Improve handling over-writing already existing views

pom.xml

@@ -9,7 +9,7 @@
 
     <groupId>org.embl.mobie</groupId>
     <artifactId>mobie-viewer-fiji</artifactId>
-    <version>5.0.3</version>
+    <version>5.0.4</version>
 
     <!-- force javadoc generation to fetch errors:    -->
     <!-- mvn javadoc:javadoc | grep error -->

src/main/java/org/embl/mobie/command/context/AbstractTransformationCommand.java

@@ -149,8 +149,10 @@ protected void createAndSaveAffineTransformedImages(
                     affineTransformation,
                     movingImage.getName() + ", " + suffix );
 
-            MoBIE.getInstance().getViewManager().getViewsSaver().saveViewDialog( view );
-            MoBIE.getInstance().getViewManager().show( view );
+            if ( MoBIE.getInstance().getViewManager().getViewsSaver().saveViewDialog( view ) )
+            {
+                MoBIE.getInstance().getViewManager().show( view );
+            }
         }
     }
 

src/main/java/org/embl/mobie/command/view/ViewerTransformLoggerCommand.java → src/main/java/org/embl/mobie/command/view/CurrentLocationLoggerCommand.java

@@ -44,8 +44,8 @@
 import org.scijava.plugin.Plugin;
 import sc.fiji.bdvpg.scijava.command.BdvPlaygroundActionCommand;
 
-@Plugin( type = BdvPlaygroundActionCommand.class, name = ViewerTransformLoggerCommand.NAME, menuPath = CommandConstants.CONTEXT_MENU_ITEMS_ROOT + ViewerTransformLoggerCommand.NAME )
-public class ViewerTransformLoggerCommand implements BdvPlaygroundActionCommand
+@Plugin( type = BdvPlaygroundActionCommand.class, name = CurrentLocationLoggerCommand.NAME, menuPath = CommandConstants.CONTEXT_MENU_ITEMS_ROOT + CurrentLocationLoggerCommand.NAME )
+public class CurrentLocationLoggerCommand implements BdvPlaygroundActionCommand
 {
 	static { net.imagej.patcher.LegacyInjector.preinit(); }
 
@@ -79,10 +79,13 @@ public void run()
 
 			// print
 			final Gson gson = JsonHelper.buildGson( false );
-			Logger.log( "# Current location " );
-			Logger.log( "To restore the view, any of below lines can be pasted into the \'location\' text field." );
-			Logger.log( "To share views with other people we recommend \'normalizedAffine\'." );
-
+			Logger.log( "" );
+			Logger.log( "# Current location" );
+			Logger.log( "" );
+			Logger.log( "- To restore the current location, any of below lines can be pasted into MoBIE's \"location\"  field." );
+			Logger.log( "- To share views with other people we recommend \"normalizedAffine\"." );
+			Logger.log( "- Note that below \"position\" is the position of the window center (not of the mouse pointer)." );
+			Logger.log( "" );
 			Logger.log( gson.toJson( positionViewerTransform ) );
 			Logger.log( gson.toJson( affineViewerTransform ) );
 			Logger.log( gson.toJson( normalizedAffineViewerTransform ) );

src/main/java/org/embl/mobie/lib/align/TurboReg2DAligner.java

@@ -32,7 +32,6 @@
 import ij.ImagePlus;
 import ij.io.FileSaver;
 import net.imglib2.realtransform.AffineTransform3D;
-import org.embl.mobie.command.context.AutomaticRegistrationCommand;
 import org.embl.mobie.lib.transform.Transform;
 
 import java.lang.reflect.Method;

src/main/java/org/embl/mobie/lib/bdv/view/SliceViewer.java

@@ -28,13 +28,12 @@
  */
 package org.embl.mobie.lib.bdv.view;
 
-import IceInternal.Ex;
 import bdv.util.BdvHandle;
 import bdv.viewer.SourceAndConverter;
 import net.imglib2.realtransform.AffineTransform3D;
 import org.embl.mobie.DataStore;
 import org.embl.mobie.command.context.*;
-import org.embl.mobie.command.view.ViewerTransformLoggerCommand;
+import org.embl.mobie.command.view.CurrentLocationLoggerCommand;
 import org.embl.mobie.MoBIE;
 import org.embl.mobie.lib.annotation.SliceViewAnnotationSelector;
 import org.embl.mobie.lib.bdv.MobieBdvSupplier;
@@ -126,7 +125,8 @@ public synchronized BdvHandle getBdvHandle()
 
 	private void installContextMenuAndKeyboardShortCuts( )
 	{
-		final SliceViewAnnotationSelector sliceViewAnnotationSelector = new SliceViewAnnotationSelector( bdvHandle, is2D, () -> moBIE.getViewManager().getAnnotationDisplays() );
+		final SliceViewAnnotationSelector sliceViewAnnotationSelector =
+				new SliceViewAnnotationSelector( bdvHandle, is2D, () -> moBIE.getViewManager().getAnnotationDisplays() );
 
