Add view description

mobie · Jan 5, 2024 · 2d952a9 · 2d952a9
1 parent 7756015
commit 2d952a9
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Showing 14 changed files with 145 additions and 61 deletions.
diff --git a/src/main/java/org/embl/mobie/MoBIESettings.java b/src/main/java/org/embl/mobie/MoBIESettings.java
@@ -107,12 +107,19 @@ public MoBIESettings removeSpatialCalibration( Boolean removeSpatialCalibration
 		return this;
 	}
 
+	public MoBIESettings appendGroovyCode( String groovyCode )
+	{
+		this.values.groovyScript += groovyCode;
+		return this;
+	}
+
 	public MoBIESettings openedFromCLI( Boolean cli )
 	{
 		this.values.openedFromCLI = cli;
 		return this;
 	}
 
+
 	public static class Values
 	{
 		private String[] s3AccessAndSecretKey;
@@ -126,6 +133,7 @@ public static class Values
 		private String view = View.DEFAULT;
 		private Boolean removeSpatialCalibration = false;
 		private Boolean openedFromCLI = false; // started from CLI
+		private String groovyScript = "";
 
 		public Boolean getRemoveSpatialCalibration()
 		{
@@ -186,5 +194,10 @@ public Boolean isOpenedFromCLI()
 		{
 			return openedFromCLI;
 		}
+
+		public String getGroovyScript()
+		{
+			return groovyScript;
+		}
 	}
 }
diff --git a/src/main/java/org/embl/mobie/command/open/OpenMultipleImagesAndLabelsCommand.java b/src/main/java/org/embl/mobie/command/open/OpenMultipleImagesAndLabelsCommand.java
@@ -93,14 +93,53 @@ public void run()
 
 		final MoBIESettings settings = new MoBIESettings();
 		settings.removeSpatialCalibration( removeSpatialCalibration );
+		String groovyCode = generateGroovyScript();
+		settings.appendGroovyCode( groovyCode );
+//		System.out.println( groovyCode );
 
 		try
 		{
 			new MoBIE( imageList, labelsList, tablesList, null, gridType, settings );
 		}
 		catch ( IOException e )
 		{
-			e.printStackTrace();
+			throw new RuntimeException( e );
 		}
 	}
+
+	public String generateGroovyScript() {
+		StringBuilder sb = new StringBuilder();
+
+		sb.append("import org.embl.mobie.command.open.OpenMultipleImagesAndLabelsCommand\n");
+		sb.append("import java.io.File\n\n");
+
+		sb.append("OpenMultipleImagesAndLabelsCommand command = new OpenMultipleImagesAndLabelsCommand()\n");
+
+		if (image0 != null) sb.append(String.format("command.image0 = new File(\"%s\")\n",
+				image0.getAbsolutePath()));
+		if (image1 != null) sb.append(String.format("command.image1 = new File(\"%s\")\n",
+				image1.getAbsolutePath()));
+		if (image2 != null) sb.append(String.format("command.image2 = new File(\"%s\")\n",
+				image2.getAbsolutePath()));
+		if (image3 != null) sb.append(String.format("command.image3 = new File(\"%s\")\n",
+				image3.getAbsolutePath()));
+
+		if (labels0 != null) sb.append(String.format("command.labels0 = new File(\"%s\")\n",
+				labels0.getAbsolutePath()));
+		if (labels1 != null) sb.append(String.format("command.labels1 = new File(\"%s\")\n",
+				labels1.getAbsolutePath()));
+
+		if (table0 != null) sb.append(String.format("command.table0 = new File(\"%s\")\n",
+				table0.getAbsolutePath()));
+		if (table1 != null) sb.append(String.format("command.table1 = new File(\"%s\")\n",
+				table1.getAbsolutePath()));
+
+		if (removeSpatialCalibration != null) {
+			sb.append("command.removeSpatialCalibration = ").append(removeSpatialCalibration).append("\n");
+		}
+
+		sb.append("\ncommand.run()\n");
+
+		return sb.toString();
+	}
 }
diff --git a/src/main/java/org/embl/mobie/command/view/ViewerTransformLoggerCommand.java b/src/main/java/org/embl/mobie/command/view/ViewerTransformLoggerCommand.java
@@ -39,7 +39,6 @@
 import org.embl.mobie.lib.transform.viewer.NormalVectorViewerTransform;
 import org.embl.mobie.lib.transform.NormalizedAffineViewerTransform;
 import org.embl.mobie.lib.transform.viewer.PositionViewerTransform;
-import org.embl.mobie.lib.transform.TransformHelper;
 import net.imglib2.realtransform.AffineTransform3D;
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
@@ -53,30 +52,29 @@ public class ViewerTransformLoggerCommand implements BdvPlaygroundActionCommand
 	public static final String NAME = "Log Current Location";
 
