diff --git a/pom.xml b/pom.xml
index 406aa07435e93cd3a95229a7ef356a0c9f2e0b2d..99854e10bc5e81318d17c9de71e87fdf85c74c80 100644
--- a/pom.xml
+++ b/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>org.scijava</groupId>
<artifactId>pom-scijava</artifactId>
- <version>17.1.1</version>
+ <version>22.2.0</version>
<relativePath />
</parent>
@@ -93,11 +93,6 @@
<license.licenseName>gpl_v3</license.licenseName>
<license.copyrightOwners>BigDataViewer developers.</license.copyrightOwners>
- <imglib2.version>4.2.1</imglib2.version>
- <imglib2-ui.version>2.0.0-beta-32</imglib2-ui.version>
- <bigdataviewer-core.version>4.1.0</bigdataviewer-core.version>
- <SPIM_Registration.version>5.0.13</SPIM_Registration.version>
-
<!-- NB: Deploy releases to the ImageJ Maven repository. -->
<releaseProfiles>deploy-to-imagej</releaseProfiles>
</properties>
diff --git a/src/main/java/bdv/ij/OpenImagePlusPlugIn.java b/src/main/java/bdv/ij/OpenImagePlusPlugIn.java
index eb1cd985175bd3f59de2adef70aa6ea5d58c2b2c..c62b681a012a63ce6e85aa63fe1c733ebeab1853 100644
--- a/src/main/java/bdv/ij/OpenImagePlusPlugIn.java
+++ b/src/main/java/bdv/ij/OpenImagePlusPlugIn.java
@@ -51,8 +51,8 @@ public class OpenImagePlusPlugIn implements Command
{
System.setProperty( "apple.laf.useScreenMenuBar", "true" );
new ImageJ();
- IJ.run("Confocal Series (2.2MB)");
-// IJ.run("Fly Brain (1MB)");
+ IJ.run( "Confocal Series (2.2MB)" );
+// IJ.run( "Fly Brain (1MB)" );
new OpenImagePlusPlugIn().run();
}
diff --git a/src/main/java/bdv/img/imagestack/ImageStackImageLoader.java b/src/main/java/bdv/img/imagestack/ImageStackImageLoader.java
index 43affc871fe4d5f5ccc9f5a8e1b521d32dad44e4..d3f3eeda0ac51fa5fb73ef05003d98d9c1f39e4f 100644
--- a/src/main/java/bdv/img/imagestack/ImageStackImageLoader.java
+++ b/src/main/java/bdv/img/imagestack/ImageStackImageLoader.java
@@ -1,12 +1,8 @@
package bdv.img.imagestack;
import java.util.ArrayList;
+import java.util.function.Function;
-import ij.ImagePlus;
-import mpicbg.spim.data.generic.sequence.BasicImgLoader;
-import mpicbg.spim.data.generic.sequence.BasicSetupImgLoader;
-import mpicbg.spim.data.generic.sequence.ImgLoaderHint;
-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;
@@ -15,84 +11,39 @@ import net.imglib2.img.basictypeaccess.array.IntArray;
import net.imglib2.img.basictypeaccess.array.ShortArray;
import net.imglib2.img.planar.PlanarImg;
import net.imglib2.type.NativeType;
+import net.imglib2.type.NativeTypeFactory;
import net.imglib2.type.numeric.ARGBType;
import net.imglib2.type.numeric.NumericType;
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, TypedBasicImgLoader< T >
+import ij.ImagePlus;
+import mpicbg.spim.data.generic.sequence.BasicImgLoader;
+import mpicbg.spim.data.generic.sequence.BasicSetupImgLoader;
+import mpicbg.spim.data.generic.sequence.ImgLoaderHint;
+import mpicbg.spim.data.generic.sequence.TypedBasicImgLoader;
+
+public class ImageStackImageLoader< T extends NumericType< T > & NativeType< T >, A extends ArrayDataAccess< A > > implements BasicImgLoader, TypedBasicImgLoader< T >
{
public static ImageStackImageLoader< UnsignedByteType, ByteArray > createUnsignedByteInstance( final ImagePlus imp )
{
- return new ImageStackImageLoader< UnsignedByteType, ByteArray >( new UnsignedByteType(), imp )
- {
- @Override
- protected ByteArray wrapPixels( final Object array )
- {
- return new ByteArray( ( byte[] ) array );
- }
-
- @Override
- protected void linkType( final PlanarImg< UnsignedByteType, ByteArray > img )
- {
- img.setLinkedType( new UnsignedByteType( img ) );
- }
- };
+ return new ImageStackImageLoader<>( new UnsignedByteType(), imp, array -> new ByteArray( ( byte[] ) array ) );
}
