fix uses of deprecated bigdataviewer and imglib2 API

src/main/java/bdv/ij/BigDataBrowserPlugIn.java

@@ -150,7 +150,9 @@ public class BigDataBrowserPlugIn implements PlugIn
 					System.out.println( key );
 					try
 					{
-						BigDataViewer.view( datasetUrlMap.get( key ), new ProgressWriterIJ() );
+						final String filename = datasetUrlMap.get( key );
+						final String title = new File( filename ).getName();
+						BigDataViewer.open( filename, title, new ProgressWriterIJ(), ViewerOptions.options() );
 					}
 					catch ( final SpimDataException e )
 					{

src/main/java/bdv/ij/BigDataViewerPlugIn.java

 package bdv.ij;
 
-import ij.Prefs;
-import ij.plugin.PlugIn;
-
 import java.awt.FileDialog;
 import java.awt.Frame;
 import java.io.File;
@@ -15,6 +12,9 @@ import javax.swing.filechooser.FileFilter;
 
 import bdv.BigDataViewer;
 import bdv.ij.util.ProgressWriterIJ;
+import bdv.viewer.ViewerOptions;
+import ij.Prefs;
+import ij.plugin.PlugIn;
 
 public class BigDataViewerPlugIn implements PlugIn
 {
@@ -105,7 +105,7 @@ public class BigDataViewerPlugIn implements PlugIn
 			try
 			{
 				lastDatasetPath = file.getAbsolutePath();
-				BigDataViewer.view( file.getAbsolutePath(), new ProgressWriterIJ() );
+				BigDataViewer.open( file.getAbsolutePath(), file.getName(), new ProgressWriterIJ(), ViewerOptions.options() );
 			}
 			catch ( final Exception e )
 			{

src/main/java/bdv/ij/OpenImarisPlugIn.java

 package bdv.ij;
 
-import ij.ImageJ;
-import ij.Prefs;
-import ij.plugin.PlugIn;
-
 import java.awt.FileDialog;
 import java.awt.Frame;
 import java.io.File;
@@ -18,6 +14,10 @@ import bdv.BigDataViewer;
 import bdv.ij.util.ProgressWriterIJ;
 import bdv.img.imaris.Imaris;
 import bdv.spimdata.SpimDataMinimal;
+import bdv.viewer.ViewerOptions;
+import ij.ImageJ;
+import ij.Prefs;
+import ij.plugin.PlugIn;
 
 public class OpenImarisPlugIn implements PlugIn
 {
@@ -114,7 +114,7 @@ public class OpenImarisPlugIn implements PlugIn
 			{
 				lastDatasetPath = file.getAbsolutePath();
 				final SpimDataMinimal spimData = Imaris.openIms( file.getAbsolutePath() );
-				new BigDataViewer( spimData, file.getName(), new ProgressWriterIJ() );
+				BigDataViewer.open( spimData, file.getName(), new ProgressWriterIJ(), ViewerOptions.options() );
 			}
 			catch ( final IOException e )
 			{

src/main/java/bdv/ij/export/SpimRegistrationSequence.java

@@ -328,8 +328,13 @@ public class SpimRegistrationSequence
 			else
 				imgD = conf.cropSizeZ/scale;
 
-			// TODO: this should be a RealInterval
-			return FinalRealInterval.createMinSize( ( int ) min.x + cropOffsetX, (int ) min.y + cropOffsetY, ( int ) min.z + cropOffsetZ, imgW, imgH, imgD );
+			return FinalRealInterval.createMinMax(
+					( int ) min.x + cropOffsetX,
+					( int ) min.y + cropOffsetY,
+					( int ) min.z + cropOffsetZ,
+					( int ) min.x + cropOffsetX + imgW - 1,
+					( int ) min.y + cropOffsetY + imgH - 1,
+					( int ) min.z + cropOffsetZ + imgD - 1 );
 	}
 
 	protected static ViewRegistrations createViewRegistrations( final SPIMConfiguration conf, final ArrayList< ViewSetup > setups )