 	@Parameter
-	BdvHandle bdv;
+	BdvHandle bdvHandle;
 
 	@Override
 	public void run()
 	{
 		new Thread( () -> {
 
-			final int timepoint = bdv.getViewerPanel().state().getCurrentTimepoint();
-			final double[] position = BdvPlaygroundHelper.getWindowCentreInCalibratedUnits( bdv );
+			final int timepoint = bdvHandle.getViewerPanel().state().getCurrentTimepoint();
+			final double[] position = BdvPlaygroundHelper.getWindowCentreInCalibratedUnits( bdvHandle );
 
 			// position
 			final PositionViewerTransform positionViewerTransform = new PositionViewerTransform( position, timepoint );
 
 			// affine
 			final AffineTransform3D affineTransform3D = new AffineTransform3D();
-			bdv.getViewerPanel().state().getViewerTransform( affineTransform3D );
+			bdvHandle.getViewerPanel().state().getViewerTransform( affineTransform3D );
 			final AffineViewerTransform affineViewerTransform = new AffineViewerTransform( affineTransform3D.getRowPackedCopy(), timepoint );
 
 			// normalized affine
-			final AffineTransform3D normalisedViewerTransform = TransformHelper.createNormalisedViewerTransform( bdv.getViewerPanel() );
-			final NormalizedAffineViewerTransform normalizedAffineViewerTransform = new NormalizedAffineViewerTransform( normalisedViewerTransform.getRowPackedCopy(), timepoint );
+			final NormalizedAffineViewerTransform normalizedAffineViewerTransform = new NormalizedAffineViewerTransform( bdvHandle );
 
 			// normal vector
-			double[] currentNormalVector = BdvUtils.getCurrentViewNormalVector( bdv );
+			double[] currentNormalVector = BdvUtils.getCurrentViewNormalVector( bdvHandle );
 			final NormalVectorViewerTransform normalVectorViewerTransform = new NormalVectorViewerTransform( currentNormalVector, timepoint );
 
 			// print

diff --git a/src/main/java/org/embl/mobie/lib/SpimDataAdder.java b/src/main/java/org/embl/mobie/lib/SpimDataAdder.java
@@ -143,7 +143,7 @@ private void addImageView( AbstractSpimData< ? > spimData, int imageIndex, Strin
 		}
 
 		final ImageDisplay< ? > imageDisplay = new ImageDisplay<>( imageName, Arrays.asList( imageName ), color, contrastLimits );
-		final View view = new View( imageName, "images", Arrays.asList( imageDisplay ), null, false );
+		final View view = new View( imageName, "images", Arrays.asList( imageDisplay ), null, null, false, null );
 		dataset.views().put( view.getName(), view );
 	}
 
@@ -155,7 +155,7 @@ private void addSegmentationView( AbstractSpimData< ? > spimData, int setupId, S
 		final double pixelWidth = viewSetup.getVoxelSize().dimension( 0 );
 		display.setResolution3dView( new Double[]{ pixelWidth, pixelWidth, pixelWidth } );
 
-		final View view = new View( name, "segmentations", Arrays.asList( display ), null, false );
+		final View view = new View( name, "segmentations", Arrays.asList( display ), null, null, false, null );
 		dataset.views().put( view.getName(), view );
 	}
 

diff --git a/.../mobie/lib/create/DatasetJsonCreator.java → ...l/mobie/lib/create/DatasetSerializer.java b/.../mobie/lib/create/DatasetJsonCreator.java → ...l/mobie/lib/create/DatasetSerializer.java
@@ -57,7 +57,8 @@
 /**
  * Class to create and modify the metadata stored in dataset Json files
  */
-public class DatasetJsonCreator {
+public class DatasetSerializer
+{
 
     ProjectCreator projectCreator;
 
