File directory;
+    @Parameter(label = "OME-Zarr path", style = "directory")
+    public File omeZarrDirectory;
 
     protected static void openAndShow(String filePath) throws IOException {
         SpimData spimData = OMEZarrOpener.openFile(filePath);
@@ -56,7 +56,7 @@ protected static void openAndShow(String filePath) throws IOException {
     @Override
     public void run() {
         try {
-            openAndShow( directory.toString() );
+            openAndShow( omeZarrDirectory.toString() );
         } catch (IOException e) {
             e.printStackTrace();
         }

src/main/java/org/embl/mobie/lib/MoBIEHelper.java

@@ -46,7 +46,9 @@
 import org.embl.mobie.lib.source.SourceToImagePlusConverter;
 import spimdata.util.Displaysettings;
 import tech.tablesaw.api.Table;
+import vib.app.FileGroup;
 
+import java.io.File;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.ArrayList;
@@ -185,6 +187,11 @@ public static List< String > getNamedGroups( String regex )
 
 	public static Metadata getMetadataFromImageFile( String path, int channelIndex )
 	{
+		if ( ! new File( path ).exists() )
+		{
+			throw new RuntimeException( "Path does not exist: " + path );
+		}
+
 		if ( path.contains( ".zarr" ) )
 		{
 			try
@@ -193,7 +200,9 @@ public static Metadata getMetadataFromImageFile( String path, int channelIndex )
 				final SpimSource< ? > source = new SpimSource( spimData, channelIndex, "" );
 				final int levels = source.getNumMipmapLevels();
 				final ImagePlus imagePlus = new SourceToImagePlusConverter<>( source ).getImagePlus( levels - 1 );
-				return new Metadata( imagePlus );
+				Metadata metadata = new Metadata( imagePlus );
+				metadata.numChannelsContainer = spimData.getSequenceDescription().getViewSetups().size();
+				return metadata;
 			}
 			catch ( SpimDataException e )
 			{

src/main/java/org/embl/mobie/lib/SourcesFromTableCreator.java

@@ -28,13 +28,17 @@
  */
 package org.embl.mobie.lib;
 
+import ij.IJ;
 import org.embl.mobie.lib.files.ImageFileSources;
 import org.embl.mobie.lib.files.LabelFileSources;
 import org.embl.mobie.lib.io.TableImageSource;
 import org.embl.mobie.lib.table.saw.TableOpener;
 import org.embl.mobie.lib.transform.GridType;
 import tech.tablesaw.api.Table;
 
+import java.io.File;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -51,12 +55,33 @@ public SourcesFromTableCreator( String tablePath, List< String > imageColumns, L
 
 		for ( String image : imageColumns )
 		{
-			final TableImageSource tableImageSource = new TableImageSource( image );
-			imageFileSources.add( new ImageFileSources( tableImageSource.name, table, tableImageSource.columnName, tableImageSource.channelIndex, root, gridType ) );
+			if ( table.columnNames().contains( "FileName_" + image + "_IMG" ) )
+			{
+				// This is an AutoMicTools table, where the image path is distributed into the two columns (file name and folder)
+				gridType = GridType.Transformed; // To accommodate rotations
+				Path rootFolder = Paths.get( root );
+				String referenceImagePath = MoBIEHelper.getAbsoluteImagePathFromAutoMicTable( table, image, rootFolder, 0 );
+				IJ.log("Detected AutoMicTools table");
+				IJ.log("Determining number of channels of " + image + ", using " + referenceImagePath +  "...");
+				int numChannels = MoBIEHelper.getMetadataFromImageFile( referenceImagePath, 0 ).numChannelsContainer;
+				IJ.log("Number of channels is " + numChannels);
+				for ( int channelIndex = 0; channelIndex < numChannels; channelIndex++ )
+				{
+					imageFileSources.add( new ImageFileSources( image + "_C" + channelIndex, table, rootFolder, image, channelIndex, gridType ) );
+				}
+			}
+			else
+			{
+				// Default table
+				final TableImageSource tableImageSource = new TableImageSource( image );
+				imageFileSources.add( new ImageFileSources( tableImageSource.name, table, tableImageSource.columnName, tableImageSource.channelIndex, root, gridType ) );
+			}
 		}
 
 		labelSources = new ArrayList<>();
-		// see https://github.com/mobie/mobie-viewer-fiji/issues/1038
+		if ( labelColumns.isEmpty() )
+			return;
+
 		final String firstLabel = labelColumns.get( 0 );
 		for ( String label : labelColumns )
 		{

src/main/java/org/embl/mobie/lib/files/ImageFileSources.java

@@ -121,23 +121,20 @@ public ImageFileSources( String name, Table table, String pathColumn, Integer ch
 
