diff --git a/src/main/java/bdv/ij/export/imgloader/ImagePlusImgLoader.java b/src/main/java/bdv/ij/export/imgloader/ImagePlusImgLoader.java
index fbefc4ad89bcf786835780ca1350b1ac408e9a93..77ecf62a16609e4f816f6a772671ee7c663de842 100644
--- a/src/main/java/bdv/ij/export/imgloader/ImagePlusImgLoader.java
+++ b/src/main/java/bdv/ij/export/imgloader/ImagePlusImgLoader.java
@@ -1,7 +1,11 @@
package bdv.ij.export.imgloader;
+import java.util.ArrayList;
+
import ij.ImagePlus;
import mpicbg.spim.data.generic.sequence.BasicImgLoader;
+import mpicbg.spim.data.generic.sequence.BasicSetupImgLoader;
+import mpicbg.spim.data.generic.sequence.TypedBasicImgLoader;
import mpicbg.spim.data.sequence.ViewId;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.algorithm.stats.ComputeMinMax;
@@ -9,9 +13,7 @@ import net.imglib2.converter.Converters;
import net.imglib2.converter.RealUnsignedShortConverter;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;
-import net.imglib2.type.numeric.integer.UnsignedByteType;
import net.imglib2.type.numeric.integer.UnsignedShortType;
-import net.imglib2.type.numeric.real.FloatType;
import bdv.img.cache.VolatileGlobalCellCache;
import bdv.img.imagestack.ImageStackImageLoader;
import bdv.img.virtualstack.VirtualStackImageLoader;
@@ -29,7 +31,7 @@ import bdv.img.virtualstack.VirtualStackImageLoader;
*
* @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
-public class ImagePlusImgLoader< T extends RealType< T > & NativeType< T > > implements BasicImgLoader< UnsignedShortType >
+public class ImagePlusImgLoader implements TypedBasicImgLoader< UnsignedShortType >
{
public static enum MinMaxOption
{
@@ -38,49 +40,51 @@ public class ImagePlusImgLoader< T extends RealType< T > & NativeType< T > > imp
TAKE_FROM_IMAGEPROCESSOR
}
- public static ImagePlusImgLoader< UnsignedByteType > createGray8( final ImagePlus imp, final MinMaxOption minMaxOption, final double min, final double max )
+ public static ImagePlusImgLoader createGray8( final ImagePlus imp, final MinMaxOption minMaxOption, final double min, final double max )
{
if( imp.getType() != ImagePlus.GRAY8 )
throw new RuntimeException( "expected ImagePlus type GRAY8" );
if ( imp.getStack() != null && imp.getStack().isVirtual() )
- return new ImagePlusImgLoader< UnsignedByteType >( imp, VirtualStackImageLoader.createUnsignedByteInstance( imp ), minMaxOption, min, max );
+ return new ImagePlusImgLoader( imp, VirtualStackImageLoader.createUnsignedByteInstance( imp ), minMaxOption, min, max );
else
- return new ImagePlusImgLoader< UnsignedByteType >( imp, ImageStackImageLoader.createUnsignedByteInstance( imp ), minMaxOption, min, max );
+ return new ImagePlusImgLoader( imp, ImageStackImageLoader.createUnsignedByteInstance( imp ), minMaxOption, min, max );
}
- public static ImagePlusImgLoader< UnsignedShortType > createGray16( final ImagePlus imp, final MinMaxOption minMaxOption, final double min, final double max )
+ public static ImagePlusImgLoader createGray16( final ImagePlus imp, final MinMaxOption minMaxOption, final double min, final double max )
{
if( imp.getType() != ImagePlus.GRAY16 )
throw new RuntimeException( "expected ImagePlus type GRAY16" );
if ( imp.getStack() != null && imp.getStack().isVirtual() )
- return new ImagePlusImgLoader< UnsignedShortType >( imp, VirtualStackImageLoader.createUnsignedShortInstance( imp ), minMaxOption, min, max );
+ return new ImagePlusImgLoader( imp, VirtualStackImageLoader.createUnsignedShortInstance( imp ), minMaxOption, min, max );
else
- return new ImagePlusImgLoader< UnsignedShortType >( imp, ImageStackImageLoader.createUnsignedShortInstance( imp ), minMaxOption, min, max );