@@ -66,7 +67,7 @@ public class DatasetJsonCreator {
      * stored in dataset Json files
      * @param projectCreator projectCreator
      */
-    public DatasetJsonCreator( ProjectCreator projectCreator ) {
+    public DatasetSerializer( ProjectCreator projectCreator ) {
         this.projectCreator = projectCreator;
     }
 
@@ -94,9 +95,15 @@ public void addDataset( String datasetName, boolean is2D ) {
      *                  images from the viewer?
      * @param sourceTransform affine transform of image view
      */
-    public void addImage(String imageName, String datasetName,
+    public void addImage(String imageName,
+                         String datasetName,
                          String uiSelectionGroup,
-                         ImageDataFormat imageDataFormat, double[] contrastLimits, String colour, boolean exclusive, AffineTransform3D sourceTransform ) {
+                         ImageDataFormat imageDataFormat,
+                         double[] contrastLimits,
+                         String colour,
+                         boolean exclusive,
+                         AffineTransform3D sourceTransform )
+    {
         Dataset dataset = fetchDataset( datasetName );
 
         addNewImageSource( dataset, imageName, imageDataFormat );
@@ -146,7 +153,8 @@ public void addSegmentation(String imageName, String datasetName, String uiSelec
      * @param datasetName dataset name
      * @param is2D whether dataset only contains 2D images
      */
-    public void makeDataset2D( String datasetName, boolean is2D ) {
+    public void makeDataset2D( String datasetName, boolean is2D )
+    {
         Dataset dataset = projectCreator.getDataset( datasetName );
         dataset.is2D( is2D );
         writeDatasetJson( datasetName, dataset );
@@ -158,15 +166,17 @@ private Dataset fetchDataset( String datasetName )
         return dataset;
     }
 
-    private void addNewImageSource( Dataset dataset, String imageName, ImageDataFormat imageDataFormat ) {
+    private void addNewImageSource( Dataset dataset, String imageName, ImageDataFormat imageDataFormat )
+    {
         Map< ImageDataFormat, StorageLocation > imageDataLocations;
         ImageDataSource imageSource = new ImageDataSource();
         imageDataLocations = makeImageDataLocations( imageDataFormat, imageName );
         imageSource.imageData = imageDataLocations;
         dataset.sources().put( imageName, imageSource );
     }
 
-    private void addNewSegmentationSource( Dataset dataset, String imageName, ImageDataFormat imageDataFormat ) {
+    private void addNewSegmentationSource( Dataset dataset, String imageName, ImageDataFormat imageDataFormat )
+    {
         Map< ImageDataFormat, StorageLocation > imageDataLocations;
 
         SegmentationDataSource annotatedLabelMaskSource = new SegmentationDataSource();
@@ -182,7 +192,8 @@ private void addNewSegmentationSource( Dataset dataset, String imageName, ImageD
     }
 
     private Map< ImageDataFormat, StorageLocation > makeImageDataLocations( ImageDataFormat imageDataFormat,
-																			String imageName ) {
+																			String imageName )
+    {
         Map< ImageDataFormat, StorageLocation > imageDataLocations = new HashMap<>();
         StorageLocation imageStorageLocation = new StorageLocation();
         if ( imageDataFormat == ImageDataFormat.OmeZarr ) {
@@ -199,29 +210,34 @@ private Map< ImageDataFormat, StorageLocation > makeImageDataLocations( ImageDat
 
     private void addNewImageView( Dataset dataset, String imageName, String uiSelectionGroup,
 								  double[] contrastLimits, String colour, boolean exclusive,
-								  AffineTransform3D sourceTransform ) {
+								  AffineTransform3D sourceTransform )
+    {
         View view = createImageView( imageName, uiSelectionGroup, exclusive, contrastLimits, colour, sourceTransform );
         dataset.views().put( imageName, view );
     }
 
-    private void addNewSegmentationView( Dataset dataset, String imageName, String uiSelectionGroup, boolean exclusive, AffineTransform3D sourceTransform ) {
+    private void addNewSegmentationView( Dataset dataset, String imageName, String uiSelectionGroup, boolean exclusive, AffineTransform3D sourceTransform )
+    {
         View view = createSegmentationView( imageName, uiSelectionGroup, exclusive, sourceTransform );
         dataset.views().put( imageName, view );
     }
 
     private void addNewDefaultImageView( Dataset dataset, String imageName, double[] contrastLimits, String colour,
-										 AffineTransform3D sourceTransform ) {
+										 AffineTransform3D sourceTransform )
+    {
         View view = createImageView( imageName, "bookmark", true, contrastLimits, colour,
                 sourceTransform );
         dataset.views().put( View.DEFAULT, view );
     }
 
