Added a status message to ManualTransformationCommand

mobie · Jun 15, 2024 · 1b6308b · 1b6308b
1 parent 31668b6
commit 1b6308b
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Showing 5 changed files with 39 additions and 9 deletions.
diff --git a/pom.xml b/pom.xml
@@ -9,7 +9,7 @@
 
     <groupId>org.embl.mobie</groupId>
     <artifactId>mobie-viewer-fiji</artifactId>
-    <version>5.0.4</version>
+    <version>5.0.6-SNAPSHOT</version>
 
     <!-- force javadoc generation to fetch errors:    -->
     <!-- mvn javadoc:javadoc | grep error -->

diff --git a/src/main/java/org/embl/mobie/command/SpatialCalibration.java b/src/main/java/org/embl/mobie/command/SpatialCalibration.java
@@ -30,7 +30,7 @@ public void setVoxelDimensions( MoBIESettings settings, String tablePath )
                 if ( rows.columnNames().contains( PixelSizeColumns.PIXEL_SIZE ) )
                 {
                     FinalVoxelDimensions voxelDimensions = new FinalVoxelDimensions(
-                            rows.textColumn( PixelSizeColumns.PIXEL_UNIT ).get( 0 ),
+                            rows.stringColumn( PixelSizeColumns.PIXEL_UNIT ).get( 0 ),
                             rows.doubleColumn( PixelSizeColumns.PIXEL_SIZE ).get( 0 ),
                             rows.doubleColumn( PixelSizeColumns.PIXEL_SIZE ).get( 0 ),
                             rows.doubleColumn( PixelSizeColumns.PIXEL_SIZE ).get( 0 )
@@ -40,7 +40,7 @@ public void setVoxelDimensions( MoBIESettings settings, String tablePath )
                 else
                 {
                     FinalVoxelDimensions voxelDimensions = new FinalVoxelDimensions(
-                            rows.textColumn( PixelSizeColumns.PIXEL_UNIT ).get( 0 ),
+                            rows.stringColumn( PixelSizeColumns.PIXEL_UNIT ).get( 0 ),
                             rows.doubleColumn( PixelSizeColumns.PIXEL_SIZE_X ).get( 0 ),
                             rows.doubleColumn( PixelSizeColumns.PIXEL_SIZE_Y ).get( 0 ),
                             rows.doubleColumn( PixelSizeColumns.PIXEL_SIZE_Z ).get( 0 )

diff --git a/src/main/java/org/embl/mobie/command/context/ManualTransformationCommand.java b/src/main/java/org/embl/mobie/command/context/ManualTransformationCommand.java
@@ -34,6 +34,7 @@
 import org.embl.mobie.command.MoBIEManualTransformationEditor;
 import org.embl.mobie.lib.image.Image;
 import org.embl.mobie.lib.image.RegionAnnotationImage;
+import org.scijava.ItemVisibility;
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
 import org.scijava.widget.Button;
@@ -46,6 +47,9 @@
 @Plugin(type = BdvPlaygroundActionCommand.class, menuPath = CommandConstants.CONTEXT_MENU_ITEMS_ROOT + "Transform>Registration - Manual")
 public class ManualTransformationCommand extends AbstractTransformationCommand
 {
+
+	public static final String INACTIVE = "Status: Manual transform inactive.";
+
 	static { net.imagej.patcher.LegacyInjector.preinit(); }
 
 	@Parameter ( label = "Start manual transform", callback = "startManualTransform" )
@@ -57,6 +61,9 @@ public class ManualTransformationCommand extends AbstractTransformationCommand
 	@Parameter ( label = "Cancel manual transform", callback = "cancelManualTransform" )
 	public Button cancelManualTransform;
 
+	@Parameter( visibility = ItemVisibility.MESSAGE )
+	private final String status = INACTIVE;
+
 	private MoBIEManualTransformationEditor transformationEditor;
 