+ return new ImagePlusImgLoader( imp, ImageStackImageLoader.createUnsignedShortInstance( imp ), minMaxOption, min, max );
}
- public static ImagePlusImgLoader< FloatType > createGray32( final ImagePlus imp, final MinMaxOption minMaxOption, final double min, final double max )
+ public static ImagePlusImgLoader createGray32( final ImagePlus imp, final MinMaxOption minMaxOption, final double min, final double max )
{
if( imp.getType() != ImagePlus.GRAY32 )
throw new RuntimeException( "expected ImagePlus type GRAY32" );
if ( imp.getStack() != null && imp.getStack().isVirtual() )
- return new ImagePlusImgLoader< FloatType >( imp, VirtualStackImageLoader.createFloatInstance( imp ), minMaxOption, min, max );
+ return new ImagePlusImgLoader( imp, VirtualStackImageLoader.createFloatInstance( imp ), minMaxOption, min, max );
else
- return new ImagePlusImgLoader< FloatType >( imp, ImageStackImageLoader.createFloatInstance( imp ), minMaxOption, min, max );
+ return new ImagePlusImgLoader( imp, ImageStackImageLoader.createFloatInstance( imp ), minMaxOption, min, max );
}
protected final ImagePlus imp;
- protected final BasicImgLoader< T > loader;
+ protected final BasicImgLoader loader;
+
+ protected VolatileGlobalCellCache loadercache;
- protected VolatileGlobalCellCache< ? > loadercache;
+ protected final ArrayList< SetupImgLoader< ? > > setupImgLoaders;
protected double impMin;
protected double impMax;
@SuppressWarnings( "unchecked" )
- protected ImagePlusImgLoader( final ImagePlus imp,
- final BasicImgLoader< T > loader,
+ protected< T extends RealType< T > & NativeType< T > > ImagePlusImgLoader( final ImagePlus imp,
+ final TypedBasicImgLoader< T > loader,
final MinMaxOption minMaxOption,
final double min,
final double max )
@@ -88,8 +92,13 @@ public class ImagePlusImgLoader< T extends RealType< T > & NativeType< T > > imp
this.imp = imp;
this.loader = loader;
+ final int numSetups = imp.getNChannels();
+ setupImgLoaders = new ArrayList< SetupImgLoader< ? > >();
+ for ( int setupId = 0; setupId < numSetups; ++setupId )
+ setupImgLoaders.add( new SetupImgLoader< T >( loader.getSetupImgLoader( setupId ) ) );
+
if ( loader instanceof VirtualStackImageLoader )
- this.loadercache = ( ( VirtualStackImageLoader< T, ?, ? > ) loader ).getCache();
+ this.loadercache = ( ( VirtualStackImageLoader< ?, ?, ? > ) loader ).getCache();
else
this.loadercache = null;
@@ -97,14 +106,13 @@ public class ImagePlusImgLoader< T extends RealType< T > & NativeType< T > > imp
{
impMin = Double.POSITIVE_INFINITY;
impMax = Double.NEGATIVE_INFINITY;
- final T minT = loader.getImageType().createVariable();
- final T maxT = loader.getImageType().createVariable();
- final int numSetups = imp.getNChannels();
+ final T minT = loader.getSetupImgLoader( 0 ).getImageType().createVariable();
+ final T maxT = minT.createVariable();
final int numTimepoints = imp.getNFrames();
for ( int t = 0; t < numTimepoints; t++ )
for ( int s = 0; s < numSetups; ++s )
{
- ComputeMinMax.computeMinMax( loader.getImage( new ViewId( t, s ) ), minT, maxT );
+ ComputeMinMax.computeMinMax( loader.getSetupImgLoader( s ).getImage( t ), minT, maxT );
impMin = Math.min( minT.getRealDouble(), impMin );
impMax = Math.max( maxT.getRealDouble(), impMax );
if ( loadercache != null )
@@ -139,18 +147,34 @@ public class ImagePlusImgLoader< T extends RealType< T > & NativeType< T > > imp
}
}
- @Override
- public RandomAccessibleInterval< UnsignedShortType > getImage( final ViewId view )
+ public class SetupImgLoader< T extends RealType< T > & NativeType< T > > implements BasicSetupImgLoader< UnsignedShortType >
{