-    private void addNewDefaultSegmentationView( Dataset dataset, String imageName, AffineTransform3D sourceTransform ) {
+    private void addNewDefaultSegmentationView( Dataset dataset, String imageName, AffineTransform3D sourceTransform )
+    {
         View view = createSegmentationView( imageName, "bookmark", true, sourceTransform );
         dataset.views().put( View.DEFAULT, view );
     }
 
-    private List< Transformation > createSourceTransformerList( AffineTransform3D sourceTransform, List<String> sources ) {
+    private List< Transformation > createSourceTransformerList( AffineTransform3D sourceTransform, List<String> sources )
+    {
         List< Transformation > imageTransformationList = new ArrayList<>();
         Transformation imageTransformation = new AffineTransformation( "affine", sourceTransform.getRowPackedCopy(), sources );
         imageTransformationList.add( imageTransformation );
@@ -239,16 +255,17 @@ private View createImageView( String imageName, String uiSelectionGroup, boolean
 
         View view;
         if ( sourceTransform.isIdentity() ) {
-            view = new View( imageName, uiSelectionGroup, displays, null, null, isExclusive);
+            view = new View( imageName, uiSelectionGroup, displays, null, null, isExclusive, null );
         } else {
             List< Transformation > imageTransformationList = createSourceTransformerList( sourceTransform, sources );
-            view = new View( imageName, uiSelectionGroup, displays, imageTransformationList, null, isExclusive );
+            view = new View( imageName, uiSelectionGroup, displays, imageTransformationList, null, isExclusive, null );
         }
 
         return view;
     }
 
-    private View createSegmentationView( String imageName, String uiSelectionGroup, boolean isExclusive, AffineTransform3D sourceTransform ) {
+    private View createSegmentationView( String imageName, String uiSelectionGroup, boolean isExclusive, AffineTransform3D sourceTransform )
+    {
         ArrayList< Display< ? > > displays = new ArrayList<>();
         ArrayList<String> sources = new ArrayList<>();
         sources.add( imageName );
@@ -257,10 +274,10 @@ private View createSegmentationView( String imageName, String uiSelectionGroup,
         displays.add( segmentationDisplay );
 
         if ( sourceTransform.isIdentity() ) {
-            return new View( imageName, uiSelectionGroup, displays, null, null, isExclusive );
+            return new View( imageName, uiSelectionGroup, displays, null, null, isExclusive, null );
         } else {
             List< Transformation > imageTransformationList = createSourceTransformerList( sourceTransform, sources );
-            return new View( imageName, uiSelectionGroup, displays, imageTransformationList, null, isExclusive );
+            return new View( imageName, uiSelectionGroup, displays, imageTransformationList, null, isExclusive, null );
         }
     }
 
@@ -269,7 +286,8 @@ private View createSegmentationView( String imageName, String uiSelectionGroup,
      * @param datasetName dataset name
      * @param dataset dataset
      */
-    public void writeDatasetJson ( String datasetName, Dataset dataset ) {
+    public void writeDatasetJson ( String datasetName, Dataset dataset )
+    {
         try {
             String datasetJsonPath = IOHelper.combinePath( projectCreator.getProjectLocation().getAbsolutePath(),
                     datasetName, "dataset.json" );

diff --git a/src/main/java/org/embl/mobie/lib/create/ImagesCreator.java b/src/main/java/org/embl/mobie/lib/create/ImagesCreator.java
@@ -34,7 +34,6 @@
 import de.embl.cba.tables.Tables;
 import ij.IJ;
 import ij.ImagePlus;
-import ij.gui.Overlay;
 import ij.process.LUT;
 import mpicbg.spim.data.SpimData;
 import mpicbg.spim.data.SpimDataException;
@@ -645,15 +644,15 @@ private SpimData tryOpenSpimData( ImageDataFormat imageDataFormat, String filePa
     }
 
     private void updateTableAndJsonsForNewImage ( String imageName, String datasetName, String uiSelectionGroup, ImageDataFormat imageDataFormat, double[] contrastLimits, String colour, boolean exclusive, AffineTransform3D sourceTransform ) {
-        DatasetJsonCreator datasetJsonCreator = projectCreator.getDatasetJsonCreator();
-        datasetJsonCreator.addImage( imageName, datasetName, uiSelectionGroup,
+        DatasetSerializer datasetSerializer = projectCreator.getDatasetJsonCreator();
+        datasetSerializer.addImage( imageName, datasetName, uiSelectionGroup,
                 imageDataFormat, contrastLimits, colour, exclusive, sourceTransform );
     }
 
