Merge pull request #59 from PreibischLab/blk-affine-fusion

Use new BlockSupplier API for AffineFusion
PreibischLab · Sep 30, 2024 · bc05b8e · bc05b8e
2 parents 49c5389 + ec107fe
commit bc05b8e
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Showing 13 changed files with 1,469 additions and 55 deletions.
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/datasetmanager/MultiViewDatasetDefinition.java b/src/main/java/net/preibisch/mvrecon/fiji/datasetmanager/MultiViewDatasetDefinition.java
@@ -49,7 +49,7 @@ public interface MultiViewDatasetDefinition
 	 * save it as an XML file.
 	 * 
 	 * @param xmlFileName - the filename of the XML that was selected (no path!)
-	 * @return - the saved {@link SpimData} object
+	 * @return - the saved {@link SpimData2} object
 	 */
 	public SpimData2 createDataset( final String xmlFileName );
 

diff --git a/src/main/java/net/preibisch/mvrecon/fiji/plugin/Image_Fusion.java b/src/main/java/net/preibisch/mvrecon/fiji/plugin/Image_Fusion.java
@@ -61,6 +61,7 @@
 import net.preibisch.mvrecon.process.export.Calibrateable;
 import net.preibisch.mvrecon.process.export.ImgExport;
 import net.preibisch.mvrecon.process.fusion.FusionTools;
+import net.preibisch.mvrecon.process.fusion.blk.BlkAffineFusion;
 import net.preibisch.mvrecon.process.fusion.lazy.LazyAffineFusion;
 import net.preibisch.mvrecon.process.fusion.lazy.LazyNonRigidFusion;
 import net.preibisch.mvrecon.process.fusion.transformed.TransformVirtual;
@@ -245,7 +246,9 @@ else if ( fusion.getPixelType() == 1 )
 			}
 			else
 			{
-				lazy = LazyAffineFusion.init(
+				System.out.println( "Image_Fusion.fuse" );
+//				lazy = LazyAffineFusion.init(
+				lazy = BlkAffineFusion.init(
 						conv,
 						spimData.getSequenceDescription().getImgLoader(),
 						group.getViews(),
@@ -257,20 +260,6 @@ else if ( fusion.getPixelType() == 1 )
 						fusion.getBoundingBox(),
 						(RealType & NativeType)type,
 						blocksize );
-
-				// TODO: replace with LazyAffineFusion and varying blocksizes depending on the task
-				/*
-				virtual = FusionTools.fuseVirtual(
-						spimData.getSequenceDescription().getImgLoader(),
-						registrations,
-						spimData.getSequenceDescription().getViewDescriptions(),
-						group.getViews(),
-						fusion.useBlending(),
-						fusion.useContentBased(),
-						fusion.getInterpolation(),
-						fusion.getBoundingBox(),
-						fusion.adjustIntensities() ? spimData.getIntensityAdjustments().getIntensityAdjustments() : null );
-				*/
 			}
 
 			final String title = getTitle( fusion.getSplittingType(), group );

diff --git a/src/main/java/net/preibisch/mvrecon/process/export/ExportN5Api.java b/src/main/java/net/preibisch/mvrecon/process/export/ExportN5Api.java
@@ -226,7 +226,7 @@ else if ( storageType == StorageFormat.HDF5 )
 						bb.dimensionsAsLongArray(),
 						compression,
 						blocksize(),
-						this.downsampling,
+						this.downsampling == null ? new int[][] {{1,1,1}} : this.downsampling,
 						viewId,
 						path,
 						xmlOut,