- if ( loadercache != null )
- loadercache.clearCache();
- final RandomAccessibleInterval< T > img = loader.getImage( view );
- return Converters.convert( img, new RealUnsignedShortConverter< T >( impMin, impMax ), new UnsignedShortType() );
+ final BasicSetupImgLoader< T > loader;
+
+ protected SetupImgLoader( final BasicSetupImgLoader< T > loader )
+ {
+ this.loader = loader;
+ }
+
+ @Override
+ public RandomAccessibleInterval< UnsignedShortType > getImage( final int timepointId )
+ {
+ if ( loadercache != null )
+ loadercache.clearCache();
+ final RandomAccessibleInterval< T > img = loader.getImage( timepointId );
+ return Converters.convert( img, new RealUnsignedShortConverter< T >( impMin, impMax ), new UnsignedShortType() );
+ }
+
+ @Override
+ public UnsignedShortType getImageType()
+ {
+ return new UnsignedShortType();
+ }
}
@Override
- public UnsignedShortType getImageType()
+ public SetupImgLoader< ? > getSetupImgLoader( final int setupId )
{
- return new UnsignedShortType();
+ return setupImgLoaders.get( setupId );
}
}
diff --git a/src/main/java/bdv/img/imagestack/ImageStackImageLoader.java b/src/main/java/bdv/img/imagestack/ImageStackImageLoader.java
index c3014bb52f50eef2cf73fd2f70e94a59598d4026..6c5c813d6500e4e03c949610844a1378047db564 100644
--- a/src/main/java/bdv/img/imagestack/ImageStackImageLoader.java
+++ b/src/main/java/bdv/img/imagestack/ImageStackImageLoader.java
@@ -1,8 +1,11 @@
package bdv.img.imagestack;
+import java.util.ArrayList;
+
import ij.ImagePlus;
import mpicbg.spim.data.generic.sequence.BasicImgLoader;
-import mpicbg.spim.data.sequence.ViewId;
+import mpicbg.spim.data.generic.sequence.BasicSetupImgLoader;
+import mpicbg.spim.data.generic.sequence.TypedBasicImgLoader;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.img.basictypeaccess.array.ArrayDataAccess;
import net.imglib2.img.basictypeaccess.array.ByteArray;
@@ -17,7 +20,7 @@ import net.imglib2.type.numeric.integer.UnsignedByteType;
import net.imglib2.type.numeric.integer.UnsignedShortType;
import net.imglib2.type.numeric.real.FloatType;
-public abstract class ImageStackImageLoader< T extends NumericType< T > & NativeType< T >, A extends ArrayDataAccess< A > > implements BasicImgLoader< T >
+public abstract class ImageStackImageLoader< T extends NumericType< T > & NativeType< T >, A extends ArrayDataAccess< A > > implements TypedBasicImgLoader< T >, BasicImgLoader
{
public static ImageStackImageLoader< UnsignedByteType, ByteArray > createUnsignedByteInstance( final ImagePlus imp )
{
@@ -97,37 +100,59 @@ public abstract class ImageStackImageLoader< T extends NumericType< T > & Native
private final long[] dim;
+ private final ArrayList< SetupImgLoader > setupImgLoaders;
+
public ImageStackImageLoader( final T type, final ImagePlus imp )
{
this.type = type;
this.imp = imp;
this.dim = new long[] { imp.getWidth(), imp.getHeight(), imp.getNSlices() };
+ final int numSetups = imp.getNChannels();
+ setupImgLoaders = new ArrayList< SetupImgLoader >();
+ for ( int setupId = 0; setupId < numSetups; ++setupId )
+ setupImgLoaders.add( new SetupImgLoader( setupId ) );
}
protected abstract A wrapPixels( Object array );
protected abstract void linkType( PlanarImg< T, A > img );
- @Override
- public RandomAccessibleInterval< T > getImage( final ViewId view )
+ public class SetupImgLoader implements BasicSetupImgLoader< T >
{
- return new PlanarImg< T, A >( dim, type.getEntitiesPerPixel() )
+ private final int setupId;
+
+ public SetupImgLoader( final int setupId )
{
- private PlanarImg< T, A > init()
+ this.setupId = setupId;
+ }
+
+ @Override
+ public RandomAccessibleInterval< T > getImage( final int timepointId )
