Rename SpimDataImage to ImageDataImage

mobie · Feb 25, 2024 · b8aba1c · b8aba1c
1 parent 6acf91d
commit b8aba1c
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Showing 7 changed files with 20 additions and 295 deletions.
diff --git a/pom.xml.releaseBackup b/pom.xml.releaseBackup
diff --git a/release.properties b/release.properties
diff --git a/src/main/java/org/embl/mobie/MoBIE.java b/src/main/java/org/embl/mobie/MoBIE.java
@@ -50,7 +50,7 @@
 import org.embl.mobie.lib.hcs.Site;
 import org.embl.mobie.lib.image.CachedCellImage;
 import org.embl.mobie.lib.image.Image;
-import org.embl.mobie.lib.image.SpimDataImage;
+import org.embl.mobie.lib.image.ImageDataImage;
 import org.embl.mobie.lib.io.DataFormats;
 import org.embl.mobie.lib.io.StorageLocation;
 import org.embl.mobie.plugins.platybrowser.GeneSearchCommand;
@@ -712,7 +712,7 @@ private void initDataSource( DataSource dataSource, String log )
 	{
 		if ( imageDataFormat.equals( ImageDataFormat.SpimData ) )
 		{
-			return new SpimDataImage<>( ( AbstractSpimData ) storageLocation.data, storageLocation.getChannel(), name, settings.values.getRemoveSpatialCalibration() );
+			return new ImageDataImage<>( ( AbstractSpimData ) storageLocation.data, storageLocation.getChannel(), name, settings.values.getRemoveSpatialCalibration() );
 		}
 
 		if ( imageDataFormat.equals( ImageDataFormat.IlastikHDF5 ) )
@@ -728,25 +728,26 @@ private void initDataSource( DataSource dataSource, String log )
 			{
 				// the whole plate is already initialised as one big SpimData
 				// note that channel <=> setupID
-				return new SpimDataImage( site.getSpimData(), site.channel, name, settings.values.getRemoveSpatialCalibration() );
+				return new ImageDataImage( site.getSpimData(), site.channel, name, settings.values.getRemoveSpatialCalibration() );
 			}
 
 			if ( site.getImageDataFormat().equals( ImageDataFormat.OmeZarr ) )
 			{
-				return new SpimDataImage( ImageDataFormat.OmeZarr, site.absolutePath, site.channel, name, ThreadHelper.sharedQueue, settings.values.getRemoveSpatialCalibration() );
+				return new ImageDataImage( ImageDataFormat.OmeZarr, site.absolutePath, site.channel, name, ThreadHelper.sharedQueue, settings.values.getRemoveSpatialCalibration() );
 			}
 
 			if ( site.getImageDataFormat().equals( ImageDataFormat.OmeZarrS3 ) )
 			{
-				return new SpimDataImage( ImageDataFormat.OmeZarrS3, site.absolutePath, site.channel, name, ThreadHelper.sharedQueue, settings.values.getRemoveSpatialCalibration() );
+				return new ImageDataImage( ImageDataFormat.OmeZarrS3, site.absolutePath, site.channel, name, ThreadHelper.sharedQueue, settings.values.getRemoveSpatialCalibration() );
 			}
 
-			return new SpimDataImage( site, name, ThreadHelper.sharedQueue, settings.values.getRemoveSpatialCalibration()  );
+			return new ImageDataImage( site, name, ThreadHelper.sharedQueue, settings.values.getRemoveSpatialCalibration()  );
 		}
 
+		// FIXME: The image below should not be called SpimDataImage
 		final String imagePath = getImageLocation( imageDataFormat, storageLocation );
-		final SpimDataImage spimDataImage = new SpimDataImage( imageDataFormat, imagePath, storageLocation.getChannel(), name, ThreadHelper.sharedQueue, settings.values.getRemoveSpatialCalibration() );
-		return spimDataImage;
+		final ImageDataImage imageDataImage = new ImageDataImage( imageDataFormat, imagePath, storageLocation.getChannel(), name, ThreadHelper.sharedQueue, settings.values.getRemoveSpatialCalibration() );
+		return imageDataImage;
 	}
 
 	public List< DataSource > getDataSources( Set< String > names )

diff --git a/src/main/java/org/embl/mobie/lib/bdv/ScreenShotMaker.java b/src/main/java/org/embl/mobie/lib/bdv/ScreenShotMaker.java
@@ -28,6 +28,7 @@
  */
 package org.embl.mobie.lib.bdv;
 
+import bdv.SpimSource;
 import bdv.util.BdvHandle;
 import bdv.viewer.Interpolation;
 import bdv.viewer.Source;
@@ -110,6 +111,7 @@ public Roi[] getMasks()
     public void run( Double targetSamplingInXY )
     {
         List< SourceAndConverter< ? > > sacs = getVisibleSourceAndConverters();
+
         run( sacs, targetSamplingInXY );
     }
 

diff --git a/src/main/java/org/embl/mobie/lib/hcs/VirtualBioFormatsStack.java b/src/main/java/org/embl/mobie/lib/hcs/VirtualBioFormatsStack.java
@@ -4,15 +4,10 @@
 import ij.ImagePlus;
 import ij.ImageStack;
 import ij.WindowManager;
-import ij.io.Opener;
 import ij.plugin.FolderOpener;
 import ij.process.*;
 import ij.util.Tools;
-import io.scif.img.IO;
-import loci.formats.in.CellSensReader;
-import org.embl.mobie.io.SpimDataOpener;
 import org.embl.mobie.io.util.IOHelper;
-import org.embl.mobie.lib.MoBIEHelper;
 
 import java.awt.*;
 import java.awt.image.ColorModel;