diff --git a/src/main/java/net/preibisch/mvrecon/process/fusion/FusionTools.java b/src/main/java/net/preibisch/mvrecon/process/fusion/FusionTools.java
@@ -47,7 +47,6 @@
 import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
 import mpicbg.spim.data.generic.sequence.BasicImgLoader;
 import mpicbg.spim.data.generic.sequence.BasicViewDescription;
-import mpicbg.spim.data.generic.sequence.BasicViewSetup;
 import mpicbg.spim.data.registration.ViewRegistration;
 import mpicbg.spim.data.sequence.Angle;
 import mpicbg.spim.data.sequence.Channel;
@@ -64,15 +63,19 @@
 import net.imglib2.IterableInterval;
 import net.imglib2.RandomAccess;
 import net.imglib2.RandomAccessibleInterval;
-import net.imglib2.cache.img.CellLoader;
+import net.imglib2.cache.CacheLoader;
+import net.imglib2.cache.img.RandomAccessibleCacheLoader;
 import net.imglib2.cache.img.ReadOnlyCachedCellImgFactory;
 import net.imglib2.cache.img.ReadOnlyCachedCellImgOptions;
-import net.imglib2.cache.img.SingleCellArrayImg;
 import net.imglib2.cache.img.optional.CacheOptions.CacheType;
 import net.imglib2.converter.Converters;
 import net.imglib2.converter.RealTypeConverters;
 import net.imglib2.img.Img;
 import net.imglib2.img.ImgFactory;
+import net.imglib2.img.basictypeaccess.AccessFlags;
+import net.imglib2.img.basictypeaccess.array.ArrayDataAccess;
+import net.imglib2.img.cell.Cell;
+import net.imglib2.img.cell.CellGrid;
 import net.imglib2.img.imageplus.ImagePlusImgFactory;
 import net.imglib2.realtransform.AffineTransform3D;
 import net.imglib2.type.NativeType;
@@ -783,49 +786,26 @@ public static < T extends NativeType< T > > RandomAccessibleInterval< T > cacheR
 		return cacheRandomAccessibleInterval( input, -1, type, cellDim );
 	}
 
-	public static < T extends NativeType< T > > RandomAccessibleInterval< T > cacheRandomAccessibleInterval(
+	public static < T extends NativeType< T >, A extends ArrayDataAccess< A > > RandomAccessibleInterval< T > cacheRandomAccessibleInterval(
 			final RandomAccessibleInterval< T > input,
 			final long maxCacheSize,
 			final T type,
 			final int... cellDim )
 	{
-		final RandomAccessibleInterval< T > in;
-
-		if ( Views.isZeroMin( input ) )
-			in = input;
-		else
-			in = Views.zeroMin( input );
-
-		final ReadOnlyCachedCellImgOptions options;
-
-		if ( maxCacheSize > 0 )
-			options = new ReadOnlyCachedCellImgOptions().cellDimensions( cellDim ).maxCacheSize( maxCacheSize );
-		else
-			options = new ReadOnlyCachedCellImgOptions().cellDimensions( cellDim ).cacheType( CacheType.SOFTREF );
-
+		final ReadOnlyCachedCellImgOptions options = ReadOnlyCachedCellImgOptions.options()
+				.cellDimensions( cellDim )
+				.cacheType( maxCacheSize > 0 ? CacheType.BOUNDED : CacheType.SOFTREF )
+				.maxCacheSize( maxCacheSize );
 		final ReadOnlyCachedCellImgFactory factory = new ReadOnlyCachedCellImgFactory( options );
 
-		final CellLoader< T > loader = new CellLoader< T >()
-		{
-			@Override
-			public void load( final SingleCellArrayImg< T, ? > cell ) throws Exception
-			{
-				final Cursor< T > cursor = cell.localizingCursor();
-				final RandomAccess< T > ra = in.randomAccess();
-
-				while( cursor.hasNext() )
-				{
-					cursor.fwd();
-					ra.setPosition( cursor );
-					cursor.get().set( ra.get() );
-				}
-			}
-		};
-
-		final long[] dim = new long[ in.numDimensions() ];
-		in.dimensions( dim );
+		final long[] dim = input.dimensionsAsLongArray();
+		final CacheLoader< Long, Cell< A > > loader = RandomAccessibleCacheLoader.get(
+				new CellGrid( dim, cellDim ),
+				input.view().zeroMin(),
+				AccessFlags.setOf( AccessFlags.VOLATILE ) );
+		final RandomAccessibleInterval<T> copy = factory.createWithCacheLoader( dim, type, loader );
 
-		return translateIfNecessary( input, factory.create( dim, type, loader ) );
+		return translateIfNecessary( input, copy );
 	}
 
 	public static < T extends Type< T > > RandomAccessibleInterval< T > copyImg( final RandomAccessibleInterval< T > input, final ImgFactory< T > factory, final T type, final ExecutorService service  )