+ {
+ return new PlanarImg< T, A >( dim, type.getEntitiesPerPixel() )
{
- final int channel = view.getViewSetupId() + 1;
- final int frame = view.getTimePointId() + 1;
- for ( int slice = 1; slice <= dim[ 2 ]; ++slice )
- mirror.set( slice - 1, wrapPixels( imp.getStack().getPixels( imp.getStackIndex( channel, slice, frame ) ) ) );
- linkType( this );
- return this;
- }
- }.init();
+ private PlanarImg< T, A > init()
+ {
+ final int channel = setupId + 1;
+ final int frame = timepointId + 1;
+ for ( int slice = 1; slice <= dim[ 2 ]; ++slice )
+ mirror.set( slice - 1, wrapPixels( imp.getStack().getPixels( imp.getStackIndex( channel, slice, frame ) ) ) );
+ linkType( this );
+ return this;
+ }
+ }.init();
+ }
+
+ @Override
+ public T getImageType()
+ {
+ return type;
+ }
}
@Override
- public T getImageType()
+ public SetupImgLoader getSetupImgLoader( final int setupId )
{
- return type;
+ return setupImgLoaders.get( setupId );
}
}
\ No newline at end of file
diff --git a/src/main/java/bdv/img/virtualstack/VirtualStackImageLoader.java b/src/main/java/bdv/img/virtualstack/VirtualStackImageLoader.java
index 4d2f27000a020b97176f735b4f1d13119fccd483..f159c4845925f354d89f3f273a9809e21b570a62 100644
--- a/src/main/java/bdv/img/virtualstack/VirtualStackImageLoader.java
+++ b/src/main/java/bdv/img/virtualstack/VirtualStackImageLoader.java
@@ -1,6 +1,9 @@
package bdv.img.virtualstack;
+import java.util.ArrayList;
+
import ij.ImagePlus;
+import mpicbg.spim.data.generic.sequence.TypedBasicImgLoader;
import mpicbg.spim.data.sequence.ViewId;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.Volatile;
@@ -22,6 +25,7 @@ import net.imglib2.type.volatiles.VolatileUnsignedByteType;
import net.imglib2.type.volatiles.VolatileUnsignedShortType;
import net.imglib2.util.Fraction;
import bdv.AbstractViewerImgLoader;
+import bdv.AbstractViewerSetupImgLoader;
import bdv.img.cache.CacheArrayLoader;
import bdv.img.cache.CacheHints;
import bdv.img.cache.CachedCellImg;
@@ -54,7 +58,7 @@ import bdv.img.cache.VolatileImgCells.CellCache;
* @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
public abstract class VirtualStackImageLoader< T extends NativeType< T >, V extends Volatile< T > & NativeType< V >, A extends VolatileAccess >
- extends AbstractViewerImgLoader< T, V >
+ extends AbstractViewerImgLoader< T, V > implements TypedBasicImgLoader< T >
{
public static VirtualStackImageLoader< FloatType, VolatileFloatType, VolatileFloatArray > createFloatInstance( final ImagePlus imp )
{
@@ -136,77 +140,102 @@ public abstract class VirtualStackImageLoader< T extends NativeType< T >, V exte
private static AffineTransform3D[] mipmapTransforms = new AffineTransform3D[] { new AffineTransform3D() };
- private final VolatileGlobalCellCache< A > cache;
+ private final VolatileGlobalCellCache cache;
private final long[] dimensions;
private final int[] cellDimensions;
+ private final CacheArrayLoader< A > loader;
+
+ private final ArrayList< SetupImgLoader > setupImgLoaders;
+
protected VirtualStackImageLoader( final ImagePlus imp, final CacheArrayLoader< A > loader, final T type, final V volatileType )
{
super( type, volatileType );
+ this.loader = loader;
dimensions = new long[] { imp.getWidth(), imp.getHeight(), imp.getNSlices() };
cellDimensions = new int[] { imp.getWidth(), imp.getHeight(), 1 };
final int numTimepoints = imp.getNFrames();
final int numSetups = imp.getNChannels();
- cache = new VolatileGlobalCellCache< A >( loader, numTimepoints, numSetups, 1, 1 );
+ cache = new VolatileGlobalCellCache( numTimepoints, numSetups, 1, 1 );
+ setupImgLoaders = new ArrayList< SetupImgLoader >();
