Move LazySpimSource to BdvUtils

mobie · Mar 8, 2019 · ea29e3c · ea29e3c
1 parent 1363490
commit ea29e3c
Show file tree

Hide file tree

Showing 3 changed files with 6 additions and 95 deletions.
diff --git a/pom.xml b/pom.xml
@@ -142,13 +142,13 @@
 		<dependency>
 			<groupId>de.embl.cba</groupId>
 			<artifactId>table-utils</artifactId>
-			<version>0.2.04</version>
+			<version>0.2.06</version>
 		</dependency>
 
 		<dependency>
 			<groupId>de.embl.cba</groupId>
 			<artifactId>bdv-utils</artifactId>
-			<version>0.2.07</version>
+			<version>0.2.08</version>
 		</dependency>
 
 	</dependencies>

diff --git a/src/main/java/de/embl/cba/platynereis/GeneSearch.java b/src/main/java/de/embl/cba/platynereis/GeneSearch.java
@@ -2,16 +2,15 @@
 
 import bdv.VolatileSpimSource;
 import bdv.tools.transformation.TransformedSource;
-import bdv.viewer.Source;
-import de.embl.cba.bdv.utils.BdvUtils;
+
+import de.embl.cba.bdv.utils.sources.LazySpimSource;
 import de.embl.cba.platynereis.utils.Utils;
 import de.embl.cba.tables.modelview.images.ImageSourcesModel;
 import de.embl.cba.tables.modelview.images.SourceAndMetadata;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.type.NativeType;
 import net.imglib2.type.numeric.RealType;
 
-import javax.swing.*;
 import java.util.ArrayList;
 import java.util.LinkedHashMap;
 import java.util.Map;
@@ -78,12 +77,10 @@ public Map< String, Double > runSearchAndGetLocalExpression()
 
 	public RandomAccessibleInterval< ? > getRandomAccessibleInterval( SourceAndMetadata sourceAndMetadata )
 	{
-		final PlatynereisImageSourcesModel.LazySpimSource lazySpimSource =
-				( PlatynereisImageSourcesModel.LazySpimSource ) sourceAndMetadata.source();
+		final LazySpimSource lazySpimSource = ( LazySpimSource ) sourceAndMetadata.source();
 		final TransformedSource transformedSource = (TransformedSource) lazySpimSource.wrappedSource();
 		final VolatileSpimSource wrappedSource = ( VolatileSpimSource ) transformedSource.getWrappedSource();
 		final RandomAccessibleInterval< ? > rai = wrappedSource.nonVolatile().getSource( 0, 0 );
-
 		return rai;
 	}
 

diff --git a/src/main/java/de/embl/cba/platynereis/PlatynereisImageSourcesModel.java b/src/main/java/de/embl/cba/platynereis/PlatynereisImageSourcesModel.java
@@ -1,21 +1,12 @@
 package de.embl.cba.platynereis;
 
-import bdv.BigDataViewer;
-import bdv.tools.brightness.ConverterSetup;
-import bdv.viewer.Interpolation;
-import bdv.viewer.Source;
-import bdv.viewer.SourceAndConverter;
+import de.embl.cba.bdv.utils.sources.LazySpimSource;
 import de.embl.cba.tables.modelview.images.ImageSourcesModel;
 import de.embl.cba.tables.modelview.images.SourceAndMetadata;
 import de.embl.cba.tables.modelview.images.SourceMetadata;
 import mpicbg.spim.data.SpimData;
 import mpicbg.spim.data.SpimDataException;
 import mpicbg.spim.data.XmlIoSpimData;
-import mpicbg.spim.data.sequence.VoxelDimensions;
-import net.imglib2.RandomAccessibleInterval;
-import net.imglib2.RealRandomAccessible;
-import net.imglib2.realtransform.AffineTransform3D;
-import net.imglib2.type.numeric.NumericType;
 
 import java.io.File;
 import java.util.*;
@@ -128,83 +119,6 @@ private SpimData openSpimData( File file )
 		}
 	}
 
-	class LazySpimSource< T extends NumericType< T > > implements Source< T >
-	{
-		private final String name;
-		private final File file;
-		private Source< T > source;
-
-		public LazySpimSource( String name, File file )
-		{
-			this.name = name;
-			this.file = file;
-		}
-
-		public Source< T > wrappedSource()
-		{
-			if ( source == null )
-			{
-				final SpimData spimData = openSpimData( file );
-				final List< ConverterSetup > converterSetups = new ArrayList<>();
-				final List< SourceAndConverter< ? > > sources = new ArrayList<>();
-				BigDataViewer.initSetups( spimData, converterSetups, sources );
-
-				source = ( Source< T > ) sources.get( 0 ).asVolatile().getSpimSource();
-			}
-
-			return source;
-		}
-
-		@Override
-		public boolean isPresent( int t )
-		{
-			if ( t == 0 ) return true;
-			return false;
-		}
-
-		@Override
-		public RandomAccessibleInterval< T > getSource( int t, int level )
-		{
-			return wrappedSource().getSource( t, level );
-		}
-
-		@Override
-		public RealRandomAccessible< T > getInterpolatedSource( int t, int level, Interpolation method )
-		{
-			return wrappedSource().getInterpolatedSource( t, level, method );
-		}
-
-		@Override
-		public void getSourceTransform( int t, int level, AffineTransform3D transform )
-		{
-			wrappedSource().getSourceTransform( t, level, transform  );
-		}
-
-		@Override
-		public T getType()
-		{
-			return wrappedSource().getType();
-		}
-
-		@Override
-		public String getName()
-		{
-			return wrappedSource().getName();
-		}
-
-		@Override
-		public VoxelDimensions getVoxelDimensions()
-		{
-			return wrappedSource().getVoxelDimensions();
-		}
-
-		@Override
-		public int getNumMipmapLevels()
-		{
-			return wrappedSource().getNumMipmapLevels();
-		}
-	}
-
 	public void addSource( File file )
 	{
 		final String imageId = sourceName( file );