Fixes #1160

mobie · Jun 20, 2024 · f446f17 · f446f17
1 parent 98f0a6a
commit f446f17
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Showing 5 changed files with 38 additions and 15 deletions.
diff --git a/src/main/java/org/embl/mobie/command/context/CurrentLocationLoggerCommand.java b/src/main/java/org/embl/mobie/command/context/CurrentLocationLoggerCommand.java
@@ -103,7 +103,7 @@ public static void logCurrentPosition( BdvHandle bdvHandle,
 		Double distanceToRecentPosition = null;
 		if ( mousePointer == null )
 		{
-			Logger.log( "To get this please use the \"" + SHORTCUT + "\" keyboard shortcut to trigger this action." );
+			Logger.log( "Only given when using the [" + SHORTCUT + "] keyboard shortcut in the BDV window to trigger this action." );
 		}
 		else
 		{

diff --git a/src/main/java/org/embl/mobie/lib/SourcesFromTableCreator.java b/src/main/java/org/embl/mobie/lib/SourcesFromTableCreator.java
@@ -73,12 +73,19 @@ public SourcesFromTableCreator( String tablePath, List< String > imageColumns, L
 				String fileName = table.getString( 0, imageColumn);
 				String relativeFolder = table.getString( 0, imageColumn.replace(  "FileName_", "PathName_" ) );
 				String referenceImagePath = MoBIEHelper.createAbsolutePath( root, fileName, relativeFolder );
-				IJ.log( "Determining number of channels of " + imageColumn + " from " + referenceImagePath + "..." );
+				IJ.log( "Determining number of channels of \"" + imageColumn + "\" from " + referenceImagePath + "..." );
 				int numChannels = ImageDataOpener.open( referenceImagePath, ThreadHelper.sharedQueue ).getNumDatasets();
 				IJ.log( "Number of channels: " + numChannels );
 				for ( int channelIndex = 0; channelIndex < numChannels; channelIndex++ )
 				{
-					imageFileSources.add( new ImageFileSources( imageColumn + "_C" + channelIndex, table, imageColumn, channelIndex, pathMapping, root, gridType ) );
+					imageFileSources.add( new ImageFileSources(
+							imageColumn + "_C" + channelIndex,
+							table,
+							imageColumn,
+							channelIndex,
+							root,
+							pathMapping,
+							gridType ) );
 				}
 			}
 			else

diff --git a/src/main/java/org/embl/mobie/lib/bdv/view/SliceViewer.java b/src/main/java/org/embl/mobie/lib/bdv/view/SliceViewer.java
@@ -219,7 +219,8 @@ public static BdvHandle createBdv( boolean is2D, String frameTitle )
 		sOptions.interpolate = false;
 		IJ.log("BigDataViewer (BDV) initialised.");
 		IJ.log("BDV navigation mode: " + ( is2D ? "2D" : "3D" ));
-		IJ.log("BDV interpolation: Nearest neighbour (Press \"I\" in BDV window to change this)" );
+		IJ.log("BDV interpolation: Nearest neighbour");
+		IJ.log(" - Use [I] keyboard shortcut in BDV window to change this" );
 		IJ.log("" );
 
 		IBdvSupplier bdvSupplier = new MobieBdvSupplier( sOptions );

diff --git a/src/main/java/org/embl/mobie/lib/view/save/ViewSaver.java b/src/main/java/org/embl/mobie/lib/view/save/ViewSaver.java
@@ -115,7 +115,7 @@ public boolean saveViewDialog( View view )
         if ( moBIE.getViews().containsKey( view.getName() ) )
         {
             GenericDialog dialog = new GenericDialog( "Overwrite view?" );
-            dialog.addMessage( view.getName() + " exists already; are you sure you want to overwrite it?" );
+            dialog.addMessage( "A view named \"" + view.getName() + "\" exists already.\nAre you sure you want to overwrite it?" );
             dialog.showDialog();
             if ( ! dialog.wasOKed() ) {
                 return false;
@@ -206,7 +206,7 @@ private void saveNewViewToProject( View view, String viewJson ) {
         try {
             if ( viewJson.equals( "dataset.json" ) )
             {
-                saveViewToDatasetJson( view, false );
+                saveViewToDatasetJson( view );
             }
             else
             {
@@ -251,15 +251,10 @@ private void addViewToUi( View view )
         moBIE.getUserInterface().addViews( views );
     }
 
-    public void saveViewToDatasetJson( View view, boolean overwrite ) throws IOException
+    public void saveViewToDatasetJson( View view ) throws IOException
     {
         String datasetJsonPath = moBIE.absolutePath( "dataset.json");
         Dataset dataset = new DatasetJsonParser().parseDataset( datasetJsonPath );
-
-        if ( ! overwrite )
-            if ( dataset.views().containsKey( view.getName() ) )
-                throw new IOException( "View saving aborted - this view name already exists!" );
-
         writeDatasetJson( dataset, view, datasetJsonPath );
         IJ.log( "View \"" + view.getName()  + "\" written to dataset.json" );
     }

diff --git a/src/test/resources/minimal-mobie-project/data/blobs/dataset.json b/src/test/resources/minimal-mobie-project/data/blobs/dataset.json
@@ -28,7 +28,7 @@
             "sources": [
               "blobs"
             ],
-            "color": "r255-g255-b255-a255",
+            "color": "r=255,g=255,b=255,a=255",
             "contrastLimits": [
               0.0,
               255.0
@@ -37,11 +37,31 @@
             "invert": false,
             "name": "blobs",
             "opacity": 1.0,
-            "visible": true
+            "visible": true,
+            "blendingMode": "sum"
           }
         }
       ],
-      "isExclusive": false
+      "sourceTransforms": [],
+      "viewerTransform": {
+        "normalizedAffine": [
+          0.0016175016000465467,
+          0.0,
+          0.0,
+          -0.20623145400593473,
+          0.0,
+          0.0016175016000465467,
+          0.0,
+          -0.20461395240588817,
+          0.0,
+          0.0,
+          0.0016175016000465467,
+          0.0
+        ],
+        "timepoint": 0
+      },
+      "isExclusive": true,
+      "description": ""
     },
     "default": {
       "uiSelectionGroup": "bookmark",