 	@Override
@@ -71,6 +78,9 @@ public void startManualTransform()
 		transformationEditor = new MoBIEManualTransformationEditor( bdvHandle.getViewerPanel(), bdvHandle.getKeybindings() );
 		transformationEditor.setTransformableSources( movingSacs );
 		transformationEditor.setActive( true );
+
+		getInfo().getMutableInput( "status", String.class )
+				.setValue( this, "Status: You are transforming " + selectedSourceName + "...");
 	}
 
 	private void acceptManualTransform()
@@ -83,12 +93,18 @@ private void acceptManualTransform()
 		// but this is intended as the transformed image is now a new image that is stored as a new view.
 		// And this new transformed image will also be shown by the above applyTransform function.
 		transformationEditor.setActive( false );
+
+		getInfo().getMutableInput( "status", String.class )
+				.setValue( this, INACTIVE );
 	}
 
 	private void cancelManualTransform()
 	{
 		if ( transformationEditor == null ) return;
 
 		transformationEditor.setActive( false );
+
+		getInfo().getMutableInput( "status", String.class )
+				.setValue( this, INACTIVE );
 	}
 }
diff --git a/src/main/java/org/embl/mobie/lib/files/FileSourcesDataSetter.java b/src/main/java/org/embl/mobie/lib/files/FileSourcesDataSetter.java
@@ -90,7 +90,7 @@ public void addDataAndDisplaysAndViews( Dataset dataset )
 			List< String > imageNames = sources.getSources();
 			ImageDataFormat imageDataFormat = ImageDataFormat.fromPath( sources.getPath( imageNames.get( 0 ) ) );
 
-			IJ.log(sources.name + " file type: " + imageDataFormat );
+			IJ.log( "\""+ sources.name + "\" file type: " + imageDataFormat );
 
 			for ( String imageName : imageNames )
 			{
@@ -339,7 +339,15 @@ else if ( sources.getGridType().equals( GridType.Transformed ) )
 		// construct and add the view
 		//
 		final ImageZoomViewerTransform viewerTransform = new ImageZoomViewerTransform( fileSourcesList.get( 0 ).getSources().get( 0 ), 0 );
-		final View view = new View( "all images", "data", displays, transformations, viewerTransform, false, null );
+		final View view = new View(
+				"all images",
+				"data",
+				displays,
+				transformations,
+				viewerTransform,
+				false,
+				null );
+		view.overlayNames( true );
 		dataset.views().put( view.getName(), view );
 	}
 }
diff --git a/src/test/java/projects/microbial_predation/MicrobialPredation.java b/src/test/java/projects/microbial_predation/MicrobialPredation.java
@@ -14,10 +14,16 @@ public static void main( String[] args )
 
         OpenImageAndLabelsCommand command = new OpenImageAndLabelsCommand();
 
-        String root = "/Users/tischer/Documents/microbial-predation-data/";
-        command.image = new File( root + "test_timelapse_subset/.*.tif" );
-        command.labels = new File( root + "test_timelapse_results/.*_labels.tif" );
-        command.table = new File( root + "test_timelapse_results/.*_measurements.csv" );
+//        String root = "/Users/tischer/Documents/microbial-predation-data/";
+//        command.image = new File( root + "test_timelapse_subset/.*.tif" );
+//        command.labels = new File( root + "test_timelapse_results/.*_labels.tif" );
+//        command.table = new File( root + "test_timelapse_results/.*_measurements.csv" );
+//        command.spatialCalibration = SpatialCalibration.FromTable;
+
+        String root = "/Volumes/Microbial_Predation_Analysis_Dev/Interval_output";
+        command.image = new File( root, "Source/.*.tif" );
+        command.labels = new File( root , ".*_profile_labels.tif" );
+        command.table = new File( root, ".*_measurements.csv" );
         command.spatialCalibration = SpatialCalibration.FromTable;
 
         command.run();