     private void updateTableAndJsonsForNewSegmentation( String imageName, String datasetName, String uiSelectionGroup, ImageDataFormat imageDataFormat, boolean exclusive, AffineTransform3D sourceTransform ) {
         addDefaultTableForImage( imageName, datasetName, imageDataFormat );
-        DatasetJsonCreator datasetJsonCreator = projectCreator.getDatasetJsonCreator();
-        datasetJsonCreator.addSegmentation( imageName, datasetName, uiSelectionGroup, imageDataFormat, exclusive, sourceTransform );
+        DatasetSerializer datasetSerializer = projectCreator.getDatasetJsonCreator();
+        datasetSerializer.addSegmentation( imageName, datasetName, uiSelectionGroup, imageDataFormat, exclusive, sourceTransform );
     }
 
     private void copyImage ( ImageDataFormat imageFormat, SpimData spimData,

diff --git a/src/main/java/org/embl/mobie/lib/create/ProjectCreator.java b/src/main/java/org/embl/mobie/lib/create/ProjectCreator.java
@@ -68,7 +68,7 @@ public class ProjectCreator {
 
     private final DatasetsCreator datasetsCreator;
     private final ImagesCreator imagesCreator;
-    private final DatasetJsonCreator datasetJsonCreator;
+    private final DatasetSerializer datasetSerializer;
     private final ProjectJsonCreator projectJsonCreator;
     private final RemoteMetadataCreator remoteMetadataCreator;
 
@@ -103,7 +103,7 @@ public ProjectCreator( File projectLocation ) throws IOException {
         }
 
         this.datasetsCreator = new DatasetsCreator( this );
-        this.datasetJsonCreator = new DatasetJsonCreator( this );
+        this.datasetSerializer = new DatasetSerializer( this );
         this.projectJsonCreator = new ProjectJsonCreator( this );
         this.imagesCreator = new ImagesCreator( this );
         this.remoteMetadataCreator = new RemoteMetadataCreator( this );
@@ -216,8 +216,8 @@ public ImagesCreator getImagesCreator() {
         return imagesCreator;
     }
 
-    public DatasetJsonCreator getDatasetJsonCreator() {
-        return datasetJsonCreator;
+    public DatasetSerializer getDatasetJsonCreator() {
+        return datasetSerializer;
     }
 
     public ProjectJsonCreator getProjectJsonCreator() { return projectJsonCreator; }

diff --git a/src/main/java/org/embl/mobie/lib/files/FileSourcesDataSetter.java b/src/main/java/org/embl/mobie/lib/files/FileSourcesDataSetter.java
@@ -243,7 +243,7 @@ else if ( sources.getGridType().equals( GridType.Transformed ) )
 		//
 		// FIXME: Maybe the viewerTransform could be something else?
 		final ImageZoomViewerTransform viewerTransform = new ImageZoomViewerTransform( transformations.get( 0 ).getSources().get( 0 ), 0 );
-		final View gridView = new View( "all images", "data", displays, transformations, viewerTransform, false );
+		final View gridView = new View( "all images", "data", displays, transformations, viewerTransform, false, null );
 		//gridView.overlayNames( true ); // FIXME: Timepoint bug!
 		dataset.views().put( gridView.getName(), gridView );
 	}

diff --git a/src/main/java/org/embl/mobie/lib/hcs/HCSDataAdder.java b/src/main/java/org/embl/mobie/lib/hcs/HCSDataAdder.java
@@ -200,7 +200,7 @@ public void addData( Dataset dataset )
 		final ArrayList< String > wells = new ArrayList<>( wellDisplay.sources.keySet() );
 		Collections.sort( wells );
 		final ImageZoomViewerTransform viewerTransform = new ImageZoomViewerTransform( wells.get( 0 ), 0 );
-		final View view = new View( plate.getName(), "plate", displays, imageTransforms, viewerTransform, true );
+		final View view = new View( plate.getName(), "plate", displays, imageTransforms, viewerTransform, true, null );
 		dataset.views().put( view.getName(), view );
 	}