public static ImageStackImageLoader< UnsignedShortType, ShortArray > createUnsignedShortInstance( final ImagePlus imp )
{
- return new ImageStackImageLoader< UnsignedShortType, ShortArray >( new UnsignedShortType(), imp )
- {
- @Override
- protected ShortArray wrapPixels( final Object array )
- {
- return new ShortArray( ( short[] ) array );
- }
-
- @Override
- protected void linkType( final PlanarImg< UnsignedShortType, ShortArray > img )
- {
- img.setLinkedType( new UnsignedShortType( img ) );
- }
- };
+ return new ImageStackImageLoader<>( new UnsignedShortType(), imp, array -> new ShortArray( ( short[] ) array ) );
}
public static ImageStackImageLoader< FloatType, FloatArray > createFloatInstance( final ImagePlus imp )
{
- return new ImageStackImageLoader< FloatType, FloatArray >( new FloatType(), imp )
- {
- @Override
- protected FloatArray wrapPixels( final Object array )
- {
- return new FloatArray( ( float[] ) array );
- }
-
- @Override
- protected void linkType( final PlanarImg< FloatType, FloatArray > img )
- {
- img.setLinkedType( new FloatType( img ) );
- }
- };
+ return new ImageStackImageLoader<>( new FloatType(), imp, array -> new FloatArray( ( float[] ) array ) );
}
public static ImageStackImageLoader< ARGBType, IntArray > createARGBInstance( final ImagePlus imp )
{
- return new ImageStackImageLoader< ARGBType, IntArray >( new ARGBType(), imp )
- {
- @Override
- protected IntArray wrapPixels( final Object array )
- {
- return new IntArray( ( int[] ) array );
- }
-
- @Override
- protected void linkType( final PlanarImg< ARGBType, IntArray > img )
- {
- img.setLinkedType( new ARGBType( img ) );
- }
- };
+ return new ImageStackImageLoader<>( new ARGBType(), imp, array -> new IntArray( ( int[] ) array ) );
}
private final T type;
@@ -103,10 +54,13 @@ public abstract class ImageStackImageLoader< T extends NumericType< T > & Native
private final ArrayList< SetupImgLoader > setupImgLoaders;
- public ImageStackImageLoader( final T type, final ImagePlus imp )
+ private final Function< Object, A > wrapPixels;
+
+ public ImageStackImageLoader( final T type, final ImagePlus imp, final Function< Object, A > wrapPixels )
{
this.type = type;
this.imp = imp;
+ this.wrapPixels = wrapPixels;
this.dim = new long[] { imp.getWidth(), imp.getHeight(), imp.getNSlices() };
final int numSetups = imp.getNChannels();
setupImgLoaders = new ArrayList<>();
@@ -114,10 +68,6 @@ public abstract class ImageStackImageLoader< T extends NumericType< T > & Native
setupImgLoaders.add( new SetupImgLoader( setupId ) );
}
- protected abstract A wrapPixels( Object array );
-
- protected abstract void linkType( PlanarImg< T, A > img );
-
public class SetupImgLoader implements BasicSetupImgLoader< T >
{
private final int setupId;
@@ -130,18 +80,16 @@ public abstract class ImageStackImageLoader< T extends NumericType< T > & Native
@Override
public RandomAccessibleInterval< T > getImage( final int timepointId, final ImgLoaderHint... hints )
{
- return new PlanarImg< T, A >( dim, type.getEntitiesPerPixel() )
- {
- 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();
+ final int channel = setupId + 1;
+ final int frame = timepointId + 1;
+ final ArrayList< A > slices = new ArrayList<>();
+ for ( int slice = 1; slice <= dim[ 2 ]; ++slice )
+ slices.add( wrapPixels.apply( imp.getStack().getPixels( imp.getStackIndex( channel, slice, frame ) ) ) );
+ final PlanarImg< T, A > img = new PlanarImg<>( slices, dim, type.getEntitiesPerPixel() );
+ @SuppressWarnings( "unchecked" )
+ final NativeTypeFactory< T, ? super A > typeFactory = ( NativeTypeFactory< T, ? super A > ) type.getNativeTypeFactory();
+ img.setLinkedType( typeFactory.createLinkedType( img ) );
+ return img;
}
@Override