Clean up some FIXME comments

mobie · Jun 13, 2024 · 2da154a · 2da154a
1 parent a67b88e
commit 2da154a
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Showing 27 changed files with 33 additions and 951 deletions.
diff --git a/src/main/java/org/embl/mobie/DataStore.java b/src/main/java/org/embl/mobie/DataStore.java
@@ -189,7 +189,7 @@ public static void putImages( Collection< ? extends Image< ? > > images )
 
 	public static void clearImages()
 	{
-		// FIXME Caching: https://github.com/mobie/mobie-viewer-fiji/issues/813
+		// TODO: Caching: https://github.com/mobie/mobie-viewer-fiji/issues/813
 		images.clear();
 	}
 

diff --git a/src/main/java/org/embl/mobie/MoBIE.java b/src/main/java/org/embl/mobie/MoBIE.java
@@ -187,11 +187,6 @@ private void initTableSaw()
 
 	private void openMoBIEProject() throws IOException
 	{
-		// FIXME: Get rid of setS3AccessAndSecretKey,
-		//  	  currently still needed by
-		//        ProjectJsonParser() => ???
-		//        Other functions that need to read JSON files
-		//        probably some Metadata from Image fetcher methods => Use DataStore for this
 		S3Utils.setS3AccessAndSecretKey( settings.values.getS3AccessAndSecretKey() );
 
 		setProjectImageAndTableRootLocations();
@@ -557,7 +552,7 @@ public String absolutePath( String... files )
 	}
 
 	@Deprecated
-	// FIXME https://github.com/bigdataviewer/bigdataviewer-playground/issues/259#issuecomment-1279705489
+	// TODO https://github.com/bigdataviewer/bigdataviewer-playground/issues/259#issuecomment-1279705489
 	public void closeSourceAndConverter( SourceAndConverter< ? > sourceAndConverter, boolean closeImgLoader )
 	{
 		SourceAndConverterServices.getBdvDisplayService().removeFromAllBdvs( sourceAndConverter );

diff --git a/src/main/java/org/embl/mobie/command/context/AbstractTransformationCommand.java b/src/main/java/org/embl/mobie/command/context/AbstractTransformationCommand.java
@@ -123,7 +123,7 @@ protected void applyTransform( AffineTransform3D affineTransform3D )
 
         createAndSaveAffineTransformedImages( movingImages, affineTransform3D, suffix );
 
-        // FIXME close the Command UI, HOW?
+        // TODO close the Command UI, HOW?
         // https://imagesc.zulipchat.com/#narrow/stream/327238-Fiji/topic/Close.20Scijava.20Command.20UI
     }
 

diff --git a/src/main/java/org/embl/mobie/command/context/AutomaticRegistrationCommand.txt b/src/main/java/org/embl/mobie/command/context/AutomaticRegistrationCommand.txt
@@ -60,7 +60,7 @@ import java.util.*;
 
 import static sc.fiji.bdvpg.bdv.BdvHandleHelper.getWindowCentreInPixelUnits;
 
-// FIXME: Make a simplified version of this that does not do the "stack" thing
+// TODO: Make a simplified version of this that does not do the "stack" thing
 
 @Plugin(type = BdvPlaygroundActionCommand.class, menuPath = CommandConstants.CONTEXT_MENU_ITEMS_ROOT + "Transform>Registration - Automatic 2D/3D")
 public class AutomaticRegistrationCommand extends AbstractRegistrationCommand

diff --git a/src/main/java/org/embl/mobie/command/open/OpenImageAndLabelsCommand.java b/src/main/java/org/embl/mobie/command/open/OpenImageAndLabelsCommand.java
@@ -47,7 +47,7 @@ public class OpenImageAndLabelsCommand implements Command {
 
 	static { net.imagej.patcher.LegacyInjector.preinit(); }
 
-	// FIXME: https://forum.image.sc/t/scijava-ui-open-both-file-and-directory/97389
+	// TODO: https://forum.image.sc/t/scijava-ui-open-both-file-and-directory/97389
 	@Parameter( label = "Image URI", style = "both", required = false )
 	public File image;
 

diff --git a/src/main/java/org/embl/mobie/lib/SourcesFromTableCreator.java b/src/main/java/org/embl/mobie/lib/SourcesFromTableCreator.java
@@ -134,7 +134,7 @@ public SourcesFromTableCreator( String tablePath, List< String > imageColumns, L
 			StringColumn imageColumn = table.stringColumn( imageColumnName );
 			for ( String imagePath : imageColumn )
 			{
-				// FIXME It would be nice to shorten the names, e.g. by removing everything that is common to all image paths
+				// TODO: It would be nice to shorten the names, e.g. by removing everything that is common to all image paths
 				uniqueRegionNames.add( imagePath );
 			}
 			final List< String > regions = new ArrayList<>( uniqueRegionNames );

diff --git a/src/main/java/org/embl/mobie/lib/bdv/view/AnnotationSliceView.java b/src/main/java/org/embl/mobie/lib/bdv/view/AnnotationSliceView.java
@@ -108,7 +108,7 @@ private SourceAndConverter createSourceAndConverter( AbstractAnnotationDisplay<
 		final BoundarySource boundarySource = new BoundarySource( source, false, 0.0F, image.getMask() );
 		final Converter< AnnotationType< A >, ARGBType > annotationARGBConverter = new AnnotationARGBConverter<>( display.coloringModel );
 		final TransformedSource transformedBoundarySource = new TransformedSource( boundarySource );
-		// FIXME: This is an issue if those sources are transformed, because the underlying image will not know about it
+		// FIXME: If those sources are transformed the underlying image will not know about it
 
 		if ( image.getSourcePair().getVolatileSource() != null )
 		{