Update CollectionTableConstants

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

@@ -54,38 +54,13 @@ public class OpenCollectionTableCommand implements Command {
 	@Parameter( label = "Table Path", required = true )
 	public File table;
 
-
 	@Override
 	public void run()
 	{
 		DebugTools.setRootLevel( "OFF" );
 
 		final MoBIESettings settings = new MoBIESettings();
 
-		spatialCalibration.setVoxelDimensions( settings, table != null ? table.getAbsolutePath() : null  );
-
-		List< String > imageList = new ArrayList<>();
-		if ( images != null && ! images.equals( "" ) )
-		{
-			imageList = Arrays.asList( images.split( "," ) );
-			imageList = imageList.stream().map( s -> s.trim() ).collect( Collectors.toList() );
-		}
-
-		List< String > labelList = new ArrayList<>();
-		if ( labels != null && ! labels.equals( "" ) )
-		{
-			labelList = Arrays.asList( labels.split( "," ) );
-			labelList = labelList.stream().map( s -> s.trim() ).collect( Collectors.toList() );
-		}
-
-		try
-		{
-			String rootPath = root == null ? null : root.getAbsolutePath();
-			new MoBIE( table.getAbsolutePath(), imageList, labelList, rootPath, pathMapping ,gridType, settings );
-		}
-		catch ( IOException e )
-		{
-			e.printStackTrace();
-		}
+		new MoBIE( MoBIEHelper.toURI( table ), settings, true );
 	}
 }

src/main/java/org/embl/mobie/lib/table/columns/CollectionTableConstants.java

@@ -77,8 +77,9 @@ public class CollectionTableConstants
      * correspondingly many table rows with the *same URI* and the respective
      * different value in the "channel" column.
      *
-     * Notes:
-     * - One could consider to encode the channel directly within the URI: FIXME add link
+     * Discussion points:
+     * - One could consider to encode the channel directly within the URI
+     *   - see: https://forum.image.sc/t/loading-only-one-channel-from-an-ome-zarr/97798
      *
      * Supported values:
      * - Zero based positive integers
@@ -123,6 +124,10 @@ public class CollectionTableConstants
      * No transformation will be applied if
      * - this column is absent.
      * - the given value cannot be parsed.
+     *
+     * Discussion points:
+     * - If one would not have commas to separate the values also CSV would be fine as a table format
+     *   - For instance, we could use space as a separator instead of comma
      */
     public static final String AFFINE = "affine";
 

src/test/java/examples/OpenCollectionTable.java

@@ -3,6 +3,9 @@
 import net.imagej.ImageJ;
 import org.embl.mobie.MoBIE;
 import org.embl.mobie.MoBIESettings;
+import org.embl.mobie.command.open.OpenCollectionTableCommand;
+
+import java.io.File;
 
 public class OpenCollectionTable
 {
@@ -11,9 +14,11 @@ public static void main( String[] args )
         final ImageJ imageJ = new ImageJ();
         imageJ.ui().showUI();
 
-//        String tablePath = "src/test/resources/project-tables/clem-table.txt";
-        String tablePath = "src/test/resources/project-tables/blobs-table.txt";
+        String tablePath = "src/test/resources/collections/blobs-table.txt";
+        File tableFile = new File( tablePath );
 
-        new MoBIE( tablePath, new MoBIESettings(), true );
+        OpenCollectionTableCommand command = new OpenCollectionTableCommand();
+        command.table = tableFile;
+        command.run();
     }
 }

src/test/resources/collections/blobs-table.txt

@@ -0,0 +1,4 @@
+uri	name	type	affine	color	view
+/Users/tischer/Documents/mobie-viewer-fiji/src/test/resources/collections/blobs.tif	shifted blobs	intensities	(1,0,0,-80,0,1,0,0,0,0,1,0)	green	
+/Users/tischer/Documents/mobie-viewer-fiji/src/test/resources/collections/blobs.tif		intensities			segmented blobs
+/Users/tischer/Documents/mobie-viewer-fiji/src/test/resources/collections/blobs-labels.tif		labels			segmented blobs