 		// add table columns to region table
 		final List< Column< ? > > columns = table.columns();
-		final int numColumns = columns.size();
-		for ( int columnIndex = 0; columnIndex < numColumns; columnIndex++ )
-		{
-			final Column< ? > column = columns.get( columnIndex );
-
-			if ( column instanceof NumberColumn )
-			{
-				final Table summary = table.summarize( column, mean ).by( pathColumn );
-				regionTable = regionTable.joinOn( pathColumn ).leftOuter( summary );
-			}
-
-			if ( column instanceof StringColumn )
-			{
-				final Table summary = table.summarize( column, Aggregators.firstString ).by( pathColumn );
-				regionTable = regionTable.joinOn( pathColumn ).leftOuter( summary );
-			}
-		}
+        for ( final Column< ? > column : columns )
+        {
+            if ( column instanceof NumberColumn )
+            {
+                final Table summary = table.summarize( column, mean ).by( pathColumn );
+                regionTable = regionTable.joinOn( pathColumn ).leftOuter( summary );
+            }
+
+            if ( column instanceof StringColumn )
+            {
+                final Table summary = table.summarize( column, Aggregators.firstString ).by( pathColumn );
+                regionTable = regionTable.joinOn( pathColumn ).leftOuter( summary );
+            }
+        }
 	}
 
 	// For creating image sources from an AutoMicTools table

src/main/java/org/embl/mobie/lib/source/Metadata.java

@@ -34,9 +34,11 @@
 public class Metadata
 {
 	public String color = "White";
+
 	public double[] contrastLimits = null;
 	public Integer numTimePoints = null;
 	public Integer numZSlices = 1;
+	public Integer numChannelsContainer = 1; // in MoBIE each image has jsut one channel, but the container could have multiple
 
 	public Metadata()
 	{
@@ -51,6 +53,7 @@ public Metadata( ImagePlus imagePlus )
 		contrastLimits = new double[]{ imagePlus.getDisplayRangeMin(), imagePlus.getDisplayRangeMax() };
 		numTimePoints = imagePlus.getNFrames();
 		numZSlices = imagePlus.getNSlices();
+		numChannelsContainer = imagePlus.getNChannels();
 	}
 
 }

src/test/java/develop/OpenAutoMicTable.java

@@ -1,7 +1,7 @@
 package develop;
 
 import net.imagej.ImageJ;
-import org.embl.mobie.command.open.OpenAutoMicToolsTableCommand;
+import org.embl.mobie.command.open.OpenTableCommand;
 
 import java.io.File;
 
@@ -12,10 +12,14 @@ public static void main( String[] args )
         final ImageJ imageJ = new ImageJ();
         imageJ.ui().showUI();
 
-        OpenAutoMicToolsTableCommand command = new OpenAutoMicToolsTableCommand();
+        OpenTableCommand command = new OpenTableCommand();
         //command.table = new File( "/Volumes/almf/group/Aliaksandr/User_data/Furlong_CrispR/test_data_20231018/20231004/20231004-172458/summary_calculated1.txt" );
         //command.table = new File( "/Volumes/almf/group/Aliaksandr/User_data/Furlong_CrispR/test_data_20231018/20231004/20231004-172458/summary_calculated1_subset.txt" );
         command.table = new File( "/Users/tischer/Desktop/teresa/summary_calculated1_subset.txt" );
+        //command.table = new File( "/Volumes/cba/exchange/furlong_test/summary_calculated1_subset_zarr.txt" );
+        //command.images = "Result.Image.Zarr"; // Result.Image.Zarr
+        command.root = command.table.getParentFile();
+        command.images = "Result.Image"; // Result.Image.Zarr
         command.run();
     }
 }