From d1d762a8ba40ac4416cbe74351bd2f70de920405 Mon Sep 17 00:00:00 2001
From: Tobias Pietzsch <tobias.pietzsch@gmail.com>
Date: Wed, 5 Mar 2014 15:07:40 -0500
Subject: [PATCH] Utility method for computing mipmapTransform (for standard
averaging down-scaling)
---
.../bdv/img/catmaid/CatmaidImageLoader.java | 12 +++++++
.../java/bdv/img/hdf5/Hdf5ImageLoader.java | 12 ++-----
.../bdv/img/remote/RemoteImageLoader.java | 12 ++-----
src/main/java/bdv/util/MipmapTransforms.java | 32 +++++++++++++++++++
4 files changed, 48 insertions(+), 20 deletions(-)
create mode 100644 src/main/java/bdv/util/MipmapTransforms.java
diff --git a/src/main/java/bdv/img/catmaid/CatmaidImageLoader.java b/src/main/java/bdv/img/catmaid/CatmaidImageLoader.java
index f7b839f0..7eedf8a2 100644
--- a/src/main/java/bdv/img/catmaid/CatmaidImageLoader.java
+++ b/src/main/java/bdv/img/catmaid/CatmaidImageLoader.java
@@ -7,6 +7,7 @@ import net.imglib2.RandomAccessibleInterval;
import net.imglib2.img.NativeImg;
import net.imglib2.img.basictypeaccess.volatiles.array.VolatileIntArray;
import net.imglib2.img.cell.CellImg;
+import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.ARGBType;
import net.imglib2.type.volatiles.VolatileARGBType;
@@ -19,6 +20,7 @@ import bdv.img.cache.VolatileGlobalCellCache;
import bdv.img.cache.VolatileGlobalCellCache.LoadingStrategy;
import bdv.img.cache.VolatileImgCells;
import bdv.img.cache.VolatileImgCells.CellCache;
+import bdv.util.MipmapTransforms;
public class CatmaidImageLoader extends AbstractViewerImgLoader< ARGBType, VolatileARGBType >
{
@@ -42,6 +44,8 @@ public class CatmaidImageLoader extends AbstractViewerImgLoader< ARGBType, Volat
private double[][] mipmapResolutions;
+ private AffineTransform3D[] mipmapTransforms;
+
private long[][] imageDimensions;
private int[][] blockDimensions;
@@ -75,11 +79,13 @@ public class CatmaidImageLoader extends AbstractViewerImgLoader< ARGBType, Volat
numScales = Integer.parseInt( numScalesString );
mipmapResolutions = new double[ numScales ][];
+ mipmapTransforms = new AffineTransform3D[ numScales ];
imageDimensions = new long[ numScales ][];
blockDimensions = new int[ numScales ][];
for ( int l = 0; l < numScales; ++l )
{
mipmapResolutions[ l ] = new double[] { 1 << l, 1 << l, 1 };
+ mipmapTransforms[ l ] = MipmapTransforms.getMipmapTransformDefault( mipmapResolutions[ l ] );
imageDimensions[ l ] = new long[] { width >> l, height >> l, depth };
blockDimensions[ l ] = new int[] { tileWidth, tileHeight, 1 };
}
@@ -150,4 +156,10 @@ public class CatmaidImageLoader extends AbstractViewerImgLoader< ARGBType, Volat
{
return cache;
}
+
+ @Override
+ public AffineTransform3D[] getMipmapTransforms( final int setup )
+ {
+ return mipmapTransforms;
+ }
}
diff --git a/src/main/java/bdv/img/hdf5/Hdf5ImageLoader.java b/src/main/java/bdv/img/hdf5/Hdf5ImageLoader.java
index 526891d2..f3992444 100644
--- a/src/main/java/bdv/img/hdf5/Hdf5ImageLoader.java
+++ b/src/main/java/bdv/img/hdf5/Hdf5ImageLoader.java
@@ -30,6 +30,7 @@ import bdv.img.cache.VolatileGlobalCellCache;
import bdv.img.cache.VolatileGlobalCellCache.LoadingStrategy;
import bdv.img.cache.VolatileImgCells;
import bdv.img.cache.VolatileImgCells.CellCache;
+import bdv.util.MipmapTransforms;
import ch.systemsx.cisd.hdf5.HDF5DataSetInformation;
import ch.systemsx.cisd.hdf5.HDF5Factory;
import ch.systemsx.cisd.hdf5.IHDF5Reader;
@@ -140,16 +141,7 @@ public class Hdf5ImageLoader extends AbstractViewerImgLoader< UnsignedShortType,
final AffineTransform3D[] mipmapTransforms = new AffineTransform3D[ mipmapResolutions.length ];