+ for ( int setupId = 0; setupId < numSetups; ++setupId )
+ setupImgLoaders.add( new SetupImgLoader( setupId ) );
}
- protected abstract void linkType( CachedCellImg< T, A > img );
+ public class SetupImgLoader extends AbstractViewerSetupImgLoader< T, V >
+ {
+ private final int setupId;
- protected abstract void linkVolatileType( CachedCellImg< V, A > img );
+ public SetupImgLoader( final int setupId )
+ {
+ super( VirtualStackImageLoader.this.type, VirtualStackImageLoader.this.volatileType );
+ this.setupId = setupId;
+ }
- @Override
- public RandomAccessibleInterval< T > getImage( final ViewId view, final int level )
- {
- final CachedCellImg< T, A > img = prepareCachedImage( view, level, LoadingStrategy.BLOCKING );
- linkType( img );
- return img;
- }
+ @Override
+ public RandomAccessibleInterval< T > getImage( final int timepointId, final int level )
+ {
+ final CachedCellImg< T, A > img = prepareCachedImage( timepointId, setupId, level, LoadingStrategy.BLOCKING );
+ linkType( img );
+ return img;
+ }
- @Override
- public RandomAccessibleInterval< V > getVolatileImage( final ViewId view, final int level )
- {
- final CachedCellImg< V, A > img = prepareCachedImage( view, level, LoadingStrategy.BUDGETED );
- linkVolatileType( img );
- return img;
- }
+ @Override
+ public RandomAccessibleInterval< V > getVolatileImage( final int timepointId, final int level )
+ {
+ final CachedCellImg< V, A > img = prepareCachedImage( timepointId, setupId, level, LoadingStrategy.BUDGETED );
+ linkVolatileType( img );
+ return img;
+ }
- @Override
- public double[][] getMipmapResolutions( final int setup )
- {
- return mipmapResolutions;
- }
+ @Override
+ public double[][] getMipmapResolutions()
+ {
+ return mipmapResolutions;
+ }
- @Override
- public AffineTransform3D[] getMipmapTransforms( final int setup )
- {
- return mipmapTransforms;
+ @Override
+ public AffineTransform3D[] getMipmapTransforms()
+ {
+ return mipmapTransforms;
+ }
+
+ @Override
+ public int numMipmapLevels()
+ {
+ return 1;
+ }
}
@Override
- public int numMipmapLevels( final int setup )
+ public SetupImgLoader getSetupImgLoader( final int setupId )
{
- return 1;
+ return setupImgLoaders.get( setupId );
}
@Override
- public VolatileGlobalCellCache< A > getCache()
+ public VolatileGlobalCellCache getCache()
{
return cache;
}
+ protected abstract void linkType( CachedCellImg< T, A > img );
+
+ protected abstract void linkVolatileType( CachedCellImg< V, A > img );
+
/**
* (Almost) create a {@link CachedCellImg} backed by the cache. The created
* image needs a {@link NativeImg#setLinkedType(net.imglib2.type.Type)
* linked type} before it can be used. The type should be either
* {@link ARGBType} and {@link VolatileARGBType}.
*/
- protected < T extends NativeType< T > > CachedCellImg< T, A > prepareCachedImage( final ViewId view, final int level, final LoadingStrategy loadingStrategy )
+ protected < T extends NativeType< T > > CachedCellImg< T, A > prepareCachedImage( final int timepointId, final int setupId, final int level, final LoadingStrategy loadingStrategy )
{
final int priority = 0;
final CacheHints cacheHints = new CacheHints( loadingStrategy, priority, false );
- final CellCache< A > c = cache.new VolatileCellCache( view.getTimePointId(), view.getViewSetupId(), level, cacheHints );
+ final CellCache< A > c = cache.new VolatileCellCache< A >( timepointId, setupId, level, cacheHints, loader );
final VolatileImgCells< A > cells = new VolatileImgCells< A >( c, new Fraction(), dimensions, cellDimensions );
final CachedCellImg< T, A > img = new CachedCellImg< T, A >( cells );
return img;