 		sacService.registerAction( UNDO_SEGMENT_SELECTIONS, sourceAndConverters -> {
 			// TODO: Maybe only do this for the sacs at the mouse position
@@ -148,7 +148,8 @@ private void installContextMenuAndKeyboardShortCuts( )
 		actions.add( SourceAndConverterService.getCommandName( SourcesInfoCommand.class ) );
 		actions.add( SourceAndConverterService.getCommandName( ShowRasterImagesCommand.class ) );
 		actions.add( SourceAndConverterService.getCommandName( ScreenShotMakerCommand.class ) );
-		actions.add( SourceAndConverterService.getCommandName( ViewerTransformLoggerCommand.class ) );
+		// TODO https://github.com/mobie/mobie-viewer-fiji/issues/1152
+		actions.add( SourceAndConverterService.getCommandName( CurrentLocationLoggerCommand.class ) );
 		actions.add( SourceAndConverterService.getCommandName( BigWarpRegistrationCommand.class ) );
 		//actions.add( SourceAndConverterService.getCommandName( AutomaticRegistrationCommand.class ) );
 		actions.add( SourceAndConverterService.getCommandName( ManualTransformationCommand.class ) );

src/main/java/org/embl/mobie/lib/view/save/ViewSaver.java

@@ -83,15 +83,16 @@ public ViewSaver( MoBIE moBIE) {
         this.moBIE = moBIE;
     }
 
-    public void saveViewDialog( View view )
+    public boolean saveViewDialog( View view )
     {
-        final GenericDialog gd = new GenericDialog("Save view");
+        final GenericDialog gd = new GenericDialog("Save view " + ( view.getName() == null ? "" : view.getName()) );
 
         gd.addChoice("Save to", new String[]{ FileLocation.CurrentProject.toString(), FileLocation.ExternalJSONFile.toString() }, saveToProjectOrFile );
         gd.addFileField( "External JSON file", externalJsonPath, 70 );
         gd.addMessage( "" );
-        gd.addStringField("View name", view.getName() != null ? view.getName() : "", 70 );
-        gd.addStringField( "View description", view.getDescription() != null ? view.getDescription() : "", 70 );
+        if ( view.getName() == null )
+            gd.addStringField("View name", "my-new-view-name", 35 );
+        gd.addStringField( "View description", view.getDescription() != null ? view.getDescription() : "My view description....", 70 );
         gd.addCheckbox("Make view exclusive", view.isExclusive() != null ? view.isExclusive() : false );
         gd.addMessage( "" );
         gd.addChoice("Selection group", getSelectionGroupChoices(), uiSelectionChoice );
@@ -103,18 +104,27 @@ public void saveViewDialog( View view )
         // fetch primary user input
         saveToProjectOrFile = gd.getNextChoice();
         externalJsonPath = gd.getNextString();
-        view.setName( UserInterfaceHelper.tidyString( gd.getNextString() ) );
+        if ( view.getName() == null )
+            view.setName( UserInterfaceHelper.tidyString( gd.getNextString() ) );
         view.setDescription( gd.getNextString()  );
         view.setExclusive( gd.getNextBoolean() );
         uiSelectionChoice = gd.getNextChoice();
         String newSelectionGroupName = gd.getNextString();
 
+        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.showDialog();
+            if ( ! dialog.wasOKed() ) {
+                return false;
+            }
+        }
+
         // compute derived parameters
         FileLocation fileLocation = FileLocation.valueOf( saveToProjectOrFile );
         if ( view.isExclusive() )
             view.setViewerTransform( new NormalizedAffineViewerTransform( moBIE.getViewManager().getSliceViewer().getBdvHandle() ) );
-        //else
-        //    view.setViewerTransform( new NoViewerTransform() );
 
         if ( uiSelectionChoice.equals( CREATE_SELECTION_GROUP ) )
             view.setUiSelectionGroup( newSelectionGroupName );
@@ -145,6 +155,8 @@ public void saveViewDialog( View view )
             saveNewViewToProject( view, "dataset.json" );
         else if ( fileLocation == FileLocation.ExternalJSONFile )
             saveNewViewToFileSystem( view, externalJsonPath );
+
+        return true;
     }
 
     @NotNull
@@ -230,7 +242,8 @@ private void saveNewViewToProject( View view, String viewJson ) {
 //        }
 //    }
 
-    private void addViewToUi( View view ) {
+    private void addViewToUi( View view )
+    {
         moBIE.getViews().put( view.getName(), view );
         Map<String, View > views = new HashMap<>();
         views.put( view.getName(), view );
@@ -292,15 +305,11 @@ private boolean jsonExists( String jsonPath ) {
 //        }
 //    }
 
-    private void saveNewViewToAdditionalViewsJson( View view, String jsonPath ) throws IOException {
-
+    private void saveNewViewToAdditionalViewsJson( View view, String jsonPath ) throws IOException
+    {
         AdditionalViews additionalViews;
         if ( jsonExists( jsonPath ) ) {
             additionalViews = new AdditionalViewsJsonParser().getViews( jsonPath );
-            if ( additionalViews.views.containsKey( view.getName() ) ) {
-                IJ.log( "View saving aborted - this view name already exists!" );
-                return;
-            }
         } else {
             additionalViews = new AdditionalViews();
             additionalViews.views = new HashMap<>();

src/main/java/org/embl/mobie/lib/view/save/ViewSavingHelper.java

@@ -54,7 +54,7 @@ public static void writeDatasetJson( Dataset dataset, View view, String datasetJ
 
     public static void writeAdditionalViewsJson( AdditionalViews additionalViews, View view, String jsonPath ) throws IOException
     {
-        additionalViews.views.put(view.getName(), view);
+        additionalViews.views.put( view.getName(), view );
 
         if (isGithub( jsonPath )) {
             new ViewsGithubWriter( GitHubUtils.rawUrlToGitLocation( jsonPath ) ).writeViewToViewsJson( view );