for ( int level = 0; level < mipmapResolutions.length; level++ )
- {
- final AffineTransform3D mipmapTransform = new AffineTransform3D();
- final double[] resolution = mipmapResolutions[ level ];
- for ( int d = 0; d < 3; ++d )
- {
- mipmapTransform.set( resolution[ d ], d, d );
- mipmapTransform.set( 0.5 * ( resolution[ d ] - 1 ), d, 3 );
- }
- mipmapTransforms[ level ] = mipmapTransform;
- }
+ mipmapTransforms[ level ] = MipmapTransforms.getMipmapTransformDefault( mipmapResolutions[ level ] );
perSetupMipmapTransforms.add( mipmapTransforms );
final int[][] subdivisions = hdf5Reader.readIntMatrix( getSubdivisionsPath( setup ) );
diff --git a/src/main/java/bdv/img/remote/RemoteImageLoader.java b/src/main/java/bdv/img/remote/RemoteImageLoader.java
index c6d93738..9046b782 100644
--- a/src/main/java/bdv/img/remote/RemoteImageLoader.java
+++ b/src/main/java/bdv/img/remote/RemoteImageLoader.java
@@ -28,6 +28,7 @@ import bdv.img.cache.VolatileGlobalCellCache;
import bdv.img.cache.VolatileGlobalCellCache.LoadingStrategy;
import bdv.img.cache.VolatileImgCells;
import bdv.img.cache.VolatileImgCells.CellCache;
+import bdv.util.MipmapTransforms;
import com.google.gson.Gson;
@@ -67,16 +68,7 @@ public class RemoteImageLoader extends AbstractViewerImgLoader< UnsignedShortTyp
final double[][] mipmapResolutions = metadata.perSetupMipmapResolutions.get( setup );
final AffineTransform3D[] mipmapTransforms = new AffineTransform3D[ mipmapResolutions.length ];
for ( int level = 0; level < mipmapResolutions.length; level++ )
- {
- final AffineTransform3D mipmapTransform = new AffineTransform3D();
- final double[] resolution = mipmapResolutions[ level ];
- for ( int d = 0; d < 3; ++d )
- {
- mipmapTransform.set( resolution[ d ], d, d );
- mipmapTransform.set( 0.5 * ( resolution[ d ] - 1 ), d, 3 );
- }
- mipmapTransforms[ level ] = mipmapTransform;
- }
+ mipmapTransforms[ level ] = MipmapTransforms.getMipmapTransformDefault( mipmapResolutions[ level ] );
perSetupMipmapTransforms.add( mipmapTransforms );
}
cellsDimensions = metadata.createCellsDimensions();
diff --git a/src/main/java/bdv/util/MipmapTransforms.java b/src/main/java/bdv/util/MipmapTransforms.java
new file mode 100644
index 00000000..cb4dd53b
--- /dev/null
+++ b/src/main/java/bdv/util/MipmapTransforms.java
@@ -0,0 +1,32 @@
+package bdv.util;
+
+import net.imglib2.realtransform.AffineTransform3D;
+
+public class MipmapTransforms
+{
+ /**
+ * Compute the transformation (scale and shift) that maps from coordinates
+ * in a down-scaled image to coordinates in the original image. This assumes
+ * that each down-scaled pixel is the average of a block of blocks of pixels
+ * in the original image. For down-scaling by a factor of 2, pixel (0,0,0)
+ * in the down-scaled image is the average of the 8 pixel block from (0,0,0)
+ * to (1,1,1) in the original image.
+ *
+ * @param resolution
+ * the down-scaling factors in each dimension. {4,4,2} means
+ * every pixel in the down-scaled image corresponds to a 4x4x2
+ * pixel block in the original image.
+ * @return transformation from down-scaled image to original image.
+ */
+ public static AffineTransform3D getMipmapTransformDefault( final double[] resolution )
+ {
+ assert resolution.length == 3;
+ final AffineTransform3D mipmapTransform = new AffineTransform3D();
+ for ( int d = 0; d < 3; ++d )
+ {
+ mipmapTransform.set( resolution[ d ], d, d );
+ mipmapTransform.set( 0.5 * ( resolution[ d ] - 1 ), d, 3 );
+ }
+ return mipmapTransform;
+